---
_id: '1085'
abstract:
- lang: eng
text: Sex chromosomes evolve once recombination is halted between a homologous pair
of chromosomes. The dominant model of sex chromosome evolution posits that recombination
is suppressed between emerging X and Y chromosomes in order to resolve sexual
conflict. Here we test this model using whole genome and transcriptome resequencing
data in the guppy, a model for sexual selection with many Y-linked colour traits.
We show that although the nascent Y chromosome encompasses nearly half of the
linkage group, there has been no perceptible degradation of Y chromosome gene
content or activity. Using replicate wild populations with differing levels of
sexually antagonistic selection for colour, we also show that sexual selection
leads to greater expansion of the non-recombining region and increased Y chromosome
divergence. These results provide empirical support for longstanding models of
sex chromosome catalysis, and suggest an important role for sexual selection and
sexual conflict in genome evolution.
article_number: '14251'
article_processing_charge: No
author:
- first_name: Alison
full_name: Wright, Alison
last_name: Wright
- first_name: Iulia
full_name: Darolti, Iulia
last_name: Darolti
- first_name: Natasha
full_name: Bloch, Natasha
last_name: Bloch
- first_name: Vicencio
full_name: Oostra, Vicencio
last_name: Oostra
- first_name: Benjamin
full_name: Sandkam, Benjamin
last_name: Sandkam
- first_name: Séverine
full_name: Buechel, Séverine
last_name: Buechel
- first_name: Niclas
full_name: Kolm, Niclas
last_name: Kolm
- first_name: Felix
full_name: Breden, Felix
last_name: Breden
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Judith
full_name: Mank, Judith
last_name: Mank
citation:
ama: Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests
role of sexual selection in guppy sex chromosome formation. Nature Communications.
2017;8. doi:10.1038/ncomms14251
apa: Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., …
Mank, J. (2017). Convergent recombination suppression suggests role of sexual
selection in guppy sex chromosome formation. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms14251
chicago: Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin
Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith
Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection
in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing
Group, 2017. https://doi.org/10.1038/ncomms14251.
ieee: A. Wright et al., “Convergent recombination suppression suggests role
of sexual selection in guppy sex chromosome formation,” Nature Communications,
vol. 8. Nature Publishing Group, 2017.
ista: Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden
F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role
of sexual selection in guppy sex chromosome formation. Nature Communications.
8, 14251.
mla: Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role
of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications,
vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251.
short: A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm,
F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:04Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2023-09-20T11:48:16Z
day: '31'
ddc:
- '570'
- '576'
department:
- _id: BeVi
doi: 10.1038/ncomms14251
external_id:
isi:
- '000392953700001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:22Z
date_updated: 2018-12-12T10:15:22Z
file_id: '5141'
file_name: IST-2017-791-v1+1_ncomms14251.pdf
file_size: 955256
relation: main_file
file_date_updated: 2018-12-12T10:15:22Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6292'
pubrep_id: '791'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergent recombination suppression suggests role of sexual selection in guppy
sex chromosome formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '7163'
abstract:
- lang: eng
text: The de novo genome assemblies generated for this study, and the associated
metadata.
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.” 2017. doi:10.15479/AT:ISTA:7163
apa: Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:7163
chicago: Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of
the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute
of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:7163.
ieee: C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.’” Institute of Science
and Technology Austria, 2017.
ista: Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W’, Institute of Science and
Technology Austria, 10.15479/AT:ISTA:7163.
mla: Fraisse, Christelle. Supplementary Files for “The Deep Conservation of the
Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Institute
of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:7163.
short: C. Fraisse, (2017).
