The Bubalus bubalis genome was sequenced at 17X-19X depth and 91%-95% coverage through a collaboration between the National Bureau of Animal Genetic Resources (NBAGR) in Karnal; the Central Institute for Research on Buffaloes (CIRB) in Hisar; and the Animal Science Division of the Indian Council of Agricultural Research (ICAR).

Copy of data (obtained from URL http://210.212.93.84/bbu_2.0alpha/) used in database development and analysis work is available on request . (Reference: Tantia MS, Vijh RK, Bhasin V, Sikka P, Vij PK, Kataria RS, Mishra BP, Yadav SP, Pandey AK, Sethi RK, Joshi BK, Gupta SC, Pathak KML. Whole-genome sequence assembly of the water buffalo (Bubalus bubalis). The Indian Journal of Animal Sciences 2011, 81(5): 38-46).

All the 27 chromosomes (Chromosome 1-24, M, U and X) were chopped into manageable range of 50000 bp using PERL script. These fragments were given to MIcroSAtellite identification tool (MISA) to identify and find the location of perfect and compound microsatellites for all the chromosomes of buffalo genome. The STR numbers, motifs, repeat number, length of the repeat, size of the repeat, repeat type, GC content, start and end position of the repeat and STR sequence has been compiled.Chromosome wise description of the STRs have been tabulated as well as represented as graphs. The mono, di, tri, tetra, penta and hexa type of microsatellites have been plotted to show the abundance of the type in chromosomes.In addition, facility to locate the STRs on chromosomes based on the position number is incorporated which may be very useful to the animal biotechnologists. The tabulation of simple versus compound shows the proportion of the same.

 

Scientific name
Common name
Order
Chr. no.
Genome Size (MB)
GC%
Bubalis bubalus
Water Buffalo
Bovidae
27 (24+M, U and X)
21.6752
18.03

Table 1. Description of Buffalo genome

 

Type
Number
Percentage
Simple
830058
91.16
Compound
80471
8.84
Total
910529
100.00

Table 2. Distribution of microsatellite types in Buffalo genome

 

ssr1

Figure 1. Graphical view of microsatellite types in Buffalo genome

 

Motif Type
Number
Percentage (%)
Mono
535570
64.52
Di
168741
20.33
Tri
106499
12.83
Tetra
6694
0.81
Penta
12388
1.49
Hexa
166
0.02

Table 3. Motif wise distribution of microsatellites in Buffalo genome

 

Chromosome
Simple
Compound
Mono
Di
Tri
Tetra
Penta
Hexa
1
38690
12112
7672
454
1005
10
5858
2
35354
10911
7062
419
877
10
4899
3
32231
10406
6376
408
702
6
4611
4
30416
9552
6308
404
734
13
4382
5
22149
7486
4568
314
489
6
3365
6
20993
6941
4525
263
532
8
3132
7
21961
6884
4553
291
616
7
3282
8
22977
7190
4787
252
512
7
3333
9
20647
6278
4079
260
440
3
2937
10
20550
6425
4156
228
530
4
3082
11
19223
5662
3852
206
393
8
2701
12
19447
6285
3748
238
441
6
2725
13
17237
5220
3285
199
362
3
2721
14
15197
4703
2841
197
313
3
2162
15
14760
4892
2988
149
342
4
2219
16
15128
4630
3152
185
359
6
2353
17
14489
4585
2721
194
270
2
2160
18
11619
3814
2129
160
181
3
1746
19
13496
4373
2804
155
358
5
2098
20
12474
3949
2465
159
274
3
1832
21
11830
3467
2106
124
203
5
1588
22
12015
3893
2424
117
278
4
1705
23
18764
5898
3686
180
380
2
2704
24
7742
2571
1467
124
136
3
1127
M
1
0
0
0
0
0
0
U
50940
15373
9458
790
1279
26
9045
X
15239
5241
3287
224
382
9
2704

Table 4. Motif wise distribution of microsatellites in Buffalo chromosomes

 

ssr2

Figure 2. Graphical view of motif wise distribution of microsatellites in Buffalo genome

 

gc

Figure 3. Distribution of length of microsatellites in context to GC percentage

 

Class
Frequency of GC content

Percentage

0-10
570674
68.751
11-20
245
0.030
21-30
2878
0.347
31-40
21998
2.650
41-50
127175
15.321
51-60
60
0.007
61-70
89233
10.750
71-80
441
0.053
81-90
15
0.002
91-100
17339
2.089

Table 5. Proportion of GC content in STRs at various ranges

 

ssr3

Figure 4. Graphical view of proportion of GC content in STRs at various ranges

 

Size of STRs
Number of STRs
<10
153185
11-13
276065
14-16
207831
17-25
162575
>25
110873

Table 6. Frequencies of STRs based on their sizes

 

ssr4

Figure 5. Graphical view of STR frequencies based on their sizes

 

Repeats class
Number of STRs
Percentage
5-15
719655
86.699
16-25
105393
12.697
26-35
4672
0.563
36-45
279
0.034
46-55
33
0.004
56-65
14
0.002
66-75
7
0.001
76-85
5
0.001

Table 7. Proportion of STRs based on Repeats’ classes