Resolution of the enigmatic phylogenetic relationship of the critically endangered Western Swamp Tortoise Pseudemydura umbrina (Pleurodira: Chelidae) using a complete mitochondrial genome

Xiuwen Zhang; Peter J Unmack; Gerald Kuchling; Yinan Wang; Arthur Georges

doi:10.1016/j.ympev.2017.07.019

Resolution of the enigmatic phylogenetic relationship of the critically endangered Western Swamp Tortoise Pseudemydura umbrina (Pleurodira: Chelidae) using a complete mitochondrial genome

Mol Phylogenet Evol. 2017 Oct:115:58-61. doi: 10.1016/j.ympev.2017.07.019. Epub 2017 Jul 25.

Authors

Xiuwen Zhang¹, Peter J Unmack², Gerald Kuchling³, Yinan Wang⁴, Arthur Georges⁵

Affiliations

¹ Institute for Applied Ecology, University of Canberra, ACT 2601, Australia. Electronic address: xiuwen.zhang@canberra.edu.au.
² Institute for Applied Ecology, University of Canberra, ACT 2601, Australia. Electronic address: peter.unmack@canberra.edu.au.
³ School of Animal Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia. Electronic address: gerald.kuchling@uwa.edu.au.
⁴ Institute for Applied Ecology, University of Canberra, ACT 2601, Australia. Electronic address: yinan.wang.yn@gmail.com.
⁵ Institute for Applied Ecology, University of Canberra, ACT 2601, Australia. Electronic address: georges@aerg.canberra.edu.au.

PMID: 28754240
DOI: 10.1016/j.ympev.2017.07.019

Abstract

Pseudemydura umbrina is one of the most endangered turtle species in the world, and the imperative for its conservation is its distinctive morphology and relict status among the Chelidae. We use Illumina sequencing to obtain the complete mitogenome for resolving its uncertain phylogenetic position. A novel nuclear paralogue confounded the assembly, and resolution of the authentic mitogenome required further Sanger sequencing. The P. umbrina mitogenome is 16,414bp comprising 37 genes organized in a conserved pattern for other vertebrates. The nuclear paralogue is 547bp, 97.8% identity to the corresponding mitochondrial sequence. Particular features of the mitogenome include an nd3 174+1A frameshift, loss of DHC loop in tRNA^Ser (AGN), and a light-strand replication initiation site in Wancy region that extends into an adjacent tRNA gene. Phylogenetic analysis showed that P. umbrina is the monotypic sister lineage to the remaining Australasian Chelidae, a lineage probably dating back to the Cretaceous.

Keywords: Complete mitogenome; ND3 frameshift; Numt; Phylogenetic analysis; Pleurodira.

MeSH terms

Animals
Endangered Species
Genome, Mitochondrial*
Phylogeny
RNA, Transfer / classification
RNA, Transfer / genetics
RNA, Transfer / metabolism
Turtles / classification*
Turtles / genetics

Substances

RNA, Transfer