Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions

Lei, Yi; Zhou, Yu; Price, Megan; Song, Zhaobin

doi:10.1186/s12864-021-07752-6

Table 2 Microsatellite distribution as frequency, density and GC content of different fish genomes

From: Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions

Repeat type	Species	Abbreviation	Total numbers	Total length (bp)	Relative abundace (loci/Mb)	Relative Density (bp/Mb)	Coverage degree (%)	G + C
Repeat type	Species	Abbreviation	Total numbers	Total length (bp)	Relative abundace (loci/Mb)	Relative Density (bp/Mb)	Coverage degree (%)	Length (bp)	content (%)
Mono- (1-nt)	D. rerio	Drer	207,951	3,278,888	155.12	2445.81	0.24	156,865	4.78
	O. niloticus	Onil	85,303	1,316,072	98.69	1522.59	0.15	139,335	10.59
	O. latipes	Olat	76,805	1,120,875	131.94	1925.44	0.19	198,155	17.68
	T. rubripes	Ttub	34,748	504,976	129.25	1878.28	0.19	264,888	52.46
	I. punctatus	Ipun	176,856	2,991,388	237.37	4013.86	0.40	343,854	11.49
	C. semilaevis	Csem	97,303	1,483,637	232.06	3539.85	0.35	231,161	15.58
	E. lucius	Eluc	45,139	667,053	62.88	928.80	0.08	326,439	48.94
	O. mykiss	Omyk	90,887	1,336,990	51.64	759.16	0.08	690,373	51.64
	N. furzeri	Nfur	50,594	805,921	71.06	1131.40	0.11	364,314	45.20
	L. oculatus	Locu	26,639	347,118	39.34	517.74	0.04	80,197	23.10
	A. mexicanus	Amex	170,345	3,398,972	189.44	3753.31	0.38	266,645	7.84
	C. carpio	Ccar	186,935	2,883,267	230.83	3558.04	0.37	84,049	2.91
	P. reticulata	Pret	119,330	1,775,344	188.83	2810.96	0.23	66,159	3.73
	O. kisutch	Okis	96,581	1,542,599	59.64	952.88	0.09	993,999	64.44
Di- (2-nt)	D. rerio	Drer	382,761	14,766,368	285.51	11,014.63	1.10	3,485,035	23.60
	O. niloticus	Onil	123,095	3,294,102	142.41	3811.02	0.38	1,337,732	40.61
	O. latipes	Olat	25,449	515,736	43.72	885.93	0.09	203,111	39.38
	T. rubripes	Trub	63,408	12,729,440	235.85	6432.72	4.73	837,010	6.58
	I. punctatus	Ipun	359,022	10,686,166	484.03	14,362.27	1.42	3,777,407	35.35
	C. semilaevis	Csem	127,607	2,668,806	2998.81	6238.79	0.63	1,071,149	40.14
	E. lucius	Eluc	150,812	3,215,024	212.80	4533.65	0.41	1,466,606	45.62
	O. mykiss	Omyk	390,181	11,517,856	225.44	7684.48	0.66	5,186,111	45.03
	N. furzeri	Nfur	186,289	6,543,766	261.89	9175.17	0.91	3,065,853	46.85
	L. oculatus	Locu	16,853	289,242	30.03	527.85	0.03	122,671	42.41
	A. mexicanus	Amex	446,448	12,194,636	498.90	13,549.68	1.36	3,706,651	30.40
	C. carpio	Ccar	181,614	5,801,364	224.78	7173.27	0.72	2,057,824	35.47
	P. reticulata	Pret	70,237	1,810,180	110.24	2843.81	0.28	858,108	47.40
	O. kisutch	Okis	502,660	12,625,074	310.50	7784.45	0.78	6,023,864	47.71
Tri- (3-nt)	D. rerio	Drer	140,175	3,374,835	104.56	2517.38	0.25	262,890	7.79
	O. niloticus	Onil	33,649	662,808	38.93	766.82	0.08	166,799	25.17
	O. latipes	Olat	15,732	295,236	27.02	507.16	0.05	104,498	35.39
	T. rubripes	Ttub	12,671	262,275	47.13	975.54	0.10	117,321	44.73
	I. punctatus	Ipun	91,842	2,466,039	123.29	3302.90	0.32	324,772	13.17
	C. semilaevis	Csem	48,581	1,052,241	114.46	2478.47	0.25	408,981	38.87
	E. lucius	Eluc	11,632	208,425	15.88	284.64	0.03	62,534	30.03
	O. mykiss	Omyk	37,290	704,511	21.39	404.12	0.05	210,431	29.87
	N. furzeri	Nfur	39,742	918,591	55.80	1288.97	0.13	221,669	24.13
	L. oculatus	Locu	26,590	644,715	35.80	822.92	0.08	93,309	14.47
	A. mexicanus	Amex	61,775	2,572,995	69.16	2833.21	0.29	333,193	12.95
	C. carpio	Ccar	53,774	1,273,065	66.86	1588.10	0.16	127,770	10.04
	P. reticulata	Pret	24,815	616,578	39.01	966.24	0.10	144,894	23.50
	O. kisutch	Okis	34,901	643,725	21.72	401.60	0.04	213,491	33.16
Tetra- (4-nt)	D. rerio	Drer	243,740	8,195,596	181.81	6113.32	0.61	2,326,652	28.39
	O. niloticus	Onil	32,971	731,160	38.14	845.90	0.08	210,529	28.79
