Mitochondrial genome of Chinese grass shrimp, Palaemonetes sinensis and comparison with other Palaemoninae species

Yingying Zhao,Xiaodong Li,Yingdong Li,Xiaochen Zhu,Weibin Xu,Hua Wei,Zhibin Han,Jing Dong

doi:10.1038/s41598-019-53539-x

Yingying Zhao, Xiaodong Li + Show 6 more

Open Access

https://doi.org/10.1038/s41598-019-53539-x

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Abstract

The mitogenome of Chinese grass shrimp, Palaemonetes sinensis, was determined through Illumina sequencing, and the basic characteristics and gene arrangement were analyzed. The mitogenome of P. sinensis was 15955 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and one control region, with tightly packed. 33 of these genes were encoded on the heavy strand, and the remainders encoded on the light strand. The composition of P. sinensis mitogenome presented a strong A + T bias, which account for 66.7%. All PCGs were initiated by a canonical ATN codon, except nad5, which was initiated by GTG. The termination codons of the PCGs were TAA, TAG and T–. The secondary structures of 22 tRNAs of P. sinensis had the typical clover structure, except of trnS1 owing to the lack of dihydroxyuridine (DHU) arm. Gene order comparison of P. sinensis and previously-sequenced Palaemoninae revealed a unique translocation between trnT and trnP in Macrobrachium. The phylogenetic analyses showed that three Exopalaemon species formed a monophyletic group and then clustered with two Palaemon species and P. sinensis successively whereas Macrobrachium clustered with Palaemon capensis in the other clade.

Highlights

Palaemonidae, as the second most species-rich family in Caridean, including 134 genera and 934 extant species[1], is widely distributed in almost any aquatic habitat
Compared with the other Palaemoninae species, P. sinensis mitogenome was slightly smaller than that of Palaemon serenus (15,967 bp), but it is in the range of the known Palaemoninae mitogenomes (15,694–15,967 bp)
Like most of Caridea, the mitogenomes of P. sinensis in this study were closely aligned, with only a small number of base overlapping between adjacent genes, indicating that RNA transcription and protein translation were more efficient (Table 1)

Summary

Introduction

Palaemonidae, as the second most species-rich family in Caridean, including 134 genera and 934 extant species[1], is widely distributed in almost any aquatic habitat. Most molecular studies on Palaemoninae are based on the analysis of partial sequences of 16S rRNA and fragment of the nuclear genes histone[3] (H3)[6,7]. Analysis of other gene sequences (both from mitogenome and nuclear genome) are necessary to improve the understanding of phylogenetic relationship amongst Palaemonid shrimps.

Results

Conclusion