Sequencing and Characterisation of Complete Mitochondrial DNA Genome for Trigonopoma pauciperforatum (Cypriniformes: Cyprinidae: Danioninae) with Phylogenetic Consideration.

Hung Hui Chung,Tommy Tsan-Yuk Lam,Leonard Whye Kit Lim,Yee Ling Chong,Yunshi Liao

doi:10.21315/tlsr2020.31.1.7

Hung Hui Chung, Tommy Tsan-Yuk Lam + Show 3 more

Open Access

https://doi.org/10.21315/tlsr2020.31.1.7

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Abstract

The Trigonopoma pauciperforatum or the redstripe rasbora is a cyprinid commonly found in marshes and swampy areas with slight acidic tannin-stained water in the tropics. In this study, the complete mitogenome sequence of T. pauciperforatum was first amplified in two parts using two pairs of overlapping primers and then sequenced. The size of the mitogenome is 16,707 bp, encompassing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other family members. The heavy strand accommodates 28 genes while the light strand houses the remaining nine genes. Most protein-coding genes utilise ATG as start codon except for COI gene which uses GTG instead. The terminal associated sequence (TAS), central conserved sequence block (CSB-F, CSB-D and CSB-E) as well as variable sequence block (CSB-1, CSB-2 and CSB-3) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of T. pauciperforatum from the basal region of the major clade, where its evolutionary relationships with Boraras maculatus, Rasbora cephalotaenia and R. daniconius are poorly resolved as suggested by the low bootstrap values. This work contributes towards the genetic resource enrichment for peat swamp conservation and comprehensive in-depth comparisons across other phylogenetic researches done on the Rasbora-related genus.

Highlights

The redstripe rasbora (Trigonopoma pauciperforatum) (Weber & de Beaufort, 1916) is grouped under the subfamiliy Danioninae in the Cyprinidae family
This study had shed light on the landscape of the complete mitochondrial genome of T. pauciperforatum beside further dissecting on the genetic contents and revealing the molecular phylogenetic relationship across 13 other closely related members of the Danioninae subfamily
The raw data for phylogenetic analysis was collected from GenBank database which includes 13 other closely related members of the Danioninae subfamily with complete mitochondrial genomic DNA available publicly; Acheilognathus typus and Danio rerio were selected as the outgroup

Summary

Introduction

The redstripe rasbora (Trigonopoma pauciperforatum) (Weber & de Beaufort, 1916) is grouped under the subfamiliy Danioninae in the Cyprinidae family It has the distinctive thick striking red neon stripe which aligns in parallel to its spine, starting from the side of its jaw, crossing upper part of the eye and up till before its tail fin (Weber & de Beaufort, 1916). Females have bigger bellies than males in general because this species is egg-spawning fish This red-striped rasbora fish can be found abundantly in school around stagnant fresh waters (rivers, drainages, lakes and streams) of South East Asia, including Peninsular Malaysia, Sarawak and Sumatra (Ward, 2003). The type locality of this species is Sumatra Their natural habitat has heavily grown and overhanging vegetation with minimal lighting. Adult fish can grow up to the length of >6 centimetre (Ward, 2003)

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