	O. latipes	Olat	22,084	776,628	37.94	1334.10	0.13	250,470	32.25
	T. rubripes	Trub	16,187	541,848	60.21	2015.43	0.20	231,326	42.69
	I. punctatus	Ipun	108,518	2,422,148	145.59	3347.91	0.32	526,093	21.72
	C. semilaevis	Csem	34,100	768,504	79.96	1807.35	0.18	277,262	36.08
	E. lucius	Eluc	21,952	411,372	30.05	562.93	0.05	191,704	46.60
	O. mykiss	Omyk	70,423	1,850,584	40.46	1062.57	0.11	826,372	44.65
	N. furzeri	Nfur	55,909	1,531,664	78.34	2142.29	0.21	530,688	34.65
	L. oculatus	Locu	4439	92,396	7.76	153.69	0.01	35,673	38.61
	A. mexicanus	Amex	84,721	3,160,820	95.30	3525.04	0.35	884,624	27.99
	C. carpio	Ccar	62,915	1,749,772	77.78	2162.41	0.22	374,219	21.39
	P. reticulata	Pret	32,055	1,138,844	50.22	1777.93	0.18	421,839	37.04
	O. kisutch	Okis	90,546	2,527,184	55.65	1551.12	0.16	1,163,069	46.02
Penta- (5-nt)	D. rerio	Drer	35,377	1,419,895	26.39	1059.14	0.11	104,811	7.38
	O. niloticus	Onil	12,089	316,950	13.99	366.69	0.04	69,140	21.81
	O. latipes	Olat	4973	145,115	8.54	249.28	0.02	36,644	25.25
	T. rubripes	Ttub	3871	164,760	14.40	612.83	0.06	87,874	53.33
	I. punctatus	Ipun	9556	234,630	12.84	315.11	0.03	50,793	21.65
	C. semilaevis	Csem	5828	186,075	13.57	428.73	0.04	54,885	29.50
	E. lucius	Eluc	1140	26,200	1.55	35.77	0.00	11,874	45.32
	O. mykiss	Omyk	13,985	342,135	7.96	194.80	0.02	122,566	35.82
	N. furzeri	Nfur	10,079	275,340	14.04	382.28	0.04	76,366	27.74
	L. oculatus	Locu	2292	56,690	3.10	73.65	0.01	20,527	36.21
	A. mexicanus	Amex	16,919	1,094,190	18.90	1187.90	0.12	282,448	25.81
	C. carpio	Ccar	15,817	686,070	19.57	850.94	0.08	79,829	11.64
	P. reticulata	Pret	3815	125,295	5.97	195.30	0.02	32,651	26.06
	O. kisutch	Okis	17,343	428,935	10.64	263.32	0.03	166,246	38.76
Hexa- (6-nt)	D. rerio	Drer	2080	58,950	1.55	43.97	0.00	19,507	33.09
	O. niloticus	Onil	966	26,856	1.12	31.07	0.00	8832	32.89
	O. latipes	Olat	485	13,884	0.83	23.85	0.00	5484	39.50
	T. rubripes	Trub	1127	34,446	4.19	128.12	0.01	18,573	53.92
	I. punctatus	Ipun	1671	44,820	2.24	59.92	0.01	15,581	34.76
	C. semilaevis	Csem	2996	106,962	7.08	252.92	0.03	50,107	48.85
	E. lucius	Eluc	712	23,232	1.01	33.21	0.00	11,962	51.49
	O. mykiss	Omyk	4590	140,352	2.66	81.33	0.01	71,447	50.91
	N. furzeri	Nfur	1664	44,028	2.33	61.70	0.01	20,000	45.42
	L. oculatus	Locu	1565	53,070	1.84	62.81	0.01	23,037	43.41
	A. mexicanus	Amex	2179	193,794	2.43	209.55	0.02	60,384	31.16
	C. carpio	Ccar	1724	69,300	2.13	88.33	0.01	20,736	29.92
	P. reticulata	Pret	786	21,594	1.23	33.73	0.00	11,193	51.83
	O. kisutch	Okis	5178	169,488	3.20	104.70	0.01	85,527	50.46
Total	D. rerio	Drer	1,012,084	31,094,532	754.94	23,194.25	2.31	6,355,760	20.44
	O. niloticus	Onil	288,073	6,347,948	333.28	7344.09	0.73	1,932,367	30.44
	O. latipes	Olat	145,528	2,867,474	249.99	4925.76	0.48	798,362	27.84
	T. rubripes	Trub	132,012	14,237,745	491.03	12,042.92	5.29	1,556,992	10.94
	I. punctatus	Ipun	747,465	18,845,191	1005.36	25,401.97	2.50	5,038,500	26.74
	C. semilaevis	Csem	316,415	6,266,225	3445.94	14,746.11	1.48	2,093,545	33.41
	E. lucius	Eluc	231,387	4,551,306	324.17	6379.00	0.57	2,071,119	45.51
	O. mykiss	Omyk	607,356	15,892,428	349.55	10,186.46	0.93	7,107,300	44.72
	N. furzeri	Nfur	344,277	10,119,310	483.46	14,181.81	1.41	4,278,890	42.28
	L. oculatus	Locu	78,378	1,483,231	117.87	2158.66	0.18	375,414	25.31
	A. mexicanus	Amex	782,387	22,615,407	874.13	25,058.69	2.52	5,533,945	24.47
	C. carpio	Ccar	502,779	12,462,838	621.95	15,421.09	1.56	2,744,427	22.02
	P. reticulata	Pret	251,038	5,487,835	395.50	8627.97	0.81	1,534,844	27.97
	O. kisutch	Okis	747,209	17,937,005	461.35	11,058.07	1.11	8,646,196	48.20

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