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Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.).

Dubey A, Farmer A, Schlueter J, Cannon SB, Abernathy B, Tuteja R, Woodward J, Shah T, Mulasmanovic B, Kudapa H, Raju NL, Gothalwal R, Pande S, Xiao Y, Town CD, Singh NK, May GD, Jackson S, Varshney RK - DNA Res. (2011)

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: Centre of Excellence in Genomics (CEG), Building #300, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, India.

ABSTRACT
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.

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Related in: MedlinePlus

Distribution of differentially expressed genes in SMD- and FW-responsive genotypes. Differential expression was calculated based on Log 2 value, with a threshold of less than −2 to greater than +2 number of differentially expressed gene was calculated for three SMD- and two FW-parental combinations. Comparison of expression values from susceptible parent to the resistant gave an estimate of up- and down-regulated genes in each cross.
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DSR007F3: Distribution of differentially expressed genes in SMD- and FW-responsive genotypes. Differential expression was calculated based on Log 2 value, with a threshold of less than −2 to greater than +2 number of differentially expressed gene was calculated for three SMD- and two FW-parental combinations. Comparison of expression values from susceptible parent to the resistant gave an estimate of up- and down-regulated genes in each cross.

Mentions: Since the numbers of Illumina tags mapped to the transcriptome assembly varied among genotypes, the data were normalized per million reads. For the SMD study, a numerical comparison of SMD-responsive reads generated from three resistant (ICPL 20096, BSMR 736 and ICPL 7035) and three susceptible (ICPL 332, TAT 10 and TTB 7) genotypes representing three mapping populations was conducted. The Log 2 threshold for this analysis was taken as −2 to +2. The number of TUSs showing expression differences at these cutoffs ranged from 7505 (BSMR 736 × TAT 10) to 10 497 (ICPL 20096 × ICPL 332). In the case of the TTB 7 × ICPL 7035 combination, the number of differentially expressed genes was 9402. Similarly, in the FW study, a comparison was made between the specific parental combinations used to develop two different mapping populations (with the same thresholds) to find TUSs with differential expression. The number of TUSs with significant differentially expressed genes ranged from 6673 (ICPB 2049 × ICPL 99050) to 11 518 (ICPL 87119 × ICPL 87091) (Fig. 3).Figure 3.


Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.).

Dubey A, Farmer A, Schlueter J, Cannon SB, Abernathy B, Tuteja R, Woodward J, Shah T, Mulasmanovic B, Kudapa H, Raju NL, Gothalwal R, Pande S, Xiao Y, Town CD, Singh NK, May GD, Jackson S, Varshney RK - DNA Res. (2011)

Distribution of differentially expressed genes in SMD- and FW-responsive genotypes. Differential expression was calculated based on Log 2 value, with a threshold of less than −2 to greater than +2 number of differentially expressed gene was calculated for three SMD- and two FW-parental combinations. Comparison of expression values from susceptible parent to the resistant gave an estimate of up- and down-regulated genes in each cross.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3111231&req=5

DSR007F3: Distribution of differentially expressed genes in SMD- and FW-responsive genotypes. Differential expression was calculated based on Log 2 value, with a threshold of less than −2 to greater than +2 number of differentially expressed gene was calculated for three SMD- and two FW-parental combinations. Comparison of expression values from susceptible parent to the resistant gave an estimate of up- and down-regulated genes in each cross.
Mentions: Since the numbers of Illumina tags mapped to the transcriptome assembly varied among genotypes, the data were normalized per million reads. For the SMD study, a numerical comparison of SMD-responsive reads generated from three resistant (ICPL 20096, BSMR 736 and ICPL 7035) and three susceptible (ICPL 332, TAT 10 and TTB 7) genotypes representing three mapping populations was conducted. The Log 2 threshold for this analysis was taken as −2 to +2. The number of TUSs showing expression differences at these cutoffs ranged from 7505 (BSMR 736 × TAT 10) to 10 497 (ICPL 20096 × ICPL 332). In the case of the TTB 7 × ICPL 7035 combination, the number of differentially expressed genes was 9402. Similarly, in the FW study, a comparison was made between the specific parental combinations used to develop two different mapping populations (with the same thresholds) to find TUSs with differential expression. The number of TUSs with significant differentially expressed genes ranged from 6673 (ICPB 2049 × ICPL 99050) to 11 518 (ICPL 87119 × ICPL 87091) (Fig. 3).Figure 3.

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: Centre of Excellence in Genomics (CEG), Building #300, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, India.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus