Disclosure of genetic diversity of mackerel fish (<i>Scomberomorus</i> spp.) in Indonesian waters based on the mitochondrial cytochrome oxidase subunit II (COII) gene

Widayanti, R.; Limiano, J. B.; Sari, R. P.; Nugroho, S. D. L. S.; Ibrahim, A.; Pakpahan, S.; Nurjirana,

doi:10.1590/1519-6984.278322

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Brazilian Journal of Biology

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Original Article • Braz. J. Biol. 84 • 2024 • https://doi.org/10.1590/1519-6984.278322 copy

Disclosure of genetic diversity of mackerel fish (Scomberomorus spp.) in Indonesian waters based on the mitochondrial cytochrome oxidase subunit II (COII) gene

Divulgação da diversidade genética de peixes cavala (Scomberomorus spp.) em águas indonésias com base no gene mitocondrial da subunidade II da citocromo oxidase (COII)

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Mackerel fish (Scomberomorus spp.) represents a significant marine fisheries commodity in Indonesia, characterized by its high commercial value and nutritional content. To understand the intraspecific interactions and genetic variability of Scomberomorus spp., a more extensive research of Scomberomorus spp. populations, including both cultivated and wild specimens, is required. This study aimed to explore the genetic diversity of mackerel fish in Indonesian waters, focusing on the mitochondrial DNA (mtDNA) cytochrome oxidase subunit II (COII) gene, which encodes the second subunit of cytochrome c oxidase (complex IV), is essential for aerobic respiration and energy transformation. Muscle tissue samples from 18 individual mackerel fish collected from various regions in Indonesia, including Palembang, Cilacap, Rembang, Banjarmasin, Ambon, and Fak-Fak Regencies, were utilized. The genomic DNA was isolated and amplified using specific primers: CO2TF (5'-ACCGCTCTGTCACTTTCTTC-3') and CO2TR (5'-ATGTCACTAAGGGTGGTTGG-3'). Subsequently, the obtained amplicons were subjected to sequencing. The sequence data were then analyzed using the MEGA11 and DnaSP 6 software. Our findings revealed 120 variable sites within the 691 base pairs of mtDNA COII sequences, resulting in a nucleotide diversity (Pi) of 0.07169. Furthermore, we identified eight haplotypes, demonstrating a haplotype diversity (Hd) of 0.8889. Remarkably, all mackerel samples from Palembang and Cilacap clustered into discrete haplotypes, specifically haplotype 1 and haplotype 2, respectively. Our phylogenetic analysis delineated three distinct clades. Clade I, closely related to Scomberomorus cavalla, encompassed all individuals from Ambon, Palembang, Rembang, and one from Banjarmasin. Clade II, associated with Scomberomorus niphonius, included individuals from Cilacap and two from Banjarmasin. Clade III, linked to Scomberomorus semifasciatus, exclusively consisted of individuals from Fak-Fak (Papua). In conclusion, Indonesian waters harbor diverse genetic variations within Scomberomorus spp., and population relationships based on the mtDNA COII gene exhibit notable complexities. Future research endeavors should focus on further elucidating the diversity and relationships among Scomberomorus spp. in diverse Indonesian populations.

Keywords:
COX2 gene; marine biodiversity; mackerel; phylogenetic; Scomberomorus spp

Traits	Value
Sample number	18
Number of sites	691
G+C contents	0.4468
Number of invariable (monomorphic) sites	571
Number of variable (polymorphic) sites (S)	120
Nucleotide diversity (Pi)	0.07169
Number of haplotypes (h)	8
Haplotype diversity (Hd)	0.8889
Haplotype members:
Haplotype 1 (Hap 1)	5 (Palembang1, Palembang2, Palembang3, Rembang1, Banjarmasin1)
Haplotype 2 (Hap 2)	3 (Cilacap1, Cilacap2, Cilacap3)
Haplotype 3 (Hap 3)	1 (Rembang1)
Haplotype 4 (Hap 4)	2 (Rembang3, Ambon1)
Haplotype 5 (Hap 5)	2 (Banjarmasin2, Banjarmasin3)
Haplotype 6 (Hap 6)	2 (Ambon2, Ambon3)
Haplotype 7 (Hap 7)	2 (Papua1, Papua3)
Haplotype 8 (Hap 8)	1 (Papua2)

