Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.

A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTrans...

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Autores principales:	Himabindu Kudapa, Sarwar Azam, Andrew G Sharpe, Bunyamin Taran, Rong Li, Benjamin Deonovic, Connor Cameron, Andrew D Farmer, Steven B Cannon, Rajeev K Varshney
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/087447918e4348bdad2dfeee5cf6a828
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spelling	oai:doaj.org-article:087447918e4348bdad2dfeee5cf6a8282021-11-18T08:36:12ZComprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.1932-620310.1371/journal.pone.0086039https://doaj.org/article/087447918e4348bdad2dfeee5cf6a8282014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24465857/?tool=EBIhttps://doaj.org/toc/1932-6203A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.Himabindu KudapaSarwar AzamAndrew G SharpeBunyamin TaranRong LiBenjamin DeonovicConnor CameronAndrew D FarmerSteven B CannonRajeev K VarshneyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e86039 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Himabindu Kudapa Sarwar Azam Andrew G Sharpe Bunyamin Taran Rong Li Benjamin Deonovic Connor Cameron Andrew D Farmer Steven B Cannon Rajeev K Varshney Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
description	A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.
format	article
author	Himabindu Kudapa Sarwar Azam Andrew G Sharpe Bunyamin Taran Rong Li Benjamin Deonovic Connor Cameron Andrew D Farmer Steven B Cannon Rajeev K Varshney
author_facet	Himabindu Kudapa Sarwar Azam Andrew G Sharpe Bunyamin Taran Rong Li Benjamin Deonovic Connor Cameron Andrew D Farmer Steven B Cannon Rajeev K Varshney
author_sort	Himabindu Kudapa
title	Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
title_short	Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
title_full	Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
title_fullStr	Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
title_full_unstemmed	Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
title_sort	comprehensive transcriptome assembly of chickpea (cicer arietinum l.) using sanger and next generation sequencing platforms: development and applications.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/087447918e4348bdad2dfeee5cf6a828
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Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.

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