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Statistics
Genus Vigna is one of the important fabaceae family crops, mainly found in the region of Asia and Africa. Approximately genus Vigna contains >100 species which are geographically widespread and morphologically diverse, mainly found in tropical regions and warm temperate.
The genome size of all the Vigna species are small and may vary from species to species ranging from 416 to 1394Mb.Till now, several genome assemblies of three Vigna species such as Mungbean (Vigna radiata), Adzuki bean (Vigna angularis var. angularis) and (Cowpea) Vigna unguiculata are available in NCBI. We have downloaded all the assembly data from NCBI and identified simple sequence repeats from genome using perl script of MIcroSAtellite identification tool (MISA)(http://pgrc.ipk-gatersleben.de/misa/). Further, mined literature for identification of experimentally validated markers and deposited in the database.
Information of genomic data available in public domain (NCBI)
Species |
Cultivars |
Accession no. |
Assembly level |
V. radiata |
VC1973A |
GCA_000741045.2 |
Chromosome |
RIL59 |
GCA_001584445.1 |
Scaffold |
V. angularis |
Jingnong 6 |
GCA_001190045.1 |
Chromosome |
Kyungwonpat |
GCA_001723775.1 |
Chromosome |
IT213134 |
GCA_000465365.1 |
Scaffold |
V. unguiculata |
IT97K-499-35 |
GCA_001687525.1 |
Scaffold |
Description of Vigna species mentioned in NCBI
Species |
Cultivars |
Size (Mb) |
GC% |
Genes |
Proteins |
V. radiata |
VC1973A |
463.638 |
34.40 |
29938 |
42284 |
RIL59 |
454.907 |
32.00 |
- |
- |
V. angularis |
Jingnong 6 |
467.301 |
34.62 |
29474 |
37769 |
Kyungwonpat |
444.439 |
31.77 |
- |
- |
IT213134 |
291.824 |
33.10 |
- |
- |
V. unguiculata |
IT97K-499-35 |
695.046 |
13.6 |
|
|
Details of Markers identified from genome assemblies of Vigna species
Species |
Cultivars |
Total |
Simple |
Compound |
V. radiata |
VC1973A |
200178 |
174113 |
26065 |
RIL59 |
200642 |
173405 |
27237 |
V. angularis |
Jingnong6 |
147634 |
130521 |
17113 |
Kyungwonpat |
143109 |
126601 |
16508 |
IT213134 |
92467 |
82406 |
10061 |
V. unguiculata |
IT97K-499-35 |
92189 |
85308 |
6881 |
Motifwise Distribution of all the Vigna species
|
V. radiata |
V. angularis |
V. unguiculata |
Unit size |
VC1973A |
RIL59 |
Jingnong6 |
Kyungwonpat |
IT213134 |
IT97K-499-35 |
Mono |
127648 |
127845 |
86204 |
78016 |
54256 |
59935 |
Di |
51742 |
50825 |
42703 |
48685 |
25646 |
21813 |
Tri |
17872 |
18956 |
16534 |
14560 |
11330 |
9260 |
Tetra |
1827 |
1822 |
1212 |
1200 |
867 |
872 |
Penta |
912 |
1003 |
734 |
414 |
231 |
187 |
Hexa |
177 |
191 |
247 |
234 |
137 |
122 |
Chromosome-wide distribution of three full genome assemblies V. radiata (cv. VC1973A), V. angularis (cv. Jingnong6) and V. angularis (cv. kyungwonpat)
|
V. radiata
(cv. VC1973A) |
V. angularis
(cv. Jingnong6) |
V. angularis
(cv. kyungwonpat) |
chromosome 1 |
13356 |
13466 |
9033 |
chromosome 2 |
9965 |
10756 |
7946 |
chromosome 3 |
6579 |
11862 |
7532 |
chromosome 4 |
8380 |
9574 |
8112 |
chromosome 5 |
16077 |
8518 |
4285 |
chromosome 6 |
13598 |
6171 |
12358 |
chromosome 7 |
23165 |
10689 |
3547 |
chromosome 8 |
18112 |
7978 |
3688 |
chromosome 9 |
8033 |
9501 |
4467 |
chromosome 10 |
8739 |
10750 |
2740 |
chromosome 11 |
8599 |
6955 |
9282 |
Unplaced scaffolds |
39510 |
24301 |
53611 |
Chromosome-wide distribution of three full genome assemblies V. radiata (cv. VC1973A), V. angularis (cv. Jingnong6) and V. angularis (cv. kyungwonpat)
Abundant repeat types in V. radiata genome assemblies
