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Legume Genomics and Genetics 2014, Vol.5, No.7, 1-7
http://lgg.biopublisher.ca
5
Figure 4 WEGO Tool Result
A total of 192 unigenes were annotated with 87
pathways in the KEGG database (http://www.genome.
jp/kegg/pathway.html). Many transcripts include
various pathways like metabolic pathways, plant-pathogen
interaction pathways, fatty acid metabolism pathway
and fatty acid biosynthesis.
4 SSR mining
Microsatellite markers (SSR markers) are some of the
most successful molecular markers in the construction
of a
Trigonella foenum-graecum L.
genetic map and in
diversity analysis (Zhang et al). For identification of
SSRs, all transcripts were searched with perl script
MISA. We identified a total of 3107 SSRs in 2191
transcripts (Table 5). The mono-nucleotide SSRs
represented the largest fraction of SSRs identified
followed by tri-nucleotide and di-nucleotide SSRs.
Although only a small fraction of tetra-, penta- and
hexa-nucleotide SSRs were identified in transcripts,
the number is quite significant.
5 Plant Transcription Factor
Further, transcription factor encoding transcripts were
identified by sequence comparison to known
transcription factor gene families. Result shows that
Table 5 Statistics of SSRs identified in transcripts
SSR Mining:
Total number of sequences examined:
7256
Total size of examined sequences (bp):
3226271
Total number of identified SSRs:
3107
Number of SSR containing sequences: 2191
Number of sequences containing more than one SSR: 747
Number of SSRs present in compound formation: 747
Distribution to different repeat type classes:
Mono-nucleotide
2589
Di-nucleotide
235
Tri-nucleotide
243
Tetra-nucleotide
28
Penta-nucleotide
10
Hexa-nucleotide
2
transcription factor genes distributed with at least 45
families were identified (Figure 5). The overall
distribution of transcription factor encoding transcripts
among the various known protein families is very
similar with that of other legumes as predicted earlier
(Libault et al., 2009).
6 Conclusion
This study is focus on
Trigonella foenum-graecum
L.
species (
SRR066197
) from NCBI database for de novo
Transcriptome analysis by RNA-seq using next-generation