contributor:
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2019-12-09T23:03:03Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-02-21T13:47:47Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.15479/AT:ISTA:7163
file:
- access_level: open_access
checksum: 3cae8a2e3cbf8703399b9c483aaba7f3
content_type: application/zip
creator: cfraisse
date_created: 2019-12-10T08:46:46Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7164'
file_name: Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip
file_size: 841375478
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '614'
relation: research_paper
status: public
status: public
title: Supplementary Files for "The deep conservation of the Lepidoptera Z chromosome
suggests a non canonical origin of the W"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5571'
abstract:
- lang: eng
text: "This folder contains all the data used in each of the main figures of \"The
genomic characterization of the t-haplotype, a mouse meiotic driver, highlights
its complex history and specialized biology\" (Kelemen, R., Vicoso, B.), as well
as in the supplementary figures. \r\n"
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Data for “The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.” 2017.
doi:10.15479/AT:ISTA:78
apa: Vicoso, B. (2017). Data for “The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:78
chicago: Vicoso, Beatriz. “Data for ‘The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:78.
ieee: B. Vicoso, “Data for ‘The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.’” Institute
of Science and Technology Austria, 2017.
ista: Vicoso B. 2017. Data for ‘The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:78.
mla: Vicoso, Beatriz. Data for “The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:78.
short: B. Vicoso, (2017).
contributor:
- contributor_type: contact_person
first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
datarep_id: '78'
date_created: 2018-12-12T12:31:36Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2024-02-21T13:48:16Z
day: '06'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:78
file:
- access_level: open_access
checksum: 4520eb2b8379417ee916995719158f16
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:00Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5618'
file_name: IST-2017-78-v1+1_Data.zip
file_size: 143697895
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '11'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '542'
relation: research_paper
status: public
status: public
title: Data for "The genomic characterization of the t-haplotype, a mouse meiotic
driver, highlights its complex history and specialized biology"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5572'
abstract:
- lang: eng
text: Code described in the Supplementary Methods of "The genomic characterization
of the t-haplotype, a mouse meiotic driver, highlights its complex history and
specialized biology" (Kelemen, R., Vicoso, B.)
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Code for “The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.” 2017.
doi:10.15479/AT:ISTA:79
apa: Vicoso, B. (2017). Code for “The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:79
chicago: Vicoso, Beatriz. “Code for ‘The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:79 .
ieee: B. Vicoso, “Code for ‘The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.’” Institute
of Science and Technology Austria, 2017.
ista: Vicoso B. 2017. Code for ‘The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:79 .
mla: Vicoso, Beatriz. Code for “The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:79 .
short: B. Vicoso, (2017).
datarep_id: '79'
date_created: 2018-12-12T12:31:36Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2024-02-21T13:48:28Z
day: '06'
ddc:
- '576'
department:
- _id: BeVi
doi: '10.15479/AT:ISTA:79 '
file:
- access_level: open_access
checksum: 3e70a7bcd6ff0c38b79e4c8a7d137034
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:15Z
date_updated: 2020-07-14T12:47:05Z
file_id: '5643'
file_name: IST-2017-79-v1+1_Code.zip
file_size: 49823
relation: main_file
file_date_updated: 2020-07-14T12:47:05Z
has_accepted_license: '1'
month: '11'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '542'
relation: research_paper
status: public
status: public
title: Code for "The genomic characterization of the t-haplotype, a mouse meiotic
driver, highlights its complex history and specialized biology"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '614'
abstract:
- lang: eng
text: 'Moths and butterflies (Lepidoptera) usually have a pair of differentiated
WZ sex chromosomes. However, in most lineages outside of the division Ditrysia,
as well as in the sister order Trichoptera, females lack a W chromosome. The W
is therefore thought to have been acquired secondarily. Here we compare the genomes
of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three
models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex
chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment
of a B chromosome). We show that the gene content of the Z is highly conserved
across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes
moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome
fusion). Our comparative genomics analysis therefore supports the secondary acquisition
of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme
stability of well-differentiated sex chromosomes.'
article_number: '1486'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Marion A
full_name: Picard, Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z
chromosome suggests a non canonical origin of the W. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-01663-5
apa: Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation
of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5
chicago: Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation
of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5.
ieee: C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the
Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W. Nature Communications.
