Characterisation of the complete mitochondrial genome of Helice wuana (Grapsoidea: Varunidae) and comparison with other Brachyuran crabs

Abstract

The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The genome composition is highly A+T biased 68.42%, and exhibits a negative AT-skew (-0.036) and GC-skew (-0.269) among Brachyura crabs. Gene rearrangements were detected, as was tandem duplication followed by random loss, which explains the translocation of mitochondrial genes. Phylogenetic analysis showed that H. wuana and H. tientsinensis clustered on one branch with high nodal support values. These results confirm that the placement of H. wuana within the Varunidae family of Thoracotrematan crabs. This study will provided a better understanding for gene rearrangements and crab evolution in the further.

Comparative Mitochondrial Genome Analyses of Sesarmid and Other Brachyuran Crabs Reveal Gene Rearrangements and Phylogeny

“…The mitogenome composition (A: 36.61%, T: 38.20%, C: 15.13%, G: 10.06%) was strongly A + T biased which accounts for 74.81%, and exhibited with negative AT-skew (-0.021). The AT-skew of the mitogenomes of most crabs were negative, for example, H. wuana (Tang et al, 2018), S. sinensis (Tang et al, 2017), H. tientsinensis (Xin et al, 2017b), C. sinensis (Xin et al, 2017a), the AT-skew value of mitogenomes in other crabs had also been calculated and counted in related studies (Xin et al, 2017a,b). The genes were typical of animal mitogenomes, with 22 tRNA genes, 13 PCGs, 2 rRNA genes, and a CR ( Table 2).…”

“…The AT-skew of the mitogenomes of most crabs were negative, for example, H . wuana ( Tang et al, 2018 ), S. sinensis ( Tang et al, 2017 ), H . tientsinensis ( Xin et al, 2017b ), C .…”

“…The complete mitogenome was obtained using a combination of conventional PCR and long PCR to amplify overlapping fragments spanning the entire mitogenome. Initially, conserved sequences, such as cox1 , cox3 , nad5 , nad4 , and rrnS , were amplified by conventional PCR using universal primers synthesized by Beijing Sunbiotech ( Tang et al, 2003 , 2017 , 2018 ; Liu et al, 2015 ; Xin et al, 2017a , b ).…”

“…The mitogenome has a simple structure, haploid nature, maternal inheritance, and rapid evolutionary rate ( Liu et al, 2015 ). The mitogenomes are closed circular double-stranded molecules in the range of 14–18 kb in most bilaterian animals, including 13 protein-coding genes (PCGs; cox1–3 , cob , nad1–6 and nad4L , atp6 , and atp8 ), 2 rRNA genes, 22 tRNA genes, and an AT-rich region (control region) ( Tang et al, 2003 , 2017 , 2018 ; Xin et al, 2017a , b ). The taxonomy of Sesarmid crabs has been studied extensively and benefited from recent refinements in species of Perisesarma and Sesarmops ( Li et al, 2019 ; Shih et al, 2019 ; Ng et al, 2020 ).…”

The complete mitochondrial genome sequence of Metaplax longipes (Grapsoidea: Varunidae)

“…Mitogenomic DNA of M. longipes was extracted from muscle tissue sample using an Aidlab Genomic DNA Extraction Kit (Aidlab Co., Beijing, China) and stored at À20 C until needed for PCR amplification. For amplification of the whole mitogenome of M. longipes, a set of universal primers were used to amplify a range of segments of the entire mitogenome (Tang et al 2003(Tang et al , 2017(Tang et al , 2018Simon et al 2006;Xin et al 2017). Subsequently, specific primers were designed using Primer Premier 5.0 and synthesized by Beijing Sunbiotech.…”