title: The complete mitochondrial genome sequences of Chelodina rugosa and Chelus fimbriata (Pleurodira: Chelidae): implications of a common absence of initiation sites (O(L)) in pleurodiran turtles.
abstract: Within the order Testudines, while phylogenetic analyses have been performed on the suborder Cryptodira with complete mitochondrial genomes (mitogenomes), mitogenomic information from another important suborder Pleurodira has been inadequate. In the present study, complete mitochondrial DNA (mtDNA) sequences of two chelid turtles Chelodina rugosa and Chelus fimbriata were firstly determined, the lengths of which were 16,582 and 16,661 bp respectively. As the typical vertebrate mitogenome, both mtDNAs consist of 13 protein coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a long noncoding region (control region, CR). However, the initiation sites for light-strand replication (O(L)), which has been identified in all reported Cryptodire mitogenomes, were not found in the putative position of the two chelid turtles and African helmeted turtle Pelomedusa subrufa. The results suggested that the absence of mitogenomic initiation sites (O(L)) could be a characteristic of Pleurodira. Phylogenetic relationships of chelid turtles and other turtles were reconstructed using the reported mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) analyses suggested the monophyly of Pleurodira and Cryptodira as well as a sister group relationship between the two chelid turtles with strong statistical support. This phylogenetic framework was also utilized to estimate divergence dates among lineages using relaxed-clock methods combined with fossil evidence. Divergence estimates revealed that genus Chelodina diverged from genus Chelus in Late Cretaceous (~83 million years ago (mya)), and the time is consistent with the vicariance of the fragments which was caused by Gondwana split.
authors.affiliation: Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, 1 East Beijing Road, Wuhu, 241000 Anhui, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Wang
authors.forename: Xuming
authors.initials: X
authors.lastname: Zhou
authors.forename: Liuwang
authors.initials: L
authors.lastname: Nie
authors.forename: Xingquan
authors.initials: X
authors.lastname: Xia
authors.forename: Luo
authors.initials: L
authors.lastname: Liu
authors.forename: Yuan
authors.initials: Y
authors.lastname: Jiang
authors.forename: Zhengfeng
authors.initials: Z
authors.lastname: Huang
authors.forename: Wanxin
authors.initials: W
authors.lastname: Jing
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial / Q000235:genetics*; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D024363:Transcription Initiation Site; D014426:Turtles / Q000235:genetics*