The complete mitochondrial genomes of Umalia orientalis and Lyreidus brevifrons: The phylogenetic position of the family Raninidae within Brachyuran crabs.
The complete mitochondrial genome (mitogenome) sequences of two primitive crabs, Umalia orientalis and Lyreidus brevifrons (Decapoda: Brachyura: Raninidae) were determined. The mitogenomes of the two species are 15,466 and 16,112bp in length with AT content of 68.0% and 70.6%, respectively. Each genome contains 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes. The gene arrangement of U. orientalis is the same with those reported for most brachyuran species. Nevertheless, the gene arrangement of L. brevifrons differs from that of U. orientalis in having an additional non-coding region. The newly found non-coding region is located between nad3 and trnA with 641bp in length. Its nucleotide composition and secondary structure are similar to the typical control region. In L. brevifrons, the secondary structures of trnS-AGN and trnI are significantly different from those in U. orientalis and other brachyuran species. The start codon for cox1 is ATG in all reported Eubrachyura mitogenomes, while a common start codon ACG is found in the Podotremata. Phylogenetic analyses for crustacean decapods based on the nucleotide and amino acid of 13 PCGs indicate that Homolidae is more primitive in Brachyura, and Raninidae is a sister group to Eubrachyura. This implies that Raninidae is closer to Eubrachyura than to Homolidae, and Podotremata may be a paraphyletic assemblage. The results also indicate that the subfamily Lyreidinae is closer to Notopodinae than to Ranininae within Raninidae. The novel mitogenome data provides useful information for refining the phylogenetic relationships within Brachyura.
EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
Guohui
G
Shi
EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao 266071, China. Electronic address: zhxcui@qdio.ac.cn.
Zhaoxia
Z
Cui
EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
Min
M
Hui
EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
Yuan
Y
Liu
Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
Tin-Yam
TY
Chan
EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
Chengwen
C
Song
D000818:Animals; D003386:Brachyura / Q000145:classification* / Q000235:genetics*; D004247:DNA / Q000235:genetics; D054629:Genome, Mitochondrial; D010802:Phylogeny
D004247:DNA
Mitochondrial genome; Non-coding region; Phylogenetics; Podotremata; Raninidae