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

 

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

 

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

 

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

 

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

 

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