New insights into Oniscidea (Crustacea: Isopoda) mitogenome structural features and phylogenetic placement of targeted taxa using mitogenomic and nuclear data

Abstract Among Isopoda suborders the Oniscidea has the highest species richness, and is also the largest terrestrial group in the Crustacea. Terrestrial isopods are an excellent case to study adaptations related to sea-land transition. However, the monophyly of Oniscidea and the relationships of the main lineages has been debated over the last three decades. Aiming to further explore structural features of mitochondrial genome and investigate the phylogenetic relationships within Oniscidea, the mitogenomes and a series of nuclear markers of the oniscids Ligia exotica and Mongoloniscus sinensis were sequenced. The nuclear genome was represented by four nuclear genes analyzed in a separate dataset. The mitogenomes of L. exotica and M. sinensis were 16,018 and 14,978 bp in length, respectively. Both included 13 protein-coding genes, 2 rRNA genes, and 21 and 19 tRNA genes respectively, missing one and three tRNA genes respectively compared to the isopod ground pattern. The M. sinensis mitogenome had higher average A+T content (~75.3%) than any other isopod studied to date. Phylogenetic analyses confirmed the assignment of M. sinesis to Agnaridae, as well as the sister-group relationship of the family with Porcellionidae, one of the more derived Crinochaeta clades. On the other hand, the basal position of Ligia within Oniscidea and the close evolutionary relationship with the aquatic groups Valvifera, Shaperomatida and some Cymothoidea that were included in our analysis, is indicated.

Download Full-text

The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes

ZooKeys ◽

10.3897/zookeys.925.47820 ◽

2020 ◽

Vol 925 ◽

pp. 73-88

Author(s):

Chaoyi Hu ◽

Shuaibin Wang ◽

Bisheng Huang ◽

Hegang Liu ◽

Lei Xu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Gc Content ◽

Sister Group ◽

Rrna Genes ◽

Sister Group Relationship ◽

Trna Genes ◽

Protein Coding ◽

Generation Sequencing ◽

Simple Sequence

Scolopendra mutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S. mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S. mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S. mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S. mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.

Download Full-text

Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽

10.3897/zookeys.1070.72742 ◽

2021 ◽

Vol 1070 ◽

pp. 13-30

Author(s):

Wanqing Zhao ◽

Dajun Liu ◽

Qian Jia ◽

Xin Wu ◽

Hufang Zhang

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Purifying Selection ◽

Sister Group ◽

Start Codon ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

Download Full-text

Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus

Bioscience Reports ◽

10.1042/bsr20182349 ◽

2019 ◽

Vol 39 (8) ◽

Author(s):

Jian-Qiu Li ◽

Li Li ◽

Bao-Quan Fu ◽

Hong-Bin Yan ◽

Wan-Zhong Jia

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Evolutionary Relationship ◽

Sister Group ◽

Trna Genes ◽

Mammal Species ◽

Qinghai Province ◽

Loop Region ◽

Mt Genome

AbstractThe plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (OL region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNASer (GCU). The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.

Download Full-text

Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi (Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina

International Journal of Molecular Sciences ◽

10.3390/ijms20205167 ◽

2019 ◽

Vol 20 (20) ◽

pp. 5167 ◽

Cited By ~ 15

Author(s):

Qiang Li ◽

Yuanhang Ren ◽

Xiaodong Shi ◽

Lianxin Peng ◽

Jianglin Zhao ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Intron Loss ◽

Rrna Genes ◽

Trna Genes ◽

Evolutionary Time ◽

Dynamic Changes ◽

Protein Coding ◽

Tree Topologies ◽

Nuclear Genomes

In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.

Download Full-text

Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

International Journal of Molecular Sciences ◽

10.3390/ijms19082383 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2383 ◽

Cited By ~ 8

Author(s):

Qixiang Lu ◽

Wenqing Ye ◽

Ruisen Lu ◽

Wuqin Xu ◽

Yingxiong Qiu

Keyword(s):

Gene Order ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Early Pleistocene ◽

Disjunct Distribution ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Intergenic Spacers ◽

Protein Coding Genes

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

Download Full-text

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

Plants ◽

10.3390/plants9091116 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1116 ◽

Cited By ~ 1

Author(s):

