Development and characterization of microsatellite <i>loci</i> of <i>Microglanis cottoides</i> (Siluriformes: Pseudopimelodidae) and cross-species amplification

Souza-Shibatta, Lenice; Ferreira, Dhiego Gomes; Oliveira, Claudio; Almeida, Fernanda Simões de; Shibatta, Oscar Akio; Sofia, Silvia Helena

doi:10.1590/S1679-62252013000300011

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Original Articles • Neotrop. ichthyol. 11 (03) • Sept 2013 • https://doi.org/10.1590/S1679-62252013000300011 linkcopy

Development and characterization of microsatellite loci of Microglanis cottoides (Siluriformes: Pseudopimelodidae) and cross-species amplification

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Thirteen microsatellite loci were isolated and characterized in Microglanis cottoides. Of these, two were monomorphic and 11 were polymorphic. These polymorphic loci tested on 24 individuals from a wild population produced a total of 108 different alleles, with levels of variability high, ranging from 2 to 20, with an average of 8.3 alleles per locus. The observed and expected heterozygosity ranged from 0.125 to 0.958 and from 0.119 to 0.931, respectively. A high combined probability of paternity exclusion value and a low probability combined genetic identity value obtained show that the set of loci described herein displays good suitability for paternity studies and differentiation of M. cottoides. Additionally, all thirteen microsatellite primers developed for M. cottoides were tested in four other Pseudopimelodidae species and successful cross-species amplification was achieved for the majority of loci.

Brazilian Eastern basin; Catfish; Enriched genomic library; Genetic marker; SSR

Locus	Sequence	Primers (5'- 3')	T_a(ºC)	k	Allele size range (pb)	Ho	He	(Q)	(I)	PIC	F _IS	GenBank
Mcot01	(GT)₇	F: TCATGATGGCGACTGAACTC	48	1	244	0.000	0.000	0.000	1.000	0.000	-	KF134914
Mcot01	(GT)₇	R: TTATTGCGTGTGCTTTCTGG	48	1	244	0.000	0.000	0.000	1.000	0.000	-	KF134914
Mcot02	(AC)₉	F: AACTGCCTGCAAAACAACC	54	8	110 - 126	0.792	0.786	0.593	0.074	0.758	0.014	KF134915
Mcot02	(AC)₉	R: TTACCCTGACAACCAGCTCAC	54	8	110 - 126	0.792	0.786	0.593	0.074	0.758	0.014	KF134915
Mcot03	(TG)₁₆	F: AGCCCAATCTGTCTGAGAGC	54	17	183 - 221	0.917	0.915	0.828	0.013	0.909	0.019	KF134916
Mcot03	(TG)₁₆	R: ATCATCACCACGTGGAACAC	54	17	183 - 221	0.917	0.915	0.828	0.013	0.909	0.019	KF134916
Mcot04	(TG)₁₈	F: AGCGGCTGTAATAGGCTGTG	48	20	159 - 211	0.917	0.931	0.861	0.008	0.927	0.037	KF134917
Mcot04	(TG)₁₈	R: CGGCTGTTCTTCCTTTACAG	48	20	159 - 211	0.917	0.931	0.861	0.008	0.927	0.037	KF134917
Mcot05	(GTAAAA)₃	F: CGTTGAAGAGTAACACAGACGTG	54	2	126 - 132	0.458	0.430	0.168	0.417	0.337	-0.045	KF134918
Mcot05	(GTAAAA)₃	R: AAGCGGAGGTTCAATTTCG	54	2	126 - 132	0.458	0.430	0.168	0.417	0.337	-0.045	KF134918
Mcot06	(GT)₇	F: TCATGATGGCGACTGAACTC	48	1	245	0.000	0.000	0.000	1.000	0.000	-	KF134919
Mcot06	(GT)₇	R: TTATTGCGTGTGCTTTCTGG	48	1	245	0.000	0.000	0.000	1.000	0.000	-	KF134919
Mcot07	(GT)₁₀	F: TTCACTCAAGAGGCAGCTGTAG	54	15	127 - 183	0.917	0.875	0.759	0.025	0.865	-0.026	KF134920
Mcot07	(GT)₁₀	R: ACCGTGTTCGTCGCTAATG	54	15	127 - 183	0.917	0.875	0.759	0.025	0.865	-0.026	KF134920
Mcot08	(AC)₁₉	F: CGCAGCACACCAGACTTATG	54	17	156 - 204	*0.792	0.908	0.815	0.015	0.901	^**0.148	KF134921
Mcot08	(AC)₁₉	R: TCATGGGTAACGACACCAAG	54	17	156 - 204	*0.792	0.908	0.815	0.015	0.901	^**0.148	KF134921
Mcot09	(TGAA)₄	F: CAGGTGGGTTCCGGATTAAC	54	7	97 - 125	0.958	0.681	0.428	0.156	0.627	-0.388	KF134922
Mcot09	(TGAA)₄	R: CAGTAGAGACTCTCATAACAATGCAC	54	7	97 - 125	0.958	0.681	0.428	0.156	0.627	-0.388	KF134922
Mcot10	(ATGA)₆	F: GTGGGATCCGGATTAACCTC	48	7	118 - 138	0.667	0.666	0.409	0.170	0.607	0.019	KF134923
Mcot10	(ATGA)₆	R: AAATAACAGGAAAGTTTTTATCCACTC	48	7	118 - 138	0.667	0.666	0.409	0.170	0.607	0.019	KF134923
Mcot11	(GT)₅	F: TCATTTGGAACCAGGACTCTG	54	4	165 - 188	0.417	0.386	0.215	0.400	0.363	-0.057	KF134924
Mcot11	(GT)₅	R: GGAATCGAACCCATGAACTC	54	4	165 - 188	0.417	0.386	0.215	0.400	0.363	-0.057	KF134924
Mcot12	(ATGA)₆	F: GTGGGATCCGGATTAACCTC	60	5	166 - 182	0.375	0.641	0.393	0.180	0.589	^**0.432	KF134925
Mcot12	(ATGA)₆	R: CCGTCAGTATGTCAGTCAGTCAG	60	5	166 - 182	0.375	0.641	0.393	0.180	0.589	^**0.432	KF134925
Mcot13	(TGT)₈	F: GAAGGTGTGGATTGAGAGCAG	60	3	125- 131	0.125	0.119	0.0598	0.780	0.115	-0.029	KF134926
Mcot13	(TGT)₈	R: CAGATTACCCATCCGTCCAT	60	3	125- 131	0.125	0.119	0.0598	0.780	0.115	-0.029	KF134926
All loci				108	8.3	0.580	0.579	0.999	2.16x10^-6	0.538	0.021

