Restrepo-Escobar, Natalia; Márquez, Edna J.

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Sumário

Original article • Neotrop. ichthyol. 18 (01) • 2020 • https://doi.org/10.1590/1982-0224-2019-0079 copiar

Microsatellite loci development for three catfish species from northwestern South America

Autoría SCIMAGO INSTITUTIONS RANKINGS

RESUMEN

Las especies de bagres neotropicales Ageneiosus pardalis, Pimelodus grosskopfii y Sorubim cuspicaudus, son importantes recursos pesqueros en Colombia y han mostrado disminuciones históricas en sus capturas. En este estudio se empleó la secuenciación genómica de próxima generación y análisis bioinformático para desarrollar entre 18 y 24 loci microsatélites para estas especies. Los loci microsatélites mostraron altos valores del contenido de información polimórfica CIP (A. pardalis: 0.601-0.903, P. grosskopfii: 0.748-0.946 and S. cuspicaudus: 0.383-0.876) y el número promedio de alelos/locus mostró un rango de 7-15 para A. pardalis, 9-30 para P. grosskopfii y 5-14 para S. cuspicaudus. Los valores promedio de heterocigosidad observada y esperada fueron respectivamente 0.757 ± 0.035 y 0.834 ± 0.015 para A. pardalis; 0.596 ± 0.040 y 0.881 ± 0.009 para P. grosskopfii; y 0.747 ± 0.031y 0.757 ± 0.025 para S. cuspicaudus. Los loci microsatélites desarrollados en este trabajo pueden ser útiles para estimar la diversidad genética y la estructura poblacional de estos tres bagres neotropicales en estudios futuros.

Palabras clave:
Peces de agua dulce; Marcadores Moleculares; Secuenciación de próxima generación; Siluriformes

Sociedade Brasileira de Ictiologia Neotropical Ichthyology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura, Universidade Estadual de Maringá., Av. Colombo, 5790, 87020-900, Phone number: +55 44-3011-4632 - Maringá - PR - Brazil
E-mail: neoichth@nupelia.uem.br

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[1] Edited by

Guillermo Orti

Locus	Repeat motif	Primer sequence for forward (F) and reverse (R) (5’→3’)	Ra	Na	Ho	He	P	PIC
Apar03	(ATT)_n	F: TTTAGAAGCAGCCTGGATGG R: CTTGACTTTGGGAAATGGGC	186-219	11	0.920	0.882	0.965	0.870
Apar25	(TCTG)_n	F: CCGGCTGTTCAATTTGTGG R: CACAGAGTAGAAGAGCTCACTTTGG	256-316	9	0.700	0.622	0.909	0.601
Apar11	(ATGG)_n	F: CACCAATGTATCCCCATCCC R: TTCAAGTACTGGCTACAAGCTGC	208-268	15	0.920	0.895	0.904	0.886
Apar36	(AATAG)_n	F: GAAGGAAATCACAGCCCTCG R: TCTGCTGGAAGGTGGAGAGG	230-280	8	0.800	0.825	0.832	0.801
Apar18	(ATCT)_n	F: GCATCTGCACCTCATATTTGC R: TGAGCTATTTCTGATTGGCTGG	206-266	13	0.860	0.871	0.816	0.858
Apar05	(ATT)_n	F: GGGAGGGAGAGGAGGATAGC R: GAAGGTAGGTGTTGGCAATGG	192-234	15	0.820	0.798	0.799	0.783
Apar35	(AATAG)_n	F: CCCTTTAAGCAAATTGTCTTCAGC R: CACCATCTGTCCTGTCCTGC	179-209	7	0.780	0.752	0.797	0.715
Apar22	(ATCT)_n	F: CAGAGGCTATTGTTCAGGCG R: TCATTGGGGTGGTGATATGC	235-271	10	0.800	0.850	0.612	0.833
Apar20	(ATCT)_n	F: TCCAACCATTACTGCATCCC R: GGTGATCGTTGGATGATTTGC	179-226	11	0.820	0.871	0.591	0.857
Apar21	(ATCT)_n	F: CACTGTGTGATCTCTCTGTGTTGG R: GAGATATTTCTTGAATTTCCTTCGG	173-225	13	0.920	0.891	0.494	0.881
Apar27	(AATG)_n	F: TCACCAAAGTGAAGCTGTTGC R: CAAACCAAGGACCTTCTCGC	146-178	9	0.900	0.827	0.416	0.806
Apar30	(ATATC)_n	F: GAACCTTGATTTTGCCCACG R: GCCAACATCAGGAAAGGGG	172-222	11	0.820	0.844	0.414	0.827
Apar04	(ATC)_n	F: CCTGCACTTCAACACTTCACC R: GAGAGAGTAAATGAGGGAAAGCG	256-298	10	0.880	0.844	0.401	0.826
Apar34	(ATCAC)_n	F: ACACTGCATCCCATCACACC R: TCCTCCTGGTCTTCTCACAGG	191-251	12	0.800	0.809	0.386	0.786
Apar23	(ATCT)_n	F: TCTTTGGTAACCCACCACCC R: ATGTGCAATGGGGATCTGC	241-269	8	0.860	0.814	0.295	0.791
Apar28	(ATGG)_n	F: AACTCCATGTCTGCTTCGGC R: CTGCTATTGCAGCCCATCC	273-301	8	0.600	0.698	0.179	0.666
Apar12	(ATCT)_n	F: GATTCCAGGATGCAGTTGAGG R: AGCGATTGCACACCATAACC	247-299	14	0.780	0.886	0.129	0.876
Apar31	(AATAG)_n	F: CTGGAGGGATGCAAACTGC R: GGGAATTCCGTTATTTTCAAGC	151-236	10	0.560	0.843	0.000	0.825
Apar14	(ATCT)_n	F: TTCCGGTATCGTGCATTTCC R: AACAATTGGGTGCCTAAGACG	165-221	15	0.500	0.910	0.000	0.903
Apar32	(ATTAG)_n	F: TTGCACTTCTGGTTGGATGC R: TCCAAAGCAAATGGTCATGG	151-216	13	0.540	0.900	0.000	0.892
Apar19	(ATCT)_n	F: TCAGCTAAGGCAAGTTGTTTGC R: GGGATTTCCTATATCGGCAGC	190-250	15	0.320	0.885	0.000	0.874
Across loci				11.286±0.574	0.757± 0.035	0.834± 0.015	0.000	0.817

