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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 and read depth of sequence tags in the contigs. Number of 454 STRs aligning to form a contig ranged from 2 to >1000. A total of 36 152 contigs showed a read depth ranging from 2 to 5 tags, followed by 6755 contigs with read depth 6–10 tags, 5517 contigs with read depth 11–100 tags and 290 contigs with read depth ranging from 100 to 1000 tags. A maximum of 12 contigs showed a read depth of >1000 tags.
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DSR007F1: Distribution and read depth of sequence tags in the contigs. Number of 454 STRs aligning to form a contig ranged from 2 to >1000. A total of 36 152 contigs showed a read depth ranging from 2 to 5 tags, followed by 6755 contigs with read depth 6–10 tags, 5517 contigs with read depth 11–100 tags and 290 contigs with read depth ranging from 100 to 1000 tags. A maximum of 12 contigs showed a read depth of >1000 tags.

Mentions: The CcTA includes 48 726 (38.1%) contigs (average length 273 bp, maximum length 2067 bp) and 79 028 (61.9%) singletons (average length 198 bp, maximum length 1720 bp). A total of 3021 contigs (6.1%) were longer than 500 bp. Details about length distribution and read depth of contigs are given in Table 1 and Fig. 1, respectively. The overall redundancy of the library was calculated at 25.2%, suggesting that the normalization process was effective and that the libraries generated have the potential to uncover many more unique transcripts. These results support that FLX/454-based gene discovery represents a viable and perhaps favourable alternative to Sanger-based sequencing of EST libraries, when a diverse sampling of genes is more important than obtaining full transcript-length contigs.15,24Table 1.


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 and read depth of sequence tags in the contigs. Number of 454 STRs aligning to form a contig ranged from 2 to >1000. A total of 36 152 contigs showed a read depth ranging from 2 to 5 tags, followed by 6755 contigs with read depth 6–10 tags, 5517 contigs with read depth 11–100 tags and 290 contigs with read depth ranging from 100 to 1000 tags. A maximum of 12 contigs showed a read depth of >1000 tags.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSR007F1: Distribution and read depth of sequence tags in the contigs. Number of 454 STRs aligning to form a contig ranged from 2 to >1000. A total of 36 152 contigs showed a read depth ranging from 2 to 5 tags, followed by 6755 contigs with read depth 6–10 tags, 5517 contigs with read depth 11–100 tags and 290 contigs with read depth ranging from 100 to 1000 tags. A maximum of 12 contigs showed a read depth of >1000 tags.
Mentions: The CcTA includes 48 726 (38.1%) contigs (average length 273 bp, maximum length 2067 bp) and 79 028 (61.9%) singletons (average length 198 bp, maximum length 1720 bp). A total of 3021 contigs (6.1%) were longer than 500 bp. Details about length distribution and read depth of contigs are given in Table 1 and Fig. 1, respectively. The overall redundancy of the library was calculated at 25.2%, suggesting that the normalization process was effective and that the libraries generated have the potential to uncover many more unique transcripts. These results support that FLX/454-based gene discovery represents a viable and perhaps favourable alternative to Sanger-based sequencing of EST libraries, when a diverse sampling of genes is more important than obtaining full transcript-length contigs.15,24Table 1.

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