Page 6 - Legume Genomics and Genetics

Legume Genomics and Genetics 2014, Vol.5, No.7, 1-7
http://lgg.biopublisher.ca
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1.6 SSR mining
We employed MIcroSAtellite (MISA) (http://pgrc.ipk-
gatersleben.de/misa/) for microsatellite mining which
gives various statistical outputs of transcripts with
useful information.
1.7 Plant transcription factor
PlantTFcat: An Online Plant Transcription Factor and
Transcriptional Regulator Categorization and Analysis
Tool used for identifying plant transcription factor in
sequences (http://plantgrn.noble.org/PlantTFcat/).
Transcription factor encoding transcripts were
identified by sequence comparison to known
transcription factor gene families.
2 Result and Discussions
2.1 NGS QC Toolkit
Sequence was filtered with this tool by removing
adaptors and other contaminated materials then quality
of sequence also checked with this tool and finally
high quality filter sequence file considered for de novo
sequence assembly (Table 1).
Table 1 NGS QC Toolkit Result
File Details Original File High Quality (HQ)
Filter file
Total number of reads 627117 609237
Total number of bases 146335656 141577237
Percentage of HQ reads -- 97.15%
2.2 De novo Sequence Assembly
CLC GENOMICS WORKBENCH 7 considered for
de novo sequence assembly with by default
parameters like Mismatch Cost=2, Insertion Cost=3,
Deletion Cost=3, Length Fraction=0.5, Similarity
Fraction=0.8, Word size=21 and finally 7256 contigs
generated with average value of 445 by this software
and other details are shown in Table 2.
Table 2 Contig measurement
Description Length
N75 348
N50 470
N25 667
Minimum 86
Maximum 3231
Average 445
Count (Contigs) 7256
3 Functional annotation with BLASTX and
blast2GO
3.1 BLASTX
BLASTX was performed to align the contigs against
non-redundant sequences database using an E value
threshold of 10-6. Out of 7256 transcript contigs, 1983
were having BLAST hits to known proteins with high
significant similarity and 167 had no BLAST hits
(Table 3). Out of total transcripts contigs, Table 4 and
Figure 1 shows that species distribution in which 2515
sequences showed significant similarity with
Medicago truncatula and least similarity was found
with Solanum lycopersicum (11).
Table 3 Blast Result
Without Blast Results 167
Without Blast Hits 2656
With Blast Results 1983
With Mapping Results 192
Annotated Sequences 2258
Total Sequences 7256
Table 4 Blast Result of Species Distribution
Species Blast Hit
Medicago truncatula 2515
Cicer arietinum 923
Glycine max 184
Phaseolus vulgaris 97
Lotus japonicas 65
Medicago sativa 44
Pisum sativum 42
Vitis vinifera 38
Populus trichocarpa 30
Theobroma cacao 24
Ricinus communis 23
Morus notabilis 20
Erythranthe guttata 20
Trigonella foenum-graecum 19
Cucumis sativus 18
Prunus persica 16
Citrus clementina 16
Jatropha curcas 15
Trifolium pratense 15
Arabidopsis lyrata 14
Citrus sinensis 14
Eutrema salsugineum 14
Arabidopsis thaliana 13
Eucalyptus grandis 13
Vicia faba 12
Solanum tuberosum 12
Zea mays 12
Fragaria vesca 11
Solanum lycopersicum 11
others 183