Sample	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18
Palembang1		0.000	0.000	0.015	0.015	0.015	0.000	0.001	0.003	0.000	0.015	0.015	0.003	0.002	0.002	0.014	0.014	0.014
Palembang2	0.000		0.000	0.015	0.015	0.015	0.000	0.001	0.003	0.000	0.015	0.015	0.003	0.002	0.002	0.014	0.014	0.014
Palembang3	0.000	0.000		0.015	0.015	0.015	0.000	0.001	0.003	0.000	0.015	0.015	0.003	0.002	0.002	0.014	0.014	0.014
Cilacap1	0.130	0.130	0.130		0.000	0.000	0.015	0.015	0.015	0.015	0.004	0.004	0.015	0.015	0.015	0.016	0.016	0.016
Cilacap2	0.130	0.130	0.130	0.000		0.000	0.015	0.015	0.015	0.015	0.004	0.004	0.015	0.015	0.015	0.016	0.016	0.016
Cilacap3	0.130	0.130	0.130	0.000	0.000		0.015	0.015	0.015	0.015	0.004	0.004	0.015	0.015	0.015	0.016	0.016	0.016
Rembang1	0.000	0.000	0.000	0.130	0.130	0.130		0.001	0.003	0.000	0.015	0.015	0.003	0.002	0.002	0.014	0.014	0.014
Rembang2	0.001	0.001	0.001	0.128	0.128	0.128	0.001		0.003	0.001	0.015	0.015	0.003	0.003	0.003	0.014	0.014	0.014
Rembang3	0.004	0.004	0.004	0.132	0.132	0.132	0.004	0.006		0.003	0.015	0.015	0.000	0.001	0.001	0.015	0.015	0.015
Banjarmasin1	0.000	0.000	0.000	0.130	0.130	0.130	0.000	0.001	0.004		0.015	0.015	0.003	0.002	0.002	0.014	0.014	0.014
Banjarmasin2	0.130	0.130	0.130	0.012	0.012	0.012	0.130	0.128	0.131	0.130		0.000	0.015	0.015	0.015	0.016	0.016	0.016
Banjarmasin3	0.130	0.130	0.130	0.012	0.012	0.012	0.130	0.128	0.131	0.130	0.000		0.015	0.015	0.015	0.016	0.016	0.016
Ambon1	0.004	0.004	0.004	0.132	0.132	0.132	0.004	0.006	0.000	0.004	0.131	0.131		0.001	0.001	0.015	0.015	0.015
Ambon2	0.003	0.003	0.003	0.134	0.134	0.134	0.003	0.004	0.001	0.003	0.133	0.133	0.001		0.000	0.014	0.014	0.014
Ambon3	0.003	0.003	0.003	0.134	0.134	0.134	0.003	0.004	0.001	0.003	0.133	0.133	0.001	0.000		0.014	0.014	0.014
Papua1	0.117	0.117	0.117	0.139	0.139	0.139	0.117	0.119	0.123	0.117	0.135	0.135	0.123	0.121	0.121		0.001	0.000
Papua2	0.119	0.119	0.119	0.139	0.139	0.139	0.119	0.121	0.125	0.119	0.135	0.135	0.125	0.123	0.123	0.001		0.001
Papua3	0.117	0.117	0.117	0.139	0.139	0.139	0.117	0.119	0.123	0.117	0.135	0.135	0.123	0.121	0.121	0.000	0.001

Location	1	2	3	4	5	6
Palembang		0.0148	0.0009	0.0099	0.0021	0.0137
Cilacap	0.1270		0.0147	0.0059	0.0148	0.0154
Rembang	0.0019	0.1270		0.0098	0.0015	0.0138
Banjarmasin	0.0849	0.0501	0.0855		0.0100	0.0130
Ambon	0.0034	0.1301	0.0031	0.0881		0.0139
Papua	0.1175	0.1359	0.1199	0.1275	0.1218

Individual	Sites
										1	1	1	1	1	1	2
	3	3	3	4	4	5	5	5	7	2	4	5	7	8	8	3
	3	6	7	6	7	0	2	3	2	9	4	2	0	7	9	0
Palembang1	L	A	L	V	S	L	N	S	I	A	I	I	I	S	P	A
Palembang2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Palembang3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Cilacap1	M	S	.	I	T	F	D	I	.	T	.	.	.	A	S	.
Cilacap2	M	S	.	I	T	F	D	I	.	T	.	.	.	A	S	.
Cilacap3	M	S	.	I	T	F	D	I	.	T	.	.	.	A	S	.
Rembang1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Rembang2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Rembang3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Banjarmasin1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Banjarmasin2	M	S	.	I	T	.	D	.	.	T	.	.	.	A	S	.
Banjarmasin3	M	S	.	I	T	.	D	.	.	T	.	.	.	A	S	.
Ambon1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Ambon2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Ambon3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Papua1	.	.	.	L	T	.	.	.	V	.	.	.	V	.	.	.
Papua2	.	.	.	L	T	.	.	.	V	.	.	.	V	.	.	.
Papua3	.	.	.	L	T	.	.	.	V	.	.	.	V	.	.	.
NC 008109 S. cavalla	.	.	.	.	.	.	.	.	.	.	.	.	V	.	.	.
NC 033531 S. concolor	.	T	.	.	T	.	.	.	.	.	.	.	V	.	.	.
NC 016420 S. niphonius	.	.	F	I	T	.	.	.	.	T	V	V	.	.	.	T
NC 021391 S. semifasciatus	.	.	.	L	T	.	.	.	V	.	.	.	V	.	.	.
NC 033887 S. sierra	.	T	.	.	T	.	.	.	.	.	.	.	V	.	.	.

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