Characterization of the Mitochondrial Genome of Cambaroides schrenckii (Astacidea: Cambaridae) and Its Phylogenetic Implications

Abstract

Background: Cambaroides schrenckii is an endangered freshwater crayfish in China, belonging to the genus Cambaroides, that can act as a complementary host for paragonimus. The objective of this study was to examine the complete mitochondrial genome characteristics and their evolutionary relationships within the Astacidea.

Methods: The analysis of gene rearrangements and evolutionary relationships was conducted through the sequencing of the mitochondrial genome of C. schrenckii.

Results: C. schrenckii mitochondrial genome length was 15,572, comprising thirteen PCGs, two rRNAs, 22 tRNAs, and one d-loop region of C. schrenckii. The mitochondrial genome of C. schrenckii exhibits an A + T content of 69.61% and a G + C content of 30.39%. Among the thirteen PCGs, cytb, nad3, and nad6 have a start codon of ATT, while the other ten PCGs have ATC, ATA, and ATG start codons. All 22 tRNA genes displayed a typical cloverleaf secondary structure. Gene rearrangement analysis showed that seven gene arrangements were identified based on PCGs in the infraorder Astacidea, with type I being the most common.

Conclusions: The relationship between the American Cambaridae is closer to Astacidae than the Asian Cambaridae. The present study provides a theoretical basis for further discussions of developmental relationships in the infraorder Astacidea.

Keywords: Astacidea; Cambaroides schrenckii; mitochondrial genome; phylogenetic analysis.

Figure 1

C. schrenckii mitochondrial genome arrangement. PCGs are shown as blue arrows, rRNA genes as purple arrows, tRNA genes as red arrows, and control region as grey arrows. Ticks in the inner cycle indicate the sequence length. The black ring indicates the GC content (outward and inward peaks showing above or below average GC content, respectively). The purple-green ring indicates the GC skew [(G − C)/(G + C)], purple (between 0 and 1), green (between −1 and 0)].

Figure 2

A + T content and nucleotide skew of genes, individual elements, and the complete mitochondrial genome of ten Astacoidea.

Figure 3

Sliding window analysis of the complete mitochondrial genome sequences of five Astacoidea. A sliding window of 300 bp (in 10 bp overlapping steps) was used to estimate nucleotide diversity Pi (π) across the alignments. Nucleotide diversity was plotted against the mid-point positions of each window. Each gene boundary is identified.

Figure 4

Relative synonymous codon usage (RSCU) of 13 protein coding genes of C. schrenckii, C. dauricus, C. japonicus, Cambaroides wladiwostokiensis, and C. similis. The termination codon is not given.

Figure 5

Comparison of the mitochondrial genome organisation of infraorder Astacidea. The circular mitochondrial genome was linearized at the 5′ end of cox1 gene for illustration purpose. Non-coding regions were not shown. Red triangular represent gene or gene fragments positional change. Red rhombus represent the duplicated gene fragments. Positions of the inverted blocks are shown with thick grey solid lines. Inversion is specified by the rotating arrow with red lines. The transposition route is indicated by a dashed line.

Figure 6

Phylogenetic relationships of C. schrenckii with other 42 representative Astacidea based on concatenated amino acid sequences of 13 protein coding genes analysed by maximum likelihood (ML) and Bayesian inference (BI) using C. haematocheir as the outgroup. Red dots on nodes indicate BPP = 100/1.00.