Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

Huang, Shiao-Wei; Lin, You-Yu; You, En-Min; Liu, Tze-Tze; Shu, Hung-Yu; Wu, Keh-Ming; Tsai, Shih-Feng; Lo, Chu-Fang; Kou, Guang-Hsiung; Ma, Gwo-Chin; Chen, Ming; Wu, Dongying; Aoki, Takashi; Hirono, Ikuo; Yu, Hon-Tsen

doi:10.1186/1471-2164-12-242

BMC Genomics

Table 2 Characterization of microsatellites in the P. monodon genome^a

From: Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

Motif	Unit	Counts^b	# FES^c	% FES^d	Bases (bp)^e	Bases^f	Max length^g	Mean length^h	STD lengthⁱ	Mean repeat no.^j	RA (%)^k	RF (%)^l
A	1	159	158	0.76	7,467	0.07	376	46.96	35.63	46.96	0.81	1.88
AC	2	1153	1095	5.23	118,430	1.07	783	102.71	93.67	51.36	12.85	13.66
AG	2	1424	1395	6.67	198,119	1.78	763	139.13	104.88	69.56	21.50	16.87
AT	2	912	896	4.28	87,832	0.79	604	96.31	70.28	48.15	9.53	10.80
CG	2	91	91	0.43	3,995	0.04	142	43.90	10.94	21.95	0.43	1.08
AAC	3	125	114	0.54	10,390	0.09	457	83.12	65.03	27.71	1.13	1.48
AAG	3	265	255	1.22	27,823	0.25	720	104.99	111.32	35.00	3.02	3.14
AAT	3	915	881	4.21	130,973	1.18	751	143.14	121.98	47.71	14.21	10.84
ACC	3	111	108	0.52	7,814	0.07	584	70.40	77.28	23.47	0.85	1.32
ACG	3	69	67	0.32	5,163	0.05	184	74.83	32.98	24.94	0.56	0.82
ACT	3	182	181	0.86	13,809	0.12	659	75.87	72.91	25.29	1.50	2.16
AGC	3	169	163	0.78	8,098	0.07	159	47.92	19.98	15.97	0.88	2.00
AGG	3	333	321	1.53	25,140	0.23	422	75.50	68.45	25.17	2.73	3.95
ATC	3	545	536	2.56	50,116	0.45	596	91.96	66.43	30.65	5.44	6.46
CCG	3	68	55	0.26	5,940	0.05	564	87.35	140.92	29.12	0.64	0.806
AAAC	4	17	17	0.08	996	0.01	120	58.59	33.20	14.65	0.11	0.20
AAAG	4	89	88	0.42	7,128	0.06	249	80.09	31.49	20.02	0.77	1.05
AAAT	4	95	93	0.44	7,572	0.07	372	79.71	60.36	19.93	0.82	1.13
AAGC	4	9	9	0.04	707	0.01	348	78.56	101.09	19.64	0.08	0.11
AAGG	4	33	31	0.15	4,890	0.04	642	148.18	169.76	37.05	0.53	0.39
AATG	4	11	11	0.05	923	0.01	131	83.91	31.85	20.98	0.10	0.13
ACAG	4	46	46	0.22	7,787	0.07	639	169.28	155.00	42.32	0.85	0.55
ACAT	4	82	79	0.38	10,505	0.10	659	128.11	133.48	32.03	1.14	0.97
ACGC	4	18	18	0.09	1,250	0.01	140	69.44	33.17	17.36	0.14	0.21
ACGG	4	89	89	0.43	3,789	0.03	116	42.57	9.40	10.64	0.41	1.05
ACTC	4	34	34	0.16	5,470	0.05	727	160.88	157.78	40.22	0.59	0.40
AGAT	4	76	75	0.36	10,076	0.09	743	132.58	114.86	33.14	1.09	0.90
AGCC	4	134	134	0.64	17,294	0.16	330	129.06	43.55	32.26	1.88	1.59
AGCG	4	63	62	0.30	2,054	0.02	36	32.60	2.82	8.15	0.22	0.75
AGGC	4	62	62	0.30	5,970	0.05	415	96.29	71.97	24.07	0.65	0.74
AGGG	4	97	94	0.45	13,231	0.12	618	136.40	130.46	34.10	1.44	1.15
ATCC	4	6	6	0.03	432	0.00	170	72.00	57.96	18.00	0.05	0.07
CCCG	4	29	29	0.14	1,915	0.02	82	66.03	8.26	16.51	0.21	0.34
AAAAC	5	6	6	0.03	388	0.00	96	64.67	24.05	12.93	0.04	0.07
AAAAG	5	14	14	0.07	927	0.01	115	66.21	28.21	13.24	0.10	0.17
AAAAT	5	9	9	0.04	435	0.00	60	48.33	10.05	9.67	0.05	0.11
AACCT	5	131	126	0.60	41,414	0.37	705	316.14	205.30	63.23	4.49	1.55
AAGAG	5	24	24	0.11	3,946	0.04	676	164.42	167.47	32.88	0.43	0.28
AAGGG	5	12	12	0.06	1,930	0.02	414	160.83	143.66	32.17	0.21	0.14
