Annual Report 2011-2012 - Nabi.res.in

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NATIONAL AGRI-FOOD BIOTECHNOLOGY INSTITUTE4. nsSNPs were extracted from the overall SNP result.Table 4: nsSNP statistics.Total no. of nsSNPsNo. of probe setsinvolvedInvolved probe setswith annotationNo. of nsSNPs withannotation35395 12441 12409 352335. SNPs in transcription factors were identified.Table 5: Summary of SNPs in Transcription Factors.No. of probe sets Synonymous SNPs No. of nsSNPs SNPs in domains188 776 335 1066. SNPs in pathways were also determined.Table 6: Summary of mutations in pathways.No. of pathwaysNo. of probesets involvedNo. of enzymesNo. ofsynonymousSNPsNo. of nonsynonymoussubstitutions147 2157 521 13442 45567. SNPs in starch & sucrose metabolism pathway.Table 7: SNP summary in Starch Metabolism Pathway.Pathway IDPath: map00500No. of enzymesinvolvedNo. of probe setsinvolvedNo. ofsynonymousSNPsNo. of nonsynonymoussubstitutions42 214 1840 525nsSNPs in remaining 11995 unigenes from Unigene database of NCBI is being detected.Homoeologous SNPs in chromosome1:According to SNP nomenclature, a homoeologousSNP exists if there is a difference between thethree homoeologous genomes (A, B and D) in asingle individual. Varieties 1 and 2 possess thesame homoeologous SNP and have thecharacteristic of a single individual.Figure 2: Depiction of homoeologus variation between A, B and D genome in wheat.37
NATIONAL AGRI-FOOD BIOTECHNOLOGY INSTITUTEHomoeologous SNP mining was carried outthrough the following steps (Table 8-11):1) SRA reads were retrieved from NCBI SRAdatabase and multifasta was generated.2) Reads were assembled by CLC Assembly Cellsoftware with default parameters.3) Resultant contigs were filtered to get thehomoeologs using cut-off value of minimum5 reads from each of the 3 genomes (A,B,D)producing 105 homoeologs out of which 90homoeologs have the polymorphism whichis determined by autosnpV1 script.4) SNPs in the regulatory region were identifiedusing cis regulatory motifs in PLACEdatabase.Table 8: Assembly results of hexaploid wheat chromosomeCLC versionNo. of SRAreadsSingleton Assemble reads Total no. ofcontigs4 beta 1072765 6126635 4601040 8854313.2 1072765 2850260 7877415 821609Table 9: Assembled contig summary.Total no. ofcontigsNo. of contigswith reads from1 genomeNo. of contigswith reads from2 genomesTable 10: Homoeologous SNPs summary.No. of contigshaving readsfrom allgenomesNo. of contigswith no readinformation885431 284159 71530 47205 482537821609 443337 130377 81295 166600Both 3.2 and 4 beta versions were used to compare the number of identified SNPs.No. of contigsReads from AgenomeReads from BgenomeReads from DgenomeTotal no. ofSNPs90 4254 4810 1182 1817Table 11: PLACE database screening report.No. of contigsTotal no. ofregulatory SNPsNo. of contigswith noregulatory SNPsNo. of annotatedcontigs withregulatory SNPsNo. of annotatedregulatory SNPs90 369 31 40 2505) Calculation of GC content for all the genomes from chromosome 1 (Table 12).Table 12: Nucleotide base summary and GC contents of 3 genomes.Features Genome A Genome B Genome DGC content 0.4317 0.4368 0.443038
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