8(1), 1486.
mla: Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome
Suggests a Non Canonical Origin of the W.” Nature Communications, vol.
8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5.
short: C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).
date_created: 2018-12-11T11:47:30Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-02-21T13:47:47Z
day: '01'
ddc:
- '570'
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1038/s41467-017-01663-5
external_id:
pmid:
- '29133797'
file:
- access_level: open_access
checksum: 4da2651303c8afc2f7fc419be42a2433
content_type: application/pdf
creator: dernst
date_created: 2020-03-03T15:55:50Z
date_updated: 2020-07-14T12:47:20Z
file_id: '7562'
file_name: 2017_NatureComm_Fraisse.pdf
file_size: 1201520
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7190'
pubrep_id: '910'
quality_controlled: '1'
related_material:
record:
- id: '7163'
relation: popular_science
status: public
scopus_import: 1
status: public
title: The deep conservation of the Lepidoptera Z chromosome suggests a non canonical
origin of the W
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '945'
abstract:
- lang: eng
text: While chromosome-wide dosage compensation of the X chromosome has been found
in many species, studies in ZW clades have indicated that compensation of the
Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show
complete compensation of the Z chromosome, while others lack full equalization,
but what drives these inconsistencies is unclear. Here, we compare patterns of
male and female gene expression on the Z chromosome of two closely related butterfly
species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths
species, Plodia interpunctella and Bombyx mori, which were previously found to
differ in the extent to which they equalize Z-linked gene expression between the
sexes. We find that, while some species and tissues seem to have incomplete dosage
compensation, this is in fact due to the accumulation of male-biased genes and
the depletion of female-biased genes on the Z chromosome. Once this is accounted
for, the Z chromosome is fully compensated in all four species, through the up-regulation
of Z expression in females and in some cases additional down-regulation in males.
We further find that both sex-biased genes and Z-linked genes have increased rates
of expression divergence in this clade, and that this can lead to fast shifts
in patterns of gene expression even between closely related species. Taken together,
these results show that the uneven distribution of sex-biased genes on sex chromosomes
can confound conclusions about dosage compensation and that Z chromosome-wide
dosage compensation is not only possible but ubiquitous among Lepidoptera.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in
Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular
Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190
apa: Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation
is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z
chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190
chicago: Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation
Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z
Chromosome.” Molecular Biology and Evolution. Oxford University Press,
2017. https://doi.org/10.1093/molbev/msx190.
ieee: A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous
in Lepidoptera, but counteracted by the masculinization of the Z chromosome,”
Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press,
pp. 2637–2649, 2017.
ista: Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous
in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular
Biology and Evolution. 34(10), 2637–2649.
mla: Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera,
but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology
and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49,
doi:10.1093/molbev/msx190.
short: A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017)
2637–2649.
date_created: 2018-12-11T11:49:20Z
date_published: 2017-07-06T00:00:00Z
date_updated: 2023-09-26T15:36:34Z
day: '06'
ddc:
- '570'
- '576'
department:
- _id: BeVi
doi: 10.1093/molbev/msx190
external_id:
isi:
- '000411814800016'
file:
- access_level: open_access
checksum: 009fd68043211d645ceb9d1de28274f2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:23Z
date_updated: 2020-07-14T12:48:15Z
file_id: '4810'
file_name: IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf
file_size: 462863
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '10'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2637 - 2649
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular Biology and Evolution
publication_identifier:
issn:
- '07374038'
publication_status: published
publisher: Oxford University Press
publist_id: '6472'
pubrep_id: '848'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by
the masculinization of the Z chromosome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 34
year: '2017'
...
---
_id: '1019'
abstract:
- lang: eng
text: As a consequence of its difference in copy number between males and females,
the X chromosome is subject to unique evolutionary forces and gene regulatory
mechanisms. Previous studies of Drosophila melanogaster have shown that the expression
of X-linked, testis-specific reporter genes is suppressed in the male germline.
