Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.)

被引：57

作者：

Dubey, Anuja ^{[1
,2
]}

Farmer, Andrew ^{[3
]}

Schlueter, Jessica ^{[4
]}

Cannon, Steven B. ^{[5
]}

Abernathy, Brian ^{[6
]}

Tuteja, Reetu ^{[1
]}

Woodward, Jimmy ^{[3
]}

Shah, Trushar ^{[1
]}

Mulasmanovic, Benjamin ^{[5
]}

Kudapa, Himabindu ^{[1
]}

Raju, Nikku L. ^{[1
]}

Gothalwal, Ragini ^{[2
]}

Pande, Suresh ^{[1
]}

Xiao, Yongli ^{[7
]}

Town, Chris D. ^{[7
]}

Singh, Nagendra K. ^{[8
]}

May, Gregory D. ^{[3
]}

Jackson, Scott ^{[6
]}

Varshney, Rajeev K. ^{[1
,9
]}

机构：

[1] Int Crops Res Inst Semi Arid Trop, CEG, Patancheru 502324, Greater Hyderab, India

[2] Barkatullah Univ, Bhopal 462026, India

[3] NCGR, Santa Fe, NM 87505 USA

[4] Univ N Carolina, Charlotte, NC 28223 USA

[5] USDA ARS, Corn Insects & Crop Genet Res Unit, Ames, IA 50011 USA

[6] Purdue Univ, W Lafayette, IN 47907 USA

[7] JCVI, Rockville, MD 20850 USA

[8] Natl Res Ctr Plant Biotechnol, New Delhi 110012, India

[9] CIMMYT, CGIAR Generat Challenge Programme GCP, Mexico City 06600, DF, Mexico

来源：

DNA RESEARCH | 2011年 / 18卷 / 03期

关键词：

Cajanus cajan L; next generation sequencing; transcriptome assembly; molecular markers and gene discovery; FINGER PROTEIN ZAT12; SSR-MARKERS; MICROSATELLITE MARKERS; EST RESOURCE; EXPRESSION; SEQUENCE; DISCOVERY; ALIGNMENT; STRESS; RNA;

D O I：

10.1093/dnares/dsr007

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan crop species' of the semi-arid tropic regions. FLX/454 sequencing carried out on a normalized cDNA pool prepared from 31 tissues produced 494 353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10 817 Sanger ESTs, resulted in a pigeonpea trancriptome assembly (CcTA) comprising of 127 754 tentative unique sequences (TUSs). Functional analysis of these TUSs highlights several active pathways and processes in the sampled tissues. Comparison of the CcTA with the soybean genome showed similarity to 10 857 and 16 367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)- and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW- and SMD-responsive genes. Sequence analysis of CcTA and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8137 simple sequence repeats, 12 141 single-nucleotide polymorphisms and 5845 intron-spanning regions. Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes.

引用

页码：153 / 164

页数：12

共 21 条

[21] Comparative transcriptome analysis of B. oleracea L. var. italica and B. macrocarpa Guss. genotypes under drought stress: de novo vs reference genome assembly
Privitera, Grete Francesca
Treccarichi, Simone
Nicotra, Roberta
Branca, Ferdinando
Pulvirenti, Alfredo
Piero, Angela Roberta Lo
Sicilia, Angelo
PLANT STRESS, 2024, 14

← 1 2 3 →