@article{13214,
  abstract     = {Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links.},
  author       = {Abualia, R and Riegler, Stefan and Benková, Eva},
  issn         = {2073-4409},
  journal      = {Cells},
  number       = {12},
  publisher    = {MDPI},
  title        = {{Nitrate, auxin and cytokinin - a trio to tango}},
  doi          = {10.3390/cells12121613},
  volume       = {12},
  year         = {2023},
}

@article{11587,
  abstract     = {Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.
Results: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.
Conclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.},
  author       = {Zhang, Runxuan and Kuo, Richard and Coulter, Max and Calixto, Cristiane P.G. and Entizne, Juan Carlos and Guo, Wenbin and Marquez, Yamile and Milne, Linda and Riegler, Stefan and Matsui, Akihiro and Tanaka, Maho and Harvey, Sarah and Gao, Yubang and Wießner-Kroh, Theresa and Paniagua, Alejandro and Crespi, Martin and Denby, Katherine and Hur, Asa Ben and Huq, Enamul and Jantsch, Michael and Jarmolowski, Artur and Koester, Tino and Laubinger, Sascha and Li, Qingshun Quinn and Gu, Lianfeng and Seki, Motoaki and Staiger, Dorothee and Sunkar, Ramanjulu and Szweykowska-Kulinska, Zofia and Tu, Shih Long and Wachter, Andreas and Waugh, Robbie and Xiong, Liming and Zhang, Xiao Ning and Conesa, Ana and Reddy, Anireddy S.N. and Barta, Andrea and Kalyna, Maria and Brown, John W.S.},
  issn         = {1474-760X},
  journal      = {Genome Biology},
  publisher    = {BioMed Central},
  title        = {{A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis}},
  doi          = {10.1186/s13059-022-02711-0},
  volume       = {23},
  year         = {2022},
}

@article{7603,
  abstract     = {Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.},
  author       = {Nimeth, Barbara Anna and Riegler, Stefan and Kalyna, Maria},
  issn         = {1664462X},
  journal      = {Frontiers in Plant Science},
  publisher    = {Frontiers},
  title        = {{Alternative splicing and DNA damage response in plants}},
  doi          = {10.3389/fpls.2020.00091},
  volume       = {11},
  year         = {2020},
}