Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae)

Ding, Li; Zhou, Quan; Sun, Yuanhai; Feoktistova, N. Yu.; Liao, Jicheng

doi:10.1016/j.ygeno.2019.09.016

Cited by 10 publications

(14 citation statements)

References 74 publications

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“…The A+T ratio of the D-loop was relatively lower (57.45%) than those of the whole mitogenome (59.72%), PCGs (59.47%), rRNAs (60.40%) and tRNAs (62.88%) ( Table S2 ). Similar to other vertebrate mitogenomes ( Ding et al, 2019 ; Krause et al, 2008 ; Wada et al, 2010 ), annotation of the Williams’s jerboa mitogenome showed overlapping regions and intergenic intervals between protein-coding and tRNA genes. The S. williamsi mitogenome had nine overlapping regions with a total length of 66 bp (between 1 and 43 bp) and 13 intergenic intervals with a total length of 42 bp (between 1 and 7 bp) ( Table 1 ).…”

Section: Resultssupporting

confidence: 59%

“…Because of the rich content of phylogenetically informative sites, whole mitochondrial genome (hereinafter referred to as mitogenome) data can provide more reliable and robust results ( Yang, Xue & Han, 2013 ; Yue et al, 2015 ). The data obtained from mitogenomes in recent years have enabled a better understanding of the phylogenetic relationships within various mammalian families (i.e., Bovidae and Cervidae ( Wada et al, 2010 ), Cricetidae ( Ding et al, 2019 ), Ursidae ( Krause et al, 2008 ), Viverridae ( Mitra et al, 2019 )). However, the mitogenome data of Dipodoidea species are limited; indeed, data of only a few species (e.g., Orientallactaga sibirica , Dipus sagitta , Euchoreutes naso , Eozapus setchuanus , Jaculus jaculus , Sicista concolor , Stylodipus telum ) ( Yue et al, 2015 ; Ding et al, 2016 ; Luo & Liao, 2016 ; Luo, Ding & Liao, 2016 ; Reyes et al, 2016 , ) are available.…”

Section: Introductionmentioning

confidence: 99%

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Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey

İbiş

2020

PeerJ

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Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia.

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Section: Resultssupporting

confidence: 59%

Section: Introductionmentioning

confidence: 99%

Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey

İbiş

2020

PeerJ

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“…A common feature in metazoan mitochondrial genomes is bias toward a higher representation of nucleotides As and Ts leading to a subsequent bias in corresponding encoded amino acids (Wang et al, 2018;Ding et al, 2020;Liu et al, 2020;Sun et al, 2020). At this point, DNA with a high AT-content makes the double helix less stable because the AT pair is bound by two hydrogen bonds while GC pairs are bound by three such bonds (Yakovchuk et al, 2006); therefore, the high AT-content of mitogenome could have a higher mutation rate such that may accelerate the evolutionary process for Diaptomidae (Triant and DeWoody, 2006;Ding et al, 2020). Interestingly, the A + T content of PCGs at the 3rd codon position is higher than that of 1st and 2nd codon FIGURE 4 | The evolutionary rate indicated by Ka/Ks for each PCG in the four representative mitogenomes of P. tunguidus (see Table 1).…”

Section: Discussionmentioning

confidence: 99%

“…Their characteristics conformed to the typical invertebrate mitogenome without gene insertion and deletion but with rearrangements. A common feature in metazoan mitochondrial genomes is bias toward a higher representation of nucleotides As and Ts leading to a subsequent bias in corresponding encoded amino acids ( Wang et al, 2018 ; Ding et al, 2020 ; Liu et al, 2020 ; Sun et al, 2020 ). At this point, DNA with a high AT-content makes the double helix less stable because the AT pair is bound by two hydrogen bonds while GC pairs are bound by three such bonds ( Yakovchuk et al, 2006 ); therefore, the high AT-content of mitogenome could have a higher mutation rate such that may accelerate the evolutionary process for Diaptomidae ( Triant and DeWoody, 2006 ; Ding et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Geographic Variation of Phyllodiaptomus tunguidus Mitogenomes: Genetic Differentiation and Phylogeny

Zhang

Liu

et al. 2021

Front. Genet.

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Phyllodiaptomus tunguidus (Copepoda: Calanoida) is largely endemic to and widespread in freshwater in southern China, where it inhabits a complex landscape from lowland to highland across an elevation gradient of 2000m. A deep genetic differentiation can be expected between its most distant geographic populations. Here, we sequenced nine mitogenomes from diverse populations. All mitogenomes contained 37 genes, including 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes and one control region. Their base composition, genetic distance and tRNA structure indeed revealed a wide differentiation between mitogenomes. Two P. tunguidus from Guangxi near Vietnam differed from the other seven by up to 10.1%. Their tRNA-Arg had a complete clover-leaf structure, whereas that of the others did not contain an entire dihydrouridine arm. The nine mitogenomes also differed in the length of rRNA. NJ, ML, and Bayesian analyses all split them into two clades, viz. the two P. tunguidus from Guangxi (Clade 1), and the other seven (Clade 2). Both the structure and phylogeny of the mitogenomes suggest that P. tunguidus has complex geographic origin, and its populations in Clade 1 have long lived in isolation from those in Clade 2. They currently reach the level of subspecies or cryptic species. An extensive phylogenetic analysis of Copepoda further verified that Diaptomidae is the most recently diverging family in Calanoida and that P. tunguidus is at the evolutionary apex of the family.

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“…Subsequently, this conclusion has been corroborated by phylogenetic reconstructions using a set of five nuclear exons and two mitochondrial genes 2 . Furthermore, molecular evidence has indicated that Urocricetus is phylogenetically related to dwarf hamsters of the genus Phodopus (Miller, 1910) 2 , 6 . It was suggested that both Phodopus and Urocricetus originated in East Central Asia (east of the Altai–Tian Shan boundary) having separated from each other in the early Late Miocene (~ 10.4 Mya), which is comparable to the time point of the split between chromosomally, morphologically, and genetically divergent Mesocricetus and Cricetus lineages.…”

Section: Introductionmentioning

confidence: 99%

Karyotypic and molecular evidence supports the endemic Tibetan hamsters as a separate divergent lineage of Cricetinae

Romanenko

Lebedev

Банникова

et al. 2021

Sci Rep

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The genus status of Urocricetus was defined recently based on morphological and molecular data. Even though the amount of evidence for a separate phylogenetic position of this genus among Cricetinae continues to increase, there is still no consensus on its relationship to other groups. Here we give the first comprehensive description of the U. kamensis karyotype (2n = 30, NFa = 50) including results of comparative cytogenetic analysis and detailed examination of its phylogenetic position by means of numerous molecular markers. The molecular data strongly indicated that Urocricetus is a distant sister group to Phodopus. Comparative cytogenetic data showed significant reorganization of the U. kamensis karyotype compared to karyotypes of all other hamsters investigated earlier. The totality of findings undoubtedly means that Urocricetus belongs to a separate divergent lineage of Cricetinae.

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Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae)

Cited by 10 publications

References 74 publications

Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey

Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey

Geographic Variation of Phyllodiaptomus tunguidus Mitogenomes: Genetic Differentiation and Phylogeny

Karyotypic and molecular evidence supports the endemic Tibetan hamsters as a separate divergent lineage of Cricetinae

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