Project description:Rastrelliger brachysoma (short mackerel) and Rastrelliger kanagurta (Indian mackerel) are commercially important marine species in Southeast Asia. In recent years, numbers of these two species have been decreasing in the wild, and genomic information about them is still limited. We conducted a genome survey of these two mackerel species to acquire essential genomic information using next-generation sequencing data. To obtain this genetic information, comprehensive bioinformatics analyses were performed, including de novo assembly, gene prediction, functional annotation, and phylogenetic analysis. The estimated genome sizes were around 680.14 Mbp (R. brachysoma) and 688.82 Mbp (R. kanagurta). The heterozygosity of these species was very similar (≈0.81), while the repeat content for R. kanagurta (9.30%) was slightly higher than for R. brachysoma (8.30%). Functional annotation indicated that most of the genes predicted in these two species shared very close average amino acid identities (94.06%). The phylogenetic analysis revealed close phylogenetic relationships between these two species and other scombrids. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.
Project description:Lecithocladium angustiovum is identified from the stomach (87.33%) and the intestine (12.67%) of Indonesian short mackerel (Rastrelliger brachysoma). The description includes an elongated body; a mean total length of 1018.84 µm; and an ecsoma of 47.52% of the total length. The oral and ventral sucker ratio is 1:0.63, and the pharynx length is 97.42 µm. The sequence results were obtained by 18s rDNA gene sequencing of the 354 basepair (bp) DNA segment, and the mean base composition (%) was 17.7 A; 35.7 T; 29.6 G; and 17.1 C. A phylogenetic tree was constructed to demonstrate the genetic distance between L. angustiovum and sequences from Lecithocladium excisum, Dinurus longisinus, Plerurus digitatus and Lecithochirium caesionis obtained from GenBank.
Project description:Phylogeographic patterns and population structure of the pelagic Indian mackerel, Rastrelliger kanagurta were examined in 23 populations collected from the Indonesian-Malaysian Archipelago (IMA) and the West Indian Ocean (WIO). Despite the vast expanse of the IMA and neighbouring seas, no evidence for geographical structure was evident. An indication that R. kanagurta populations across this region are essentially panmictic. This study also revealed that historical isolation was insufficient for R. kanagurta to attain migration drift equilibrium. Two distinct subpopulations were detected between the WIO and the IMA (and adjacent populations); interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the IMA and WIO regions suggest historical isolation as a result of fluctuations in sea levels during the late Pleistocene. This occurrence resulted in the evolution of a phylogeographic break for this species to the north of the Andaman Sea.