	Primers
	Mcot01	Mcot02	Mcot03	Mcot04	Mcot05	Mcot06	Mcot07	Mcot08	Mcot09	Mcot10	Mcot11	Mcot12	Mcot13
Species	Allele size range (bp) and the number of alleles per locus observed (k)
Microglanis cibelae	244-246	114-122	104-218	180-196	114-132	148-168	244-246	168-214	113-125	122-132	165	166-174	128
	k= 2	k= 4	k= 2	k= 5	k= 3	k= 5	k= 2	k= 5	k= 3	k= 4	k= 1	k= 3	k= 1
Microglanis garavelloi	232	114-124	195-197	181-191	112-132	155-161	232-256	152-172	-	116-130	184	168-172	126-129
	k= 1	k= 3	k= 1	k= 3	k= 3	k= 3	k= 2	k= 3	-	k= 3	k= 1	k= 3	k= 2
Microglanis parahybae	251	116-126	202-208	207-221	114-132	145-155	244-252	162-176	114-124	122-126	184	170-178	122
	k= 1	k= 5	k= 3	k= 4	k= 2	k= 4	k= 1	k= 5	k= 4	k= 3	k= 1	k= 3	k= 1
Pseudopimelodus pulcher	238-258	100-134	182-214	-	110-156	145-153	245-247	158-170	115-197	122-126	186-192	170-174	101-128
	k= 4	k= 5	k= 6	-	k= 2	k= 4	k= 2	k= 5	k= 5	k= 2	k= 2	k= 2	k= 5

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Sociedade Brasileira de Ictiologia Neotropical Ichthyology, Departamento de Biologia Animal e Vegetal, CCB, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Km 380, Cidade Universitária, 86055-900, Londrina, Paraná, Brazil, Phone +55(43)3371-5151 - Londrina - PR - Brazil
E-mail: neoichth@nupelia.uem.br

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