AATAT	5	14	14	0.07	1,236	0.01	258	88.29	58.22	17.66	0.13	0.17
AGAGG	5	16	15	0.07	1,873	0.02	456	117.06	116.10	23.41	0.20	0.19
AGGCG	5	25	25	0.12	922	0.01	37	36.88	0.60	7.38	0.10	0.30
AGGGG	5	20	20	0.10	1,884	0.02	215	94.20	53.84	18.84	0.20	0.24
AAAAAG	6	13	13	0.06	1,703	0.02	437	131.00	119.28	21.83	0.19	0.15
AAAAAT	6	9	9	0.04	452	0.00	62	50.22	16.36	8.37	0.05	0.11
AAACAC	6	6	6	0.03	425	0.00	133	70.83	32.20	11.81	0.05	0.07
AAAGAG	6	26	26	0.12	4,633	0.04	705	178.19	156.46	29.70	0.50	0.31
AAATAT	6	6	4	0.02	184	0.00	59	30.67	16.68	5.11	0.02	0.07
AAATGG	6	6	3	0.01	218	0.00	79	36.33	23.55	6.06	0.02	0.07
AACAAT	6	7	7	0.03	625	0.01	119	89.29	22.26	14.88	0.07	0.08
AACAGC	6	25	25	0.12	1,052	0.01	55	42.08	5.61	7.01	0.11	0.30
AAGAGC	6	8	8	0.04	352	0.00	44	44.00	0.00	7.33	0.04	0.10
AAGAGG	6	30	30	0.14	4,223	0.04	554	140.77	124.39	23.46	0.46	0.36
AAGGAG	6	28	28	0.13	3,377	0.03	318	120.61	85.98	20.10	0.37	0.33
AAGGGG	6	23	23	0.11	2,123	0.02	195	92.30	55.98	15.38	0.23	0.27
AATATT	6	7	7	0.03	370	0.00	98	52.86	30.56	8.81	0.04	0.08
AATGAT	6	45	41	0.20	5,325	0.05	453	118.33	107.96	19.72	0.58	0.53
ACACAT	6	16	16	0.08	2,716	0.02	714	169.75	190.21	28.29	0.30	0.19
ACACGC	6	14	14	0.07	1,056	0.01	136	75.43	32.56	12.57	0.12	0.17
ACACTC	6	10	10	0.05	972	0.01	172	97.20	46.96	16.20	0.11	0.12
ACAGAG	6	13	13	0.06	2,486	0.02	733	191.23	196.79	31.87	0.27	0.15
ACATAT	6	15	13	0.06	1,737	0.02	367	115.80	104.02	19.30	0.19	0.18
ACCATC	6	11	11	0.05	852	0.01	203	77.45	66.27	12.91	0.09	0.13
ACCTCC	6	8	8	0.04	587	0.01	150	73.38	50.83	12.23	0.06	0.10
ACGATG	6	9	9	0.04	424	0.00	86	47.11	22.13	7.85	0.05	0.11
ACTCTC	6	6	6	0.03	752	0.01	229	125.33	84.80	20.89	0.08	0.07
AGAGGG	6	49	49	0.23	7,856	0.07	702	160.33	138.90	26.72	0.85	0.58
AGCCGC	6	10	10	0.05	642	0.01	175	64.20	43.00	10.70	0.07	0.12
AGGATG	6	6	6	0.03	929	0.01	509	154.83	181.98	25.81	0.10	0.07
AGGGGG	6	19	19	0.09	2,064	0.02	321	108.63	73.56	18.11	0.22	0.23
CCCCCG	6	66	25	0.12	838	0.01	58	12.70	5.66	2.12	0.09	0.78

^a The characterization of microsatellites in P. monodon FESs is accomplished in terms of the occurring hits^b, the number of occurred FESs^c, the percentage frequency of repeats in terms of the total number of FES analyzed^d, the amount of repeats in terms of nucleotide length^e and as a percentage^f of total sequence (11,114,786 bp) analyzed, the maximum length^g, the standard deviationⁱ about the microsatellite mean length^h, the mean repeat number^j, the relative abundance^k, and the relative frequency^l. In total, seventy-one microsatellite types have ≧6 hits in the 20,926 FESs; the remaining 91 microsatellite types with 1~5 hits were omitted.
^kThe relative abundance (RA) is the base-pairs comprised by each repeat class [Bases (bp)^e] divided by the total length of all microsatellites (921,720 bp) ×100.
^l The relative frequency (RF) is the hits of each repeat class [Counts^b] divided by the total hits of all microsatellites (8,441 hits) ×100.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com