Mitochondrial genome of Neilupotamon papileonaceum, with its phylogenetic analysis

Abstract

The mitochondrial genome of one potamidae species Neilupotamon papileonaceum was sequenced and annotated. The mitogenome is 16,273 bp in length, containing 37 typical genes. The A + T content of the whole mitogenome is 68.9%. Most of the PCGs started with ATG and stopped with TAT, except for ATP8 and ND6 stopped with TGA, COX1, COX2, ND5, ND4, and ND4L used incomplete T as stop codon. The phylogeny tree is monophyletic among 15 related species. The relationships of N. papileonaceum, Sinopotamon yaanense, and Longpotamon yangtsekiense were closer than others. This study further enriched mitogenome database of the tribe Typhlocybini.

Keywords:

• Mitochondrial DNA
• Neilupotamon papileonaceum
• phylogenetic analysis

The Neilupotamon papileonaceum as a kind of freshwater crab belongs to Crustacea, Decapoda, Potamidae. The N. papileonaceum is distributed in Huitong County, Loudi County, Xinhua County, and Chenxi County, Hunan province, China. Their whole body is red with blue butterfly patterns on the carapace and live in caves in streams and canals (Dai 1999).

A male adult of N. papileonaceum was collected from Shuiche Town（Xinhua County, Hunan Province, China) (110°97.5′E, 27°69.9′N), in August 2018 and the specimens (No. DWNLXX-1) were stored at −80 °C in our laboratory (College of Animal Science and Technology, Hunan Agriculture University). Total genomic DNA of the N. papileonaceum was extracted from the muscle of cheliped using the Column Animal DNA out (Beijing Tiandz, Beijin, China) following the kit’s instructions. Then, the mitochondrial genome (mitogenome) of N. papileonaceum was sequenced by Illumina sequencing platform (Wuhan Biowefind Biotechnology Co., Ltd, Wuhan, China). The reads were assembled and annotated using Generous Prime (v2019.1.3.). All tRNA genes were identified by ARWEN v1.2 (Laslett and Canbäck 2008). The annotated sequences of mitogenome were submitted to GenBank with accession number MT021974. All protein condoning genes (PCGs) were aligned using MAFFT algorithm in the TranslatorX (Katoh et al. 2019), and then poorly aligned results were removed by Gblocks 9.1 b (Castresana 2000; Abascal et al. 2010).

Mitogenome of N. papileonaceum has 16,273 bp in length and including 37 typical genes (13 PCGs, 22 tRNA genes, and 2 rRNA genes). The overall nucleotide composition of the mitogenome is 34.1% for A, 21.5% for C, 9.7% for G, and 34.7% for T. The A + T content of genes is 68.9%. Most PCGs started with ATG and stopped with TAT, except for ATP8 and ND6 stopped with TGA, COX1, COX2, ND5, ND4, and ND4L used incomplete T as stop codon. The length of 22 tRNA ranges from 62 bp (tRNA-Gly and tRNA-Cys) to 72 bp (tRNA-Val). Genes of 16S rRNA and 12S rRNA are 1331 bp and 883 bp, respectively. To validate the phylogenetic position of N. papileonaceum, we perform multiple sequence alignment and MEGA 6.0 (Tamura et al. 2013) to construct a neighbor-joining tree containing complete mitochondrial genome DNA of 15 species in Decapoda, as shown in the phylogenetic tree (Figure 1).

Figure 1. Phylogenetic analysis infers the evolutionary relationship of N. papileonaceum. The tree was constructed based on neighbor-joining (NJ) tree method using Mega 6.0. (The GenBank accession number for each species is indicated after the scientific name.).

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This research was supported by the National Natural Science Foundation of China [31672640], Blue Granary [2018YFD0900200] and Healthy Pond Technology System of Aquaculture Industry in Hunan province.