Microsatellite marker development from next-generation sequencing in the New England cottontail (Sylvilagus transitionalis) and cross-amplification in the eastern cottontail (S. floridanus)

King, Timothy L.; Eackles, Michael; Aunins, Aaron; McGreevy, Thomas J.; Husband, Thomas P.; Tur, Anthony; Kovach, Adrienne I.

doi:10.1186/s13104-017-3062-2

Table 1 Characteristics of 35 microsatellite loci in n = 33 Sylvilagus transitionalis and cross-amplification in n = 6 S. floridanus

From: Microsatellite marker development from next-generation sequencing in the New England cottontail (Sylvilagus transitionalis) and cross-amplification in the eastern cottontail (S. floridanus)

Locus	Primer sequences	Repeat motif	Genbank accession number	Allele size range	A	A_e	H_e	H_o	F	P value	Number of alleles in S. floridanus
StrQ2	F: *TGTCTGGCTTATGAGAAAGGG R: ACTGCGGGACTTCATACTGC	AGC	KX530819	129–153	5	3.0	0.68	0.61	0.09	0.107	4
StrQ7	F: *TCGCTCTCTGTCTCTGCCTT R: GCCTGCACTCTCTAGCTTGG	ACT	KX530820	116–122	2	1.6	0.39	0.39	− 0.03	1.000	5
StrQ8	F: *TCCTGCCTTTGAGAGCATTT R: TGGGTGATGCCTCACTTAAT	AGAT	KX530821	149–169	6	2.8	0.65	0.66	− 0.03	0.813	5
StrQ10	F: TGATAGGAAGGTAAGTCAGTGGG R: *TGCTCTCAAGAACCCAGGAG	AGAT	KX530822	120–132	4	2.0	0.50	0.47	0.04	0.184	0
StrQ11	F: *ATCGAATTTCGTCTGCATCC R: AAGGGTAGCTCTCAAACACCA	ATCC	KX530823	188–192	2	1.2	0.14	0.15	− 0.08	1.000	5
StrQ12	F: TGATTCGGAGTGGTTATGAAGA R: *ATTGCAATGCCCAACACTG	ATC	KX530824	132–135	2	1.1	0.12	0.12	− 0.07	1.000	6
StrQ15	F: *GATGGTGGATAAGATAGAGGACA R: TATGGCTGGACCACACTCTG	AGAT	KX530825	177–193	5	2.9	0.67	0.58	0.12	0.110	4
StrQ16	F: *CAGATTGACGTTGAGCAGA R: TGCTTGCCTCTTTCAAATAAA	AGAT	KX530826	144–152	3	2.4	0.58	0.64	− 0.11	0.677	4
StrQ18	F: *ACTCAGAGATAATGCACCAAA R: AAGGGTTAGATGGCAAGGGT	ACT	KX530827	215–221	3	2.4	0.59	0.58	0.01	0.173	6
StrQ19	F: ACCATCCATGACTGGTGAAA R: *GCACATGGGACATAGAAGGC	ATCC	KX530828	154–166	3	1.9	0.47	0.31	0.32	0.016	3
StrQ20	F: TGATTGCCCAGAGAATTAGTACC R: *AGGTCTTCAGACTCACTCTGGT	ATCC	KX530829	201–217	2	1.5	0.36	0.39	− 0.12	1.000	6
StrQ21	F: *TTCAATTTGCACCAAGAAGC R: CACAAGGTAGCATACTGTGGC	ATCC	KX530830	188–192	2	2.0	0.50	0.42	0.13	0.484	3
StrQ23	F: *AGCCTGCATCCTTTAGGG R: GCATAAAGGTTAATGAATAAGATTGC	AGAT	KX530831	207–211	2	1.1	0.06	0.06	− 0.03	1.000	3*
StrQ24	F: TGCGACTATTTCCAAAGCAT R: *TTGTTAGTTTCTCACAGTGCTGC	AGAT	KX530832	200–212	4	2.4	0.60	0.61	− 0.03	0.752	4
StrQ25	F* TGCATATTTGTCTTTCATTCTCTGA R: AACAATGACAAATTACACAGCCA	AGAT	KX530833	127–135	3	1.4	0.30	0.30	− 0.04	0.631	5*
StrQ26	F* CCTCTCTGAAACTATGCCTTTC R: CCTACAGCACTCCTGACTCGT	AAGG	KX530834	144–160	5	3.4	0.71	0.65	0.08	0.806	6
StrQ27	F:*TTCATCATCTTGTTATTTCATAGAGAA R: TGGAGCTCTTGGAGTCTAATGTG	AAGG	KX530835	142–154	4	2.7	0.63	0.64	− 0.02	0.623	4
