Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

Abstract

Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is mitochondrial DNA analysis, which can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes.We determined the complete mitochondrial genome of a Central European red deer, Cervus elaphus hippelaphus, from Hungary by a next generation sequencing technology. The mitochondrial genome is 16 354 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region, all of which are arranged similar as in other vertebrates. We made phylogenetic analyses with the new sequence and 76 available mitochondrial sequences of Cervidae, using Bos taurus mitochondrial sequence as outgroup. We used 'neighbor joining' and 'maximum likelihood' methods on whole mitochondrial genome sequences; the consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Cervinae and Capreolinae, and five tribes, Cervini, Muntiacini, Alceini, Odocoileini, and Capreolini. The evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; which method could be used broadly in phylogenetic evolutionary analysis of animal taxa.

Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens

“…Based on genomic SNP markers, Hu et al (2019) suggested a different phylogenetic relationship where Tarim deer (represented by C. h. Yarkandensis ) formed a sister clade with Cervus canadensis , which was later explained as a result of frequent hybridisation amongst the Cervus group members ( Heckeberg, 2020 ). Our complete mitogenome-based phylogeny supports the inferences arrived from the cytochrome b-based phylogeny as well as other studies involving four species of red deer ( C. nippon , C. elaphus , C. canadensis and C. hanglu ) ( Zhang & Zhang, 2012 ; Frank et al, 2016 ; Li, Ba & Yang, 2016 ; Świsłocka et al, 2020 ; Mackiewicz et al, 2022 ). Given the support from the other studies, we believe that the mitogenome-based phylogeny of Hangul provides a clear relationship status within the Tarim red deer group.…”

“…Overall, the red deer group divergence period varied between 7-1 Mya across different studies ( Doan et al, 2022 ), probably due to differences in marker selection and analytical settings. For example, mitogenome-based divergence time estimation between European red deer and Tarim red deer ( C. h. Yarkandensis ) was found to be ~1.65 Mya ( Frank et al, 2016 ) and ~1.88 Mya ( Mackiewicz et al, 2022 ). Doan et al (2018) reported a divergence period of ~1.54 Mya between the western (consisting of C. elaphus and C. hanglu ) and the eastern ( C. nippon and C. canadensis ) red deer groups, whereas Zhang & Zhang (2012) along with Mackiewicz et al (2022) suggested that ~2 Mya divergence period between the same groups.…”

“…To ascertain Hangul’s phylogenetic position and estimate its divergence time, all available mitogenomes of Hangul ( and ), other cervids ( n = 13 species) and one sequence each of Muntiacini and Odocoileini were downloaded ( Wada, Nishibori & Yokohama, 2007 ; Pan et al, 2014 ; Frank et al, 2016 ) from GenBank (see Table 1 ). Upon scrutiny, it was observed that both Hangul mitogenomes from GenBank were identical and therefore only one of the sequences ( ) was used in all analyses.…”

Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

“…Being among the most important game animals for trophies, their populations have been managed, translocated and selectively hunted throughout their history and distribution area [26][27][28][29][30]. Recently a worldwide "deer industry" has been developed, whereby animals are farmed for venison and to some extent for antler products [31][32][33].…”

Identification of abnormal nuclear and mitochondrial genes in esophageal cancer cells

“…Since the initial reports in 2009 ( 6 , 7 ), NGS has aided the discovery of >50 novel disease genes in research settings. Thus, a there is a compelling requirement to extensively identify genomic abnormalities underlying ESCC by NGS, including single-nucleotide polymorphisms (SNPs), insertions/deletions (INDELs), structure variations (SVs) and other information variations ( 8 , 9 ), to elucidate its molecular basis, and to aid the development of effective targeted therapies.…”