Genetic diversity analysis in a set of Caricaceae accessions using resistance gene analogues

Sengupta, Samik; Das, Basabdatta; Acharyya, Pinaki; Prasad, Manoj; Ghose, Tapas Kumar

doi:10.1186/s12863-014-0137-0

BMC Genomic Data

Table 4 Details of homology of the DNA sequences identified in this study

From: Genetic diversity analysis in a set of Caricaceae accessions using resistance gene analogues

Marker	N	N1	GenBank Acc. No.	Genotype name of the GenBank accession	L	BLAST homology searches (Megablast)		Q	Conserved domain homology searches
Marker	N	N1	GenBank Acc. No.	Genotype name of the GenBank accession	L	Homology	E-value	Q	Homology	E- value
BDTG 11	41	31	Not assigned	Not applicable	Average length 215bp	Oryza sativa Indica Group cultivar IRGC 16339 xa5 gene, partial cds	4e-56	80%	Not found	Not applicable
BDTG 12	41	31	Not assigned	Not applicable	Average length 456bp	Oryza sativa Indica Group cultivar IRGC 27045 xa5 gene	2e-135	80%	Not found	Not applicable
		10	JM426511.1	Vasconcellea parviflora	189	Oryza nivara cultivar 106133 XA5 (xa5) gene, complete cds	1e-23	47%	Not found	Not applicable
			JM426525	Vasconcellea stipulata	215		5e-19	35%	Not found	Not applicable
			JM426506	Vasconcellea quercifolia	123		4e-29	77%	Gamma subunit of transcription initiation factor IIA	1.54e-04
			JM426460	CO5	123		1e-17	73%	Gamma subunit of transcription initiation factor IIA	6.11e-04
			JM426516	Bangalore Dwarf	115		1e-16	80%	Not found	Not applicable
			JM426495	Pusa Nanha	573	Carica papaya BAC clone 90D06, complete sequence mRNA	2e-24	17%	Cytochrome P450	3.08e-24
			HR614236	CO 1	1046	Brassica rapa subsp. pekinensis clone KBrH011C10, complete sequence	7e-64	30%	Serpentine type 7TM GPCR chemoreceptor Srz	1.74e-04
			JM170468	Pusa Giant	281	No significant similarity found	Not found	Not found	Not found	Not applicable
			JM170470	Vasconcellea pubescens	275	No significant similarity found	Not found	Not found	Not found	Not applicable
			JM170472	Vasconcellea pubescens	555	Pseudomonas pseudoalcaligenes CECT 5344 complete genome	4e-138	70%	Methyl-accepting chemotaxis protein (MCP), signaling domain	7.37e-33
BDTG 13	40	34	Not assigned	Not applicable	Average length 175	Oryza sativa isolate BDTG13-Bhasa receptor kinase (Xa26) gene	1e-16	79%	Not found	Not applicable
BDTG 13		1	HR614235.1	CO1	108	Carica papaya chloroplast, complete genome	0.080	89%	Nickel-dependent hydrogenase	1.74e-16
BDTG14	39	0	Not assigned	Not applicable	Average length 232bp	No significant similarity found	Not found	Not found	Not found	Not found
BDTG17	40	31	Not assigned	Not applicable	Average length 256bp	Oryza sativa (japonica cultivar-group) bacterial blight resistance protein XA26 (Xa26) gene, complete cds	3e-162	55%	LRR receptor-like protein kinase	1.23e-05
BDTG19	41	0	Not assigned	Not applicable	Average length 252bp	No significant similarity found	Not found	Not found	Not found	Not applicable
BDTG21	41	30	Not assigned	Not applicable	Average length 105bp	Oryza sativa Indica Group Xa21 gene for receptor kinase-like protein, complete cds, cultivar:zheda8220	4e-161	76%	LRR	6.45e-07
BDTG22	40	37	Not assigned	Not applicable	Average length 367bp	Oryza rufipogon Xa21F pseudogene, strain:W1236	0.0	82%	Not found	Not applicable
BDTG23	40	31	Not assigned	Not applicable	Average length 203bp	Oryza rufipogon Xa21F pseudogene, strain:W1236	0.0	80%	Not found	Not applicable
BDTG24	40	29	Not assigned	Not applicable	Average length 287bp	Oryza rufipogon Xa21F pseudogene, strain:W149	0.0	80%	Not found	Not applicable
BDTG25	40	35	Not assigned	Not applicable	Average length 181bp	Oryza rufipogon Xa21F pseudogene, strain:W593	0.0	79%	Not found	Not applicable
BDTG30	40	35	Not assigned	Not applicable	Average length 254bp	Oryza sativa Japonica Group Os11g0559200 (Os11g0559200) mRNA	2e-137	72%	LRR receptor-like protein kinase	3.69e-11
BDTG31	41	34	Not assigned	Not applicable	Average length 362bp		1e-173	65%	Not found	Not applicable
BDTG34	39	25	Not assigned	Not applicable	Average length 347bp	Oryza longistaminata receptor kinase-like protein gene, family	2e-110	70%	Not found	Not applicable

N – Total number of sequences obtained.
N1 – Total number of sequences producing significant homology with various sequences of Oryza sativa.
N2 – Total number of sequences allotted accession number by NCBI Genbank.
L – length of the sequence in bp.
Q – percentage of query coverage.

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ISSN: 2730-6844

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