Locus	Repeat motif	Primer sequence for forward (F) and reverse (R) (5'→3')	Ra	Na	Ho	He	P	PIC
¹ Pgrk40	(ATCT)_n	F: TTTGGTAACATTCAAGGTTTACTTGC R: AAAATAGCAACGTTCTAACTAGGGG	159-219	15	0.920	0.916	0.743	0.910
¹ Pgrk27	(ATATT)_n	F: CTTCCAAGCATGACAAGCCC R: CTCTCCACCACATCTTCCCC	264-359	16	0.920	0.866	0.517	0.852
¹ Pgrk15	(ATCT)_n	F: TGCCATCAGTGGTCTTCACC R: CCCCATCACCCTGTTCACC	268-328	14	0.760	0.852	0.225	0.840
² Pgrk14	(ATCT)_n	F: TCATGGCCTTGTACTTGTACCG R: CACCAGTTCATGCTTCTGCC	169-261	15	0.800	0.903	0.170	0.895
² Pgrk03	(ATCT)_n	F: GGATGAAAGAAAAGGATTTGGC R: GATAAGACGCGCTTACACTTGC	174-246	16	0.740	0.909	0.083	0.902
² Pgrk24	(AAAT)_n	F: ACACGCATGTCTCTTGCCC R: ACTTGTACTGCGGATGCGG	188-232	11	0.660	0.866	0.016	0.852
² Pgrk01	(ATCT)_n	F: GTCCCAGTCCTGCTTCACG R: GCTAATGGTACAACATCGCCC	156-292	30	0.760	0.948	0.002	0.946
² Pgrk19	(AAAT)_n	F: TAGTCGGTGCTAATTCGCCG R: ACTGACTGGAGACCACAGCG	201-237	10	0.520	0.810	0.000	0.787
² Pgrk12	(ATCT)_n	F: TGAGATTGGTTTATAACACAGACCG R: TGCAGCTGAAGAACTCAGGG	192-292	22	0.380	0.913	0.000	0.908
¹ Pgrk18	(ATCT)_n	F: GGATAAATATGGGTGGGTGGC R: GGAGCTGTGGAAGAGACATCG	210-282	15	0.580	0.907	0.000	0.900
² Pgrk07	(ATCT)_n	F: TGGCACATGAGTTGAAGACG R: AAACACATTGACTGATAGCCTTCC	197-265	17	0.400	0.907	0.000	0.899
³ Pgrk06	(ATCT)_n	F: GCGGGAAAAGTACAGGAAGG R: CGACGCAGCTCAGAATAAAGC	180-264	13	0.520	0.899	0.000	0.890
¹ Pgrk31	(ATT)_n	F: TGGAATTGTGCATTTCTTTGC R: GGAGGTTGAATTCCTCTGTGG	154-208	15	0.580	0.888	0.000	0.878
² Pgrk02	(ATCT)_n	F: ATCTGTCTGGCCATCCACC R: CAGATAGACGGACGCACG	77-157	15	0.400	0.879	0.000	0.867
¹ Pgrk20	(ATCT)_n	F: CAAGCTGCCTCCTGAAAACC R: GCTCATCTGTGTGAGTGGTGC	124-216	14	0.600	0.868	0.000	0.855
¹ Pgrk10	(ATCT)_n	F: TGTTGCGTAATATTCCCAGGC R: GACACAAACTGGTGAAAATCTGC	230-282	11	0.480	0.864	0.000	0.849
² Pgrk28	(AATAG)_n	F: ACTGTCTTGTGGCTTTGTGC R: TACGGGAAAATAATCCTGGG	116-226	11	0.660	0.843	0.000	0.825
² Pgrk08	(AAAT)_n	F: TTGGCGTGCAAATGAATCC R: ATGGGACCACAATCAGAGGC	261-301	9	0.340	0.771	0.000	0.748
Across loci				14.944±1.136	0.612±0.042	0.878± 0.010	0.000	0.867