Xue-Li Zhao ◽

Zhang-Ming Zhu

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Process ◽

Rrna Genes ◽

Trna Genes ◽

Sister Relationship ◽

Protein Coding ◽

Variable Regions ◽

Chloroplast Genomes ◽

Distinct Genus ◽

Relationship Of

Taxonomic and phylogenetic relationships of Christia, Urariopsis, Uraria and related genera within the tribe Desmodieae (Fabaceae: Papilionoideae) have long been controversial. Here, we report the complete chloroplast (cp) genomes of Christia vespertilionis and Urariopsis brevissima and perform comparative and phylogenetic analyses with Uraria lagopodioides and other relatives in the Desmodieae. The cp genomes of C. vespertilionis and U. brevissima are 149,656 and 149,930 bp long, with 128 unique genes (83 protein-coding genes, 37 tRNA genes and 8 rRNA genes), respectively. Comparative analyses revealed 95-129 simple sequence repeats (SSRs) and eleven highly variable regions (trnK-rbcL, rbcL-atpB, ndhJ-trnF, trnL-trnT, psbD-rpoB, accD-cemA, petA-psbL, psbE-petL, rps11-rps19, ndhF-ccsA, and rps15-ycf1) among six Desmodieae species. Phylogenetic analyses clearly resolved two subtribes (Desmodiinae and Lespedezinae) of Desmodieae as monophyletic, and the newly reported C. vespertilionis and U. brevissima clustered in subtribe Desmodiinae. A sister relationship of C. vespertilionis to U. lagopodioides was supported. Evidence was presented to support the treatment of Urariopsis as a distinct genus rather than in synonymy with Uraria. The results provide valuable information for further studies on species delimitation, phylogenetics, population genetics, and the evolutionary process of speciation in the Desmodieae.

Download Full-text

A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

Amphibia-Reptilia ◽

10.1163/15685381-00002958 ◽

2014 ◽

Vol 35 (3) ◽

pp. 331-343 ◽

Cited By ~ 5

Author(s):

Yongmin Li ◽

Huabin Zhang ◽

Xiaoyou Wu ◽

Hui Xue ◽

Peng Yan ◽

...

Keyword(s):

Nucleotide Sequence ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes

We determined the complete nucleotide sequence of the mitochondrial genome of Odorrana schmackeri (family Ranidae). The O. schmackeri mitogenome (18 302 bp) contained 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes and a single control region (CR). In the new mitogenome, the distinctive feature is the loss of tRNA-His, which could be explained by a hypothesis of gene substitution. The new sequence data was used to assess the phylogenetic relationships among 23 ranid species mostly from China using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses support two families (Ranidae, Dicroglossidae) for Chinese ranids. In Ranidae, we support the genus Amolops should be retained in the subfamily Raninae rather than in a distinct subfamily Amolopinae of its own. Meanwhile, the monophyly of the genus Odorrana was supported. Within Dicroglossidae, four tribes were well supported including Occidozygini, Dicroglossini, Limnonectini and Paini. More mitochondrial genomes and nuclear genes are required to decisively evaluate phylogenetic relationships of ranids.

Download Full-text

Mitochondrial DNA Variability withinUromastyx ornata philbyi(Agamidae: Squamata) from Southwestern Saudi Arabia

Comparative and Functional Genomics ◽

10.1155/2012/851379 ◽

2012 ◽

Vol 2012 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Sayed A. M. Amer ◽

Mohamed M. Ahmed ◽

Thomas M. Wilms ◽

Mohammed Shobrak ◽

Yoshinori Kumazawa

Keyword(s):