| Species |
Mono |
Di |
Tri |
Tetra |
Penta |
Hexa |
V. radiata VC1973A |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
(A)10 |
25847 |
(TA)6 |
1297 |
(AAT)5 |
602 |
(AAAT)5 |
116 |
(AAAAT)5 |
29 |
(AAAAAT)5 |
5 |
(T)10 |
25690 |
(AT)6 |
1181 |
(ATT)5 |
511 |
(TTTA)5 |
92 |
(ATTTT)5 |
18 |
(AAAATA)5 |
4 |
(T)11 |
10992 |
(AT)7 |
692 |
(ATA)5 |
464 |
(AATA)5 |
47 |
(TTTTA)5 |
18 |
(CAACAT)5 |
2 |
(A)11 |
10965 |
(TA)7 |
655 |
(TAT)5 |
444 |
(TTAT)5 |
45 |
(TTTAT)5 |
15 |
(CATCTT)6 |
2 |
(A)12 |
5472 |
(AT)8 |
623 |
(TTA)5 |
414 |
(TATT)5 |
40 |
(AAAAT)6 |
13 |
(AATTCA)5 |
2 |
V. radiata cv. RIL59 |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
(T)10 |
26651 |
(TA)6 |
1510 |
(AAT)5 |
629 |
(AAAT)5 |
129 |
(AAAAT)5 |
27 |
(AAAAAT)5 |
5 |
(A)10 |
26548 |
(AT)6 |
1344 |
(ATT)5 |
545 |
(TTTA)5 |
84 |
(ATTTT)5 |
26 |
(CAACAT)5 |
4 |
(A)11 |
10933 |
(AT)16 |
924 |
(ATA)5 |
491 |
(TTAT)5 |
59 |
(TTTTA)5 |
21 |
(GAAGAT)5 |
4 |
(T)11 |
10770 |
(AT)15 |
874 |
(TAT)5 |
450 |
(ATTT)5 |
52 |
(TTTAT)5 |
21 |
(AAAATA)5 |
3 |
(T)12 |
5355 |
(AT)14 |
872 |
(TTA)5 |
419 |
(AATA)5 |
46 |
(AAATA)5 |
13 |
(TTTATT)5 |
2 |
Abundant repeat types in V. angularis genome assemblies
| Species |
Mono |
Di |
Tri |
Tetra |
Penta |
Hexa |
| V.angularis cv.Jingnong6 |
R |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
|
(A)10 |
23616 |
(TA)6 |
2284 |
(AAT)5 |
676 |
(AAAT)5 |
92 |
(AAAAT)5 |
102 |
(CTCCTT)5 |
9 |
(T)10 |
23432 |
(AT)6 |
2099 |
(TAT)5 |
490 |
(TTTA)5 |
67 |
(TTTTA)5 |
86 |
(TATTTT)5 |
4 |
(A)11 |
7308 |
(TA)7 |
1903 |
(ATT)5 |
465 |
(ATTT)5 |
44 |
(AAAAT)6 |
28 |
(CACAAA)5 |
3 |
(T)11 |
7206 |
(TA)8 |
1753 |
(ATA)5 |
450 |
(TTAT)5 |
44 |
(TTTTA)6 |
23 |
(TCCTTC)5 |
3 |
(A)12 |
2794 |
(AT)7 |
1739 |
(TTA)5 |
444 |
(ATAA)5 |
39 |
(TTATT)5 |
23 |
(CTCCTG)5 |
3 |
| V.angularis cv.Kyungwonpat |
R |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
|
(T)10 |
21824 |
(TA)6 |
1487 |
(AAT)5 |
620 |
(AAAT)5 |
88 |
(AAAAT)5 |
28 |
(AGGAGA)5 |
5 |
(A)10 |
21788 |
(AT)6 |
1376 |
(TAT)5 |
475 |
(TTTA)5 |
69 |
(TTTTA)5 |
20 |
(TAAAAA)5 |
2 |
(A)11 |
6713 |
(TA)7 |
947 |
(TTA)5 |
459 |
(TTAT)5 |
40 |
(TTTAT)5 |
15 |
(TCATCC)5 |
2 |
(T)11 |
6598 |
(AT)7 |
883 |
(ATT)5 |
457 |
(AATA)5 |
38 |
(TTATT)5 |
13 |
(AGAGAA)5 |
2 |
(A)12 |
2509 |
(AT)8 |
873 |
(ATA)5 |
444 |
(ATTT)5 |
38 |
(TTTTA)6 |
10 |
(CAGATC)5 |
2 |
| V.angularis IT213134 |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
(T)10 |
15822 |
(TA)6 |
971 |
(AAT)5 |
460 |
(AAAT)5 |
59 |
(AAAAT)5 |
26 |
|
3 |
(A)10 |
15819 |
(AT)6 |
945 |
(TAT)5 |
402 |
(TTTA)5 |
50 |
(TTTTA)5 |
10 |
(CTCAGC)5 |
2 |
(T)11 |
4889 |
(AT)8 |
667 |
(ATA)5 |
373 |
(ATTT)5 |
35 |
(TTATT)5 |
8 |
(TTTTTA)7 |
2 |
(A)11 |
4837 |
(AT)9 |
666 |
(TTA)5 |
358 |
(TTAT)5 |
29 |
(AAAAT)6 |
7 |
(TTATTT)5 |
2 |
(A)12 |
1841 |
(AT)7 |
646 |
(ATT)5 |
349 |
(TATT)5 |
27 |
(AATAA)5 |
6 |
(TGAGGC)5 |
2 |
*R=repeats; F*=frequency
Abundant repeat types in V. unguiculata genome assemblies
Species |
Mono |
Di |
Tri |
Tetra |
Penta |
Hexa |
| V.unguiculata IT97K-499-35 |
R |
F |
R |
F |
R |
F |
R |
F |
R |
F |
R |
|
(A)10 |
13186 |
(AT)12 |
1297 |
(AAT)5 |
258 |
(AAAT)5 |
41 |
(ATTAT)6 |
7 |
(TGGGGA)5 |
2 |
(T)10 |
12841 |
(AT)11 |
1261 |
(ATT)5 |
230 |
(ATTT)5 |
32 |
(AATAT)6 |
5 |
(AAAAAC)5 |
2 |
(A)11 |
5598 |
(TA)11 |
1053 |
(GAA)5 |
211 |
(TTTA)5 |
31 |
(TTTTA)5 |
5 |
(TCCTCA)5 |
2 |
(T)11 |
5495 |
(TA)12 |
1035 |
(TTC)5 |
203 |
(ATTA)5 |
26 |
(TCTCT)5 |
5 |
(GATTCA)6 |
2 |
(A)12 |
2841 |
(TA)6 |
780 |
(ATA)5 |
179 |
(TAAT)5 |
25 |
(AAAAT)5 |
4 |
(TAAAAT)5 |
2 |
| 