A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.
Jeffrey Martin,Nicole V. Johnson,Stephen M. Gross,James C. Schnable,Xiandong Meng,Mei Wang,Devin Coleman-Derr,Erika Lindquist,Chia-Lin Wei,Shawn M. Kaeppler,Feng Chen,Zhong Wang +11 more
TLDR
The power of deep sequencing for large transcriptome studies is demonstrated by generating a high quality transcriptome, which provides a rich resource for the research community.Abstract:
RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.read more
Citations
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A survey of the sorghum transcriptome using single-molecule long reads
Salah E. Abdel-Ghany,Michael Hamilton,Jennifer L. Jacobi,Peter B. Ngam,Nicholas P. Devitt,Faye D. Schilkey,Asa Ben-Hur,Anireddy S. N. Reddy +7 more
TL;DR: This analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms and uncovers APA of ∼11,000 expressed genes and more than 2,100 novel genes.
Journal ArticleDOI
Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.
Silong Sun,Yingsi Zhou,Jian Chen,Junpeng Shi,Haiming Zhao,Hainan Zhao,Weibin Song,Mei Zhang,Mei Zhang,Yang Cui,Xiaomei Dong,Han Liu,Xuxu Ma,Yinping Jiao,Bo Wang,Xuehong Wei,Joshua C. Stein,Jeff C. Glaubitz,Fei Lu,Fei Lu,Guoliang Yu,Chengzhi Liang,Kevin Fengler,Bailin Li,Antoni Rafalski,Patrick S. Schnable,Doreen Ware,Doreen Ware,Edward S. Buckler,Jinsheng Lai +29 more
TL;DR: The de novo genome assembly of maize line Mo17 and comparative analysis with other sequenced maize lines show extensive gene-order variations, which should have implications for heterosis and genome evolution.
Journal ArticleDOI
An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development
Scott C. Stelpflug,Rajandeep S. Sekhon,Brieanne Vaillancourt,Candice N. Hirsch,C. Robin Buell,Natalia de Leon,Shawn M. Kaeppler +6 more
TL;DR: This comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.
Journal Article
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
TL;DR: Rnnotator, an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome, is described, demonstrating that the Rn notator pipeline is able to reconstruct full-length transcripts in the absence of a complete reference genome.
Journal ArticleDOI
The maize W22 genome provides a foundation for functional genomics and transposon biology
Nathan M. Springer,Sarah N. Anderson,Carson M. Andorf,Kevin R. Ahern,Fang Bai,Omer Barad,W. Brad Barbazuk,Hank W. Bass,Kobi Baruch,Gil Ben-Zvi,Edward S. Buckler,Edward S. Buckler,Robert Bukowski,Michael S. Campbell,Ethalinda K. S. Cannon,Paul S. Chomet,R. Kelly Dawe,Ruth Davenport,Hugo K. Dooner,Limei He Du,Chunguang Du,Katherine A. Easterling,Christine M. Gault,Jiahn-Chou Guan,Charles T. Hunter,Georg Jander,Yinping Jiao,Karen E. Koch,Guy Kol,Tobias G. Köllner,Toru Kudo,Qing Li,Fei Lu,Fei Lu,Dustin Mayfield-Jones,Wenbin Mei,Donald R. McCarty,Jaclyn M. Noshay,John L. Portwood,Gil Ronen,A. Mark Settles,Doron Shem-Tov,Jinghua Shi,Ilya Soifer,Joshua C. Stein,Michelle C. Stitzer,Masaharu Suzuki,Daniel L. Vera,Erik Vollbrecht,Julia Vrebalov,Doreen Ware,Doreen Ware,Doreen Ware,Sharon Wei,Kokulapalan Wimalanathan,Margaret R. Woodhouse,Wenwei Xiong,Thomas P. Brutnell,Thomas P. Brutnell +58 more
TL;DR: It is shown that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms.
References
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