StrQ28	F: *GGAAGAAAGGAAGAAAGGAAGA R: GGAGACTTGGATTGAATTCTGG	AAGG	KX530836	200	1	1.0	0.00	0.00	N/A	N/A	5
StrQ30	F:*CTTAATTGTAAGGAGGGTAGGAAA R: CCTCTTTCTCTCACTAATGCTGTT	AAGG	KX530837	102–138	6	3.8	0.75	0.73	0.02	0.436	0
StrQ31	F: *TCAAGCACAGAACAGAGCAG R: CCTTCTATTCCTTCTTTCTTCCTTC	AAGG	KX530838	130–134	2	2.0	0.50	0.46	0.08	0.726	5
StrQ32	F:*TGTAACTCTGCCTTCCAAATAAATAA R: GGCTGTTTAACTTGCCATGC	AAGG	KX530839	182–198	5	2.7	0.64	0.61	0.04	0.768	5
StrQ34	F:*TTAGAACGAACAAGAAAGAAAGAAA R: TCAAGTGGGAAAGGAATATCAA	AAGG	KX530840	148–156	3	2.5	0.62	0.58	0.05	0.415	4
StrQ37	F: *TTGTATGTGAACTTTGCACCG R: CACAGTCTAACTCTATCTGTCAAGAAA	AAGC	KX530841	94–106	2	1.5	0.34	0.24	0.28	0.123	6
StrQ39	F: *TCAAAGCACTTAATTCAAATCCC R: GTCTCTCCAAGCCTCCTCCT	AAGC	KX530842	192–196	2	1.9	0.48	0.33	0.29	0.135	2
StrQ41	F: *CCCTCTCTGTAACTCTGTCTTTCA R: TGAGGTACATTCAGCAGCCA	AAGG	KX530843	196–216	4	2.1	0.52	0.42	0.18	0.468	3*
StrQ42	F:*AGAAATAAAGAATAGCTTGGATAAATG R: CCTTCCTTCGTTCCTTCGTT	AAGG	KX530844	120–132	4	3.5	0.72	0.82	− 0.15	0.253	4*
StrQ43	F: *GTATCTGCCGAATGAAGTGGA R: TAGGTACAGATAATTCACTTTGGACA	AAGG	KX530845	218–230	3	1.9	0.49	0.55	− 0.13	0.637	3*
StrQ44	F:*TTATTTATTGGAAAGGTAGATAGGTGA R: TGGGTTATTGGCACTCACAA	AAGG	KX530846	230–234	2	1.3	0.26	0.24	0.06	0.551	4*
StrQ45	F: *CGACTAGGATAAATGCCACAGA R: CCCAATCCCTACACAACTAACAC	AAGG	KX530847	124	1	1.0	0.00	0.00	N/A	N/A	1
StrQ46	F:*AAATGAGGAATATTTGTTGAATGC R: AGAATGAACCAGCAAATGGG	AACT	KX530848	120–144	6	2.4	0.59	0.70	− 0.20	0.359	3
StrQ48	F: *GGGTTTGATGCTGAGGTCC R: TACATCCAGTGCACATTCGC	AACC	KX530849	118–122	2	1.1	0.06	0.06	− 0.03	1.000	2*
StrQ49	F: *ATCTTAGTGGAGAGAGTGGCTTG R: AAGTTCACCAGGCTAACTAGAGGA	AAAT	KX530850	120–132	4	3.0	0.68	0.58	0.14	0.178	1
StrQ63	F:*AAACAAGGAGATGTCACAGTAGTTTAG R: CATCCCTCTCTGTAACCTTGACTT	AATT	KX530851	126–130	2	1.3	0.24	0.21	0.10	0.467	2*
StrQ67	F: *TCTTGTCAAGTTTGTAACATGTGC R: TCAGCTTAACCCACTGTGCC	AATG	KX530852	246–254	3	1.3	0.22	0.24	− 0.12	1.000	2
StrQ72	F: *GCCTCTGCTTCTCTGTAACTTTG R: GGTTGGGAGGAGGCTTAGAG	AATC	KX530853	136	1	1.0	0.00	0.00	N/A	N/A	1

Locus refers to the name assigned to the microsatellite containing sequence. Primers sequences with a * denote which primer was tagged with an M13 tail. The number of alleles (A), effective number of alleles (A_e), unbiased heterozygosity (H_e), observed heterozygosity (H_o), and fixation index (F) were output by the GenAlEx software. The Hardy–Weinberg P value is the P value reported across loci from Genepop using Fisher’s method. The Number of alleles in S. floridanus refers the number of alleles at each locus observed in S. floridanus, where a * denotes a putatively species specific amplification pattern not observed in S. transitionalis

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ISSN: 1756-0500

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