Saudi Arabia ◽

Mitochondrial Dna ◽

Sister Group ◽

Molecular Data ◽

Sister Group Relationship ◽

Trna Genes ◽

Loop Structure ◽

Protein Coding ◽

Nadh Dehydrogenase Subunit 2 ◽

The One

Approximately 2.4 kbp of mitochondrial DNA was sequenced from 9 individuals ofUromastyx ornata philbyioriginating from Taif, Namas, Al-Baha, and Jazan in southwestern Saudi Arabia. The sequenced regions cover eight tRNA genes (tRNAGln,tRNAIle,tRNAMet,tRNATrp,tRNAAla,tRNAAsn,tRNACys, andtRNATyr) and two protein-coding genes (NADH dehydrogenase subunit 2 and cytochromeb).U. ornata philbyihad an insertion of 170 bp length betweentRNAGlnandtRNAIlegenes. The first 128 bp of this insertion was similar to the one identified earlier inU. ornata ornataand can be folded into a stem-and-loop structure, which was less stable inU. ornata philbyithan inU. ornata ornata, or the secondtRNAGlngene. The next 42 bp of the insertion was unique inU. ornata philbyiand additionally retained a stable stem-and-loop structure. Most base substitutions found in the sequenced genes were synonymous transitions rather than transversions. Tree analyses supported the sister group relationship between the twoU. ornatasubspecies and dividedU. ornata philbyiinto two groups: Taif+Namas group in the east of Sarawat and Al-Baha+Jazan group in the west of Sarawat. These molecular data are in agreement with current classification ofU. ornata.

Download Full-text

Two-Step Contractions of Inverted Repeat Region and Psai Gene Duplication from the Plastome of Croton Tiglium (Euphorbiaceae)

10.20944/preprints201807.0458.v2 ◽

2018 ◽

Author(s):

Sangjin Jo ◽

Ki-Joong Kim

Keyword(s):

Intergenic Spacer ◽

Sister Group ◽

Single Copy ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Inverted Repeat Region ◽

Protein Coding ◽

Tropical Asia ◽

Croton Tiglium

Croton L. (Euphorbiaceae) is a very specious genus and consists of about 1,250 species, mainly distributed in tropical Asia and China. The first complete plastome sequence from the genus, Croton tiglium, is reported in this study (NCBI acc. No. MH394334). The plastome is 150,021 bp in length. The lengths of LSC and SSC are 111,654 bp and 18,167 bp, respectively. However, the length of the IR region is only 10,100 bp and includes only four rrn and four trn genes, and a small part of the ycf1 gene. We propose two-step IR contractions to explain this unique IR region of the C. tiglium plastome. First, the IR contracted from rps19-rpl2 to ycf2-trnL-CAA on the LSC/IRb boundary. Second, the IR contracted from ycf2-trnL-CAA to rrn16-trnV-GAC on the LSC/IRa boundary. In addition, duplicated copies of psaI genes were discovered in the C. tiglium plastome. Both copies were located side by side between accD and ycf4 genes, but one copy was pseudogenized because of a five-basepair (TAGCT) insertion in the middle of the gene following frameshift mutation. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes have two introns. The infA gene is lost. Twelve large repeats were detected in the plastome. All large repeats are located in the LSC region. Also, 272 simple sequence repeats (SSRs) were identified. The penta-SSRs accounted for 45% of total SSRs, followed by mono- (32%), di- (12%), tetra (6%) and tri-SSRs (5%). Most of them were distributed in the large single copy (LSC) region (85%). In addition, 76% of the SSRs were located in the intergenic spacer (IGS). Phylogenetic analysis suggested that C. tiglium is a sister group of Jatropha curcas with 100% bootstrap support. Seven Euphorbiaceae species formed one clade with 100% bootstrap support.

Download Full-text

Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera: Sphingidae)

ZooKeys ◽

10.3897/zookeys.754.23404 ◽

2018 ◽

Vol 754 ◽

pp. 127-139 ◽

Cited By ~ 1

Author(s):

Jun Li ◽

Rui-Rui Lin ◽

Yao-Yao Zhang ◽

Kun-Jie Hu ◽

Ya-Qi Zhao ◽

...

Keyword(s):

Tandem Repeats ◽

Phylogenetic Analyses ◽

Rrna Genes ◽

Phylogenetic Position ◽

Trna Genes ◽

Rich Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Oxidase Subunit ◽

Relationship Of

In the present study, the complete mitogenome of Theretrajaponica was sequenced and compared with other sequenced mitogenomes of Sphingidae species. The mitogenome of T.japonica, containing 37 genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) and a region rich in adenine and thymine (AT-rich region), is a circular molecule with 15,399 base pairs (bp) in length. The order and orientation of the genes in the mitogenome are similar to those of other sequenced mitogenomes of Sphingidae species. All 13 protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome C oxidase subunit 1 gene (cox1) which is initiated by the codon CGA as observed in other lepidopteran insects. Cytochrome C oxidase subunit 2 gene (cox2) has the incomplete termination codon T and NADH dehydrogenase subunit 1 gene (nad1) terminates with TAG while the remainder terminates with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Ile and Leu2 are the most frequently used codon families and codons CGG, CGC, CCG, CAG, and AGG are absent. