De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes

PloS One
Ingrid GarbusViviana Echenique

Abstract

A long-standing goal in plant breeding has been the ability to confer apomixis to agriculturally relevant species, which would require a deeper comprehension of the molecular basis of apomictic regulatory mechanisms. Eragrostis curvula (Schrad.) Nees is a perennial grass that includes both sexual and apomictic cytotypes. The availability of a reference transcriptome for this species would constitute a very important tool toward the identification of genes controlling key steps of the apomictic pathway. Here, we used Roche/454 sequencing technologies to generate reads from inflorescences of E. curvula apomictic and sexual genotypes that were de novo assembled into a reference transcriptome. Near 90% of the 49568 assembled isotigs showed sequence similarity to sequences deposited in the public databases. A gene ontology analysis categorized 27448 isotigs into at least one of the three main GO categories. We identified 11475 SSRs, and several of them were assayed in E curvula germoplasm using SSR-based primers, providing a valuable set of molecular markers that could allow direct allele selection. The differential contribution to each library of the spliced forms of several transcripts revealed the existence of several isotigs pro...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jun 6, 1972·Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character·M D Bennett
Jul 13, 2001·The Plant Cell·U GrossniklausP J van Dijk
Sep 25, 2003·Annual Review of Plant Biology·Anna M Koltunow, Ueli Grossniklaus
Jun 19, 2004·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Malay C SahaGregory D May
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Oct 19, 2006·Proceedings of the National Academy of Sciences of the United States of America·Andrew S CatanachRoss Bicknell
Aug 31, 2007·Biostatistics·Mark D Robinson, Gordon K Smyth
Dec 14, 2007·Annual Review of Genetics·Peggy Ozias-Akins, Peter J van Dijk
Mar 4, 2008·Plant Molecular Biology·Gerardo D L CervigniViviana Echenique
Aug 2, 2008·International Journal of Plant Genomics·Luciano Carlos da MaiaAntonio Costa de Oliveira
Feb 19, 2010·Sexual Plant Reproduction·Elvira Hörandl
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Mar 6, 2010·The Plant Journal : for Cell and Molecular Biology·Anna SchallauHelmut Bäumlein
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Mar 12, 2011·Sexual Plant Reproduction·Ana Claudia OchogavíaSilvina Claudia Pessino
Jul 16, 2013·Plant Reproduction·Gianni Barcaccia, Emidio Albertini
Dec 1, 2001·Sexual Plant Reproduction·E AlbertiniM Falcinelli
Jun 19, 2014·Genetics·Melanie L Hand, Anna M G Koltunow
Jun 21, 2014·Molecular Genetics and Genomics : MGG·Chunxian ChenTom G Beckman
Apr 19, 2017·PloS One·Juan Manuel RodrigoViviana Echenique
Apr 23, 2017·BMC Genomics·Juan Pablo A OrtizSilvina C Pessino

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Citations

Jul 30, 2019·Frontiers in Plant Science·Diego ZappacostaViviana Echenique

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Datasets Mentioned

BETA
EH183417
EH195711

Methods Mentioned

BETA
Chip
PCR
electrophoresis

Software Mentioned

BLAST
Newbler assembler
PrimerSearch
SSR locator
EdgeR
Primer3
PRINSEQ
BLAST2GO
BLASTX
BLAST -

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