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Genetic characterization and phylogenetic study of Lakor goat from Southwest Maluku Regency based on mitochondrial COI gene.

ABSTRACT: Aim:This study is aimed at characterizing the genetic and phylogenetic structure of Lakor goats as indigenous livestock from the Southwest Maluku Regency based on mitochondrial COI gene sequences. Materials and Methods:The genomes of 103 follicle samples from Lakor goats, collected from Lakor Island, were analyzed. The polymerase chain reaction was used to amplify 1548 bp of the mitochondrial COI gene using two primer pairs (COIA and COIB). Following sequencing, genetic variation and phylogenetic relationship were established using MEGA version X software. Results:The results of multiple COI gene alignment of the total sequences identified four polymorphic nucleotides that function as genetic markers between individual animals within the Lakor goat population. These correspond to positions 228 (A-G), 519 (G-A), 900 (C-T), and 1266 (T-C). Phylogenetic signals based on the COI gene showed that Lakor goat breed is a monophyletic group or single clade with a bootstrap value of 100% by the neighbor-joining (NJ) and maximum likelihood (ML) evolutionary models. This data indicated that evolutionarily, the Lakor goat breed has a very close kinship with three goat breeds from China: The Meigu goat (KM 244714.1), Chinese Tibet (Capra hircus) (KJ 940969.1), and C. hircus (KP 677510.1). Phylogenetic information based on the cladistics system classified the Lakor goat as a single clade (monophyletic group). The low-genetic diversity within populations indicates that there has been an inbreeding depression occurring at a very high frequency. Conclusion:We conclude that the Lakor goat may be divided into a single clade or monophyletic group based on the COI gene sequence. Four nucleotides were identified that can be used as genetic markers among individual animals within the Lakor goat population, as well as C. hircus and others as derived from GenBank data. The Lakor goat population has a high level of inbreeding depression as a result of geographical isolation, which supports the formation of a monophyletic group with different genetic characteristics, and does not allow the introduction of males from other breeds. Phylogenetic signals indicated that Capra aegagrus (bezoar) is the ancestor of the native goats in Indonesia, including the Lakor goats.

SUBMITTER: Rumanta M

PROVIDER: S-EPMC7396349 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Genetic characterization and phylogenetic study of Lakor goat from Southwest Maluku Regency based on mitochondrial COI gene.

Rumanta Maman M Kunda Rony Marsyal RM Volkandari Slamet Diah SD Indriawati Indriawati I Kakisina Pieter P

Veterinary world 20200628 6

<h4>Aim</h4>This study is aimed at characterizing the genetic and phylogenetic structure of Lakor goats as indigenous livestock from the Southwest Maluku Regency based on mitochondrial COI gene sequences.<h4>Materials and methods</h4>The genomes of 103 follicle samples from Lakor goats, collected from Lakor Island, were analyzed. The polymerase chain reaction was used to amplify 1548 bp of the mitochondrial COI gene using two primer pairs (COIA and COIB). Following sequencing, genetic variation ...[more]

PMID: 32801575

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Project description:BackgroundThe common mudskipper (Periophthalmus kalolo Lesson, 1831) belongs to a group of fish species that exhibit amphibious lifestyles during specific daily periods. However, identifying this species poses a challenge due to its morphological similarities with other mudskipper species. These similarities have occasionally caused misidentifications of mudskippers. In Indonesia, previous studies have examined the genetic variation of common mudskippers, but these investigations have been limited to a few specific areas, particularly along the southern coast of Java. As a result, the available data remain fragmented, and no comprehensive genetic population analysis of common mudskippers on the southern coast of Java has been conducted. Therefore, our study aimed to establish DNA barcodes of COI mtDNA and explore the genetic variation and relationship among these common mudskipper populations from the southern coast of Java. We collected nine specimens from two populations, Cilacap Mangrove Forest and Kondang Bandung Beach, and supplemented our dataset with 38 previously collected COI sequences of common mudskippers from three different populations from the southern coast of Java (Pasir Mendit Beach, Bogowonto Lagoon, and Baros Beach).ResultsThe study revealed that 47 common mudskippers from five different populations are separated into three genetically distinct clades (A, B, and C). These clades display genetic divergences ranging from 0.97% to 1.91%. Each clade exhibits high levels of haplotype diversity but relatively low nucleotide diversity, suggesting a previous bottleneck in population followed by a fast expansion. However, the phylogeny, haplotype network, and principal coordinate analysis indicate overlapping populations with no geographic separation within these clades. This suggests the potential occurrence of gene flow among these populations, which might have been facilitated by past geological events.ConclusionsThese results enhance our understanding of common mudskipper biodiversity in Indonesia. Further studies involving common mudskipper populations from various geographical sites in Indonesia are required to further enrich our understanding of the variation and evolution of this species.

Dataset Information

Genetic characterization and phylogenetic study of Lakor goat from Southwest Maluku Regency based on mitochondrial COI gene.

Publications

Genetic characterization and phylogenetic study of Lakor goat from Southwest Maluku Regency based on mitochondrial COI gene.

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