Locus	Repeat motif	Primer sequence for forward (F) and reverse (R) (5’→3’)	Ra	Na	Ho	He	P	PIC
Scus22	(ATCT)_n	F: CGCCACCTTAGGAACCTACC R: GTGGTATGGTGGTGTCGAGG	180-208	8	0.800	0.808	0.932	0.784
Scus15	(TTC)_n	F: GCCTTCATATGCTTGGACCC R: TGAAGGTCCCTTTCAATGGC	201-216	6	0.620	0.637	0.913	0.599
Scus41	(ATTAC)_n	F: CAGATAAAGGACCATGCTGAGG R: CTGGATGCTCTGTGTGAGGC	161-186	6	0.780	0.689	0.895	0.636
Scus24	(ATCT)_n	F: CCTTGAGATACCTGCAGCCC R: GTTCCCTCCCTTCGTCTTCC	257-289	9	0.820	0.831	0.847	0.809
Scus17	(ATCT)_n	F: TGATAGAGGCACAGAGTGAACG R: CCTGTGTGCCTTGATGTCG	181-229	12	0.900	0.862	0.809	0.847
Scus43	(ATTAG)_n	F: TGACTCTGTGACTCTAATTCCTGC R: TCAGTTTCCCTGAGGAACCC	141-166	6	0.720	0.629	0.809	0.568
Scus28	(ATCT)_n	F: TCGGATGCAAAGTTAGACGG R: AGGATTTGTTGCCTCATGCC	252-280	8	0.820	0.803	0.794	0.774
Scus25	(ATCT)_n	F: TAAAACTGCAAGCCCCTTCG R: CAGAGTCCAAACCCTGTGGG	173-237	14	0.920	0.867	0.746	0.853
Scus23	(ATCT)_n	F: GATCTTTGTTCAGTCCACGGC R: GACGTTGTTAGCCCAGATGC	275-309	11	0.780	0.838	0.523	0.818
Scus12	(ATT)_n	F: TCTACACAAGCAGAAATGCAGC R: TCACATTGCTTGACAGATGCC	204-258	11	0.680	0.695	0.514	0.670
Scus35	(ATATT)_n	F: GTCAAAACGCATTCTGTAAATGG R: GTAGTGCTCAGCTCCAGGGC	209-249	9	0.880	0.832	0.479	0.812
Scus40	(ATCTT)_n	F: TGGAAGTAGTTGCTGCTGTTGC R: CAGAAGGCATTTACTGTCTGGC	241-276	7	0.660	0.641	0.438	0.594
Scus20	(ATCT)_n	F: GTCACATCTGGGTGTGCTGG R: GCCTGAGCTTTGGATTGAGC	249-317	14	0.940	0.887	0.321	0.876
Scus39	(ATCTT)_n	F: GGGACACTATGATTTTCCTTCAGC R: CTGTCATCCCCAGCAGTAGC	128-168	9	0.820	0.812	0.199	0.785
Scus32	(AGGGC)_n	F: AACGAGCCATGCAAGAACG R: CCCAGAAGCAGTAAGGTGTGC	222-287	14	0.820	0.861	0.122	0.848
Scus21	(ATCT)_n	F: CTACCCAATCTAGCTGCCCC R: CGACCTGGTGGGTACGTAGG	117-221	11	0.900	0.820	0.080	0.798
Scus03	(ATC)_n	F: GGATCGTTGGTGTAAATCTCTGC R: TGACTCATGGTGTGTGGTGC	114-135	7	0.520	0.575	0.052	0.536
Scus11	(ATT)_n	F: CACTTCCACCTGAACCATGC R: GCATCAGGGTTAGCACAGGC	276-288	5	0.300	0.419	0.037	0.383
Scus16	(AATG)_n	F: ACGTCATCTGGTGTCGTTGG R: CCAGAAGATCTGTGTGAACCG	104-136	9	0.620	0.780	0.026	0.748
Scus13	(ATT)_n	F: AGACGAGAGGGGTGACATGC R: AAGGTGTTGGCAGGATGAGG	272-314	9	0.740	0.809	0.024	0.783
Scus10	(ATT)_n	F: CCTGAAGAAATCCAGCCACC R: ACCACAACTCCGACTCCAGG	168-213	13	0.820	0.865	0.020	0.851
Scus18	(ATCT)_n	F: CAAGCATCAAAGCAGAAAGCC R: ATCACCATCTTGCGTTCTATCC	257-305	12	0.640	0.867	0.005	0.853
Scus37	(ATCAG)_n	F: GATCTGGGCTCTGCTTTTGG R: GCAGCACAATGAGTACTGCG	265-330	9	0.540	0.597	0.002	0.564
Scus07	(ATT)_n	F: CAACATCTGCAACCAAATGC R: GATTTTGCACCAGGACAACG	146-176	9	0.880	0.753	0.000	0.713
Across loci				9.500±0.552	0.747±0.031	0.757±0.025	0.000	0.729