However, it is not known whether this phenomenon is restricted to testis-expressed
genes or if it is a more general property of genes with tissue-specific expression,
which are also underrepresented on the X chromosome. To test this, we compared
the expression of three tissue-specific reporter genes (ovary, accessory gland
and Malpighian tubule) inserted at various autosomal and X-chromosomal locations.
In contrast to testis-specific reporter genes, we found no reduction of X-linked
expression in any of the other tissues. In accessory gland and Malpighian tubule,
we detected higher expression of the X-linked reporter genes, which suggests that
they are at least partially dosage compensated. We found no difference in the
tissue-specificity of X-linked and autosomal reporter genes. These findings indicate
that, in general, the X chromosome is not a detrimental environment for tissue-specific
gene expression and that the suppression of X-linked expression is limited to
the male germline.
article_processing_charge: No
author:
- first_name: Eliza
full_name: Argyridou, Eliza
last_name: Argyridou
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Annabella
full_name: Königer, Annabella
last_name: Königer
- first_name: John
full_name: Parsch, John
last_name: Parsch
citation:
ama: Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor
of tissue-specific gene expression in Drosophila melanogaster. Heredity.
2017;119(1):27-34. doi:10.1038/hdy.2017.12
apa: Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2017.12
chicago: Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage
Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2017.12.
ieee: E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not
a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,”
Heredity, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017.
ista: Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general
inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity.
119(1), 27–34.
mla: Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific
Gene Expression in Drosophila Melanogaster.” Heredity, vol. 119, no. 1,
Nature Publishing Group, 2017, pp. 27–34, doi:10.1038/hdy.2017.12.
short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34.
date_created: 2018-12-11T11:49:43Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2023-09-22T09:41:21Z
day: '01'
department:
- _id: BeVi
doi: 10.1038/hdy.2017.12
external_id:
isi:
- '000405397800004'
intvolume: ' 119'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 27 - 34
publication: Heredity
publication_identifier:
issn:
- 0018067X
publication_status: published
publisher: Nature Publishing Group
publist_id: '6374'
quality_controlled: '1'
related_material:
record:
- id: '9861'
relation: research_data
status: public
scopus_import: '1'
status: public
title: X-linkage is not a general inhibitor of tissue-specific gene expression in
Drosophila melanogaster
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 119
year: '2017'
...
---
_id: '9861'
abstract:
- lang: eng
text: As a consequence of its difference in copy number between males and females,
the X chromosome is subject to unique evolutionary forces and gene regulatory
mechanisms. Previous studies of Drosophila melanogaster have shown that the expression
of X-linked, testis-specific reporter genes is suppressed in the male germline.
However, it is not known whether this phenomenon is restricted to testis-expressed
genes or if it is a more general property of genes with tissue-specific expression,
which are also underrepresented on the X chromosome. To test this, we compared
the expression of three tissue-specific reporter genes (ovary, accessory gland
and Malpighian tubule) inserted at various autosomal and X-chromosomal locations.
In contrast to testis-specific reporter genes, we found no reduction of X-linked
expression in any of the other tissues. In accessory gland and Malpighian tubule,
we detected higher expression of the X-linked reporter genes, which suggests that
they are at least partially dosage compensated. We found no difference in the
tissue-specificity of X-linked and autosomal reporter genes. These findings indicate
that, in general, the X chromosome is not a detrimental environment for tissue-specific
gene expression and that the suppression of X-linked expression is limited to
the male germline.
article_processing_charge: No
author:
- first_name: Eliza
full_name: Argyridou, Eliza
last_name: Argyridou
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Annabella
full_name: Königer, Annabella
last_name: Königer
- first_name: John
full_name: Parsch, John
last_name: Parsch
citation:
ama: 'Argyridou E, Huylmans AK, Königer A, Parsch J. Data from: X-linkage is not
a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
2017. doi:10.5061/dryad.02f6r'
apa: 'Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). Data
from: X-linkage is not a general inhibitor of tissue-specific gene expression
in Drosophila melanogaster. Dryad. https://doi.org/10.5061/dryad.02f6r'
chicago: 'Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch.
“Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression
in Drosophila Melanogaster.” Dryad, 2017. https://doi.org/10.5061/dryad.02f6r.'
ieee: 'E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “Data from: X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.”
Dryad, 2017.'
ista: 'Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. Data from: X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,
Dryad, 10.5061/dryad.02f6r.'
mla: 'Argyridou, Eliza, et al. Data from: X-Linkage Is Not a General Inhibitor
of Tissue-Specific Gene Expression in Drosophila Melanogaster. Dryad, 2017,
doi:10.5061/dryad.02f6r.'
short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017).
date_created: 2021-08-10T08:12:52Z
date_published: 2017-02-14T00:00:00Z
date_updated: 2023-09-22T09:41:20Z
day: '14'
department:
- _id: BeVi
doi: 10.5061/dryad.02f6r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.02f6r
month: '02'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1019'
relation: used_in_publication
status: public
status: public
title: 'Data from: X-linkage is not a general inhibitor of tissue-specific gene expression
in Drosophila melanogaster'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '1158'
abstract:
- lang: eng
text: Speciation results from the progressive accumulation of mutations that decrease
the probability of mating between parental populations or reduce the fitness of
hybrids—the so-called species barriers. The speciation genomic literature, however,
is mainly a collection of case studies, each with its own approach and specificities,
such that a global view of the gradual process of evolution from one to two species
is currently lacking. Of primary importance is the prevalence of gene flow between
diverging entities, which is central in most species concepts and has been widely
discussed in recent years. Here, we explore the continuum of speciation thanks
to a comparative analysis of genomic data from 61 pairs of populations/species
of animals with variable levels of divergence. Gene flow between diverging gene
pools is assessed under an approximate Bayesian computation (ABC) framework. We
show that the intermediate "grey zone" of speciation, in which taxonomy
is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective
of species life history traits or ecology. Thanks to appropriate modeling of among-locus
variation in genetic drift and introgression rate, we clarify the status of the
majority of ambiguous cases and uncover a number of cryptic species. Our analysis
also reveals the high incidence in animals of semi-isolated species (when some
but not all loci are affected by barriers to gene flow) and highlights the intrinsic
difficulty, both statistical and conceptual, of delineating species in the grey
zone of speciation.
acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number
ERC grant 232971). PopPhyl project. The funder had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/
(grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent
Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful
discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch)
Center for high-performance computing of the SIB Swiss Institute of Bioinformatics
and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité."
article_number: e2000234
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light
on the grey zone of speciation along a continuum of genomic divergence. PLoS
Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Shedding light on the grey zone of speciation along a continuum of
genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation
along a Continuum of Genomic Divergence.” PLoS Biology. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Shedding light on the grey zone of speciation along a continuum of genomic divergence,”
PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding
light on the grey zone of speciation along a continuum of genomic divergence.
PLoS Biology. 14(12), e2000234.
mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along
a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234,
Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS
Biology 14 (2016).
date_created: 2018-12-11T11:50:28Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-02-23T14:11:16Z
day: '27'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234
file:
- access_level: open_access
checksum: 2bab63b068a9840efd532b9ae583f9bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:42Z
date_updated: 2020-07-14T12:44:36Z
file_id: '5164'
file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf
file_size: 2494348
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file_date_updated: 2020-07-14T12:44:36Z
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issue: '12'
language:
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month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6200'
pubrep_id: '742'
quality_controlled: '1'
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scopus_import: 1
status: public
title: Shedding light on the grey zone of speciation along a continuum of genomic
divergence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1329'
abstract:
- lang: eng
text: Daphnia species have become models for ecological genomics and exhibit interesting
features, such as high phenotypic plasticity and a densely packed genome with
many lineage-specific genes. They are also cyclic parthenogenetic, with alternating
asexual and sexual cycles and environmental sex determination. Here, we present
a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to
investigate gene expression in females and spontaneously produced males of two
clonal lines derived from lakes in Germany and the Czech Republic. We find that
only a low percentage (18%) of genes shows sex-biased expression and that there
are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore,
FBGs tend to be more conserved between species than MBGs in both sequence and
expression. These patterns may be a consequence of cyclic parthenogenesis leading
to a relaxation of purifying selection on MBGs. The two clonal lines show considerable
differences in both number and identity of sex-biased genes, suggesting that they
may have reproductive strategies differing in their investment in sexual reproduction.
Orthologs of key genes in the sex determination and juvenile hormone pathways,
which are thought to be important for the transition from asexual to sexual reproduction,
are present in D. galeata and highly conserved among Daphnia species.
acknowledgement: This study was financially supported by individual grants from the
Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6
to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L.
Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and
K. Otte for providing the necessary resources and help for maintaining Daphnia cultures
in the laboratory. H. Lainer supported us for the molecular laboratory work. D.
Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and
L. Hardulak did the orthology mapping including more insect species. This study
was financially supported by individual grants from the Volkswagen Stiftung (to
M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD
(to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium.
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Alberto
full_name: López Ezquerra, Alberto
last_name: López Ezquerra
- first_name: John
full_name: Parsch, John
last_name: Parsch
- first_name: Mathilde
full_name: Cordellier, Mathilde
last_name: Cordellier
citation:
ama: Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome
assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia
galeata. Genome Biology and Evolution. 2016;8(10):3120-3139. doi:10.1093/gbe/evw221
apa: Huylmans, A. K., López Ezquerra, A., Parsch, J., & Cordellier, M. (2016).
De novo transcriptome assembly and sex-biased gene expression in the cyclical
parthenogenetic Daphnia galeata. Genome Biology and Evolution. Oxford University
Press. https://doi.org/10.1093/gbe/evw221
chicago: Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier.
“De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical
Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution. Oxford
University Press, 2016. https://doi.org/10.1093/gbe/evw221.
ieee: A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo
transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic
Daphnia galeata,” Genome Biology and Evolution, vol. 8, no. 10. Oxford
University Press, pp. 3120–3139, 2016.
ista: Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome
assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia
galeata. Genome Biology and Evolution. 8(10), 3120–3139.
mla: Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene
Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology
and Evolution, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39,
doi:10.1093/gbe/evw221.
short: A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology
and Evolution 8 (2016) 3120–3139.
date_created: 2018-12-11T11:51:24Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:49:55Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1093/gbe/evw221
file:
- access_level: open_access
checksum: 25c7adcb452d39d3b6343ff4b57a652d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:06Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4924'
file_name: IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf
file_size: 1406265
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 3120 - 3139
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5940'
pubrep_id: '663'
quality_controlled: '1'
scopus_import: 1
status: public
title: De novo transcriptome assembly and sex-biased gene expression in the cyclical
parthenogenetic Daphnia galeata
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2016'
...
---
_id: '9862'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation
study to test the robustness of ABC in face of recent times of divergence. 2016.
doi:10.1371/journal.pbio.2000234.s016
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Simulation study to test the robustness of ABC in face of recent times
of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness
of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016.
https://doi.org/10.1371/journal.pbio.2000234.s016.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Simulation study to test the robustness of ABC in face of recent times of divergence.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation
study to test the robustness of ABC in face of recent times of divergence, Public
Library of Science, 10.1371/journal.pbio.2000234.s016.
mla: Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in
Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:20:17Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Simulation study to test the robustness of ABC in face of recent times of divergence
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9863'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions
of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Accessions of surveyed individuals, geographic locations and summary
statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic
Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Accessions of surveyed individuals, geographic locations and summary statistics.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions
of surveyed individuals, geographic locations and summary statistics, Public Library
of Science, 10.1371/journal.pbio.2000234.s017.
mla: Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations
and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:22:52Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s017
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Accessions of surveyed individuals, geographic locations and summary statistics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1513'
abstract:
- lang: eng
text: "Insects of the order Hemiptera (true bugs) use a wide range of mechanisms
of sex determination, including genetic sex determination, paternal genome elimination,
and haplodiploidy. Genetic sex determination, the prevalent mode, is generally
controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different
configurations that include additional sex chromosomes are also present. Although
this diversity of sex determining systems has been extensively studied at the
cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon
pisum has been analyzed at the genomic level, and little is known about X chromosome
biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published
DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative
analysis of the gene content and expression of the X chromosome throughout this
clade. We find that, despite showing evidence of dosage compensation, the X chromosomes
of these species show female-biased expression, and a deficit of male-biased genes,
in direct contrast to the pea aphid X. We further detect an excess of shared gene
content between these very distant species, suggesting that despite the diversity
of sex determining systems, the same chromosomal element is used as the X throughout
a large portion of the order. "
article_processing_charge: No
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage
compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268.
doi:10.1093/gbe/evv215'
apa: 'Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects:
Conservation, dosage compensation and sex-biased expression. Genome Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215'
chicago: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects:
Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology
and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.'
ieee: 'A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression,” Genome Biology and Evolution,
vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.'
ista: 'Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12),
3259–3268.'
mla: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation,
Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution,
vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.'
short: A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.
date_created: 2018-12-11T11:52:27Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:18Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evv215
ec_funded: 1
file:
- access_level: open_access
checksum: 2b56b8c2e2a1d4cc3c9cb8daba26dd9b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:29Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5284'
file_name: IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf
file_size: 858027
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 3259 - 3268
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5664'
pubrep_id: '496'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The X chromosome of hemipteran insects: Conservation, dosage compensation
and sex-biased expression'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '1577'
abstract:
- lang: eng
text: Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked
genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be
unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y
transposition must be the main source of Drosophila Y-linked genes. Here we show
how these genes were acquired. We found a previously unidentified gene (flagrante
delicto Y, FDY) that originated from a recent duplication of the autosomal gene
vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were
duplicated along with vig2, but they became pseudogenes through the accumulation
of deletions and transposable element insertions, whereas FDY remained functional,
acquired testis-specific expression, and now accounts for ∼20% of the vig2-like
mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and
DNA sequence divergence indicates that the duplication to the Y chromosome occurred
∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the
establishment of a Y-linked gene and demonstrates how the Drosophila Y has been
accumulating autosomal genes.
acknowledgement: "This work was supported by grants from Conselho Nacional de Desenvolvimento
Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes
of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski,
C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished
data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski,
B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for
help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members
of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments
on the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Carvalho, Antonio
last_name: Carvalho
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Claudia
full_name: Russo, Claudia
last_name: Russo
- first_name: Bonnielin
full_name: Swenor, Bonnielin
last_name: Swenor
- first_name: Andrew
full_name: Clark, Andrew
last_name: Clark
citation:
ama: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the
Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455.
doi:10.1073/pnas.1516543112
apa: Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth
of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1516543112
chicago: Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and
Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.”
PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.
ieee: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new
gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no.
40. National Academy of Sciences, pp. 12450–12455, 2015.
ista: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene
on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.
mla: Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila
Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015,
pp. 12450–55, doi:10.1073/pnas.1516543112.
short: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.
date_created: 2018-12-11T11:52:49Z
date_published: 2015-10-06T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '06'
department:
- _id: BeVi
doi: 10.1073/pnas.1516543112
external_id:
pmid:
- '26385968'
intvolume: ' 112'
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/
month: '10'
oa: 1
oa_version: Published Version
page: 12450 - 12455
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5594'
quality_controlled: '1'
scopus_import: 1
status: public
title: Birth of a new gene on the Y chromosome of Drosophila melanogaster
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...