Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda)

PeerJ

article

Mun Hua Tan¹  Han Ming Gan¹  Yin Peng Lee¹  Gary C.B. Poore³  Christopher M. Austin¹ 

[1] School of Science, Monash University Malaysia;Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia;Museums Victoria;School of Life and Environmental Sciences, Deakin University

关键词: True shrimps;    Mitochondrial genomics;    Codon usage;    Ghost shrimps;    Gene order;    Phylogenetics;    Shrimps;   

DOI  :  10.7717/peerj.2982

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Background Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information. Methods Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements. Results We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders. Discussion Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

【 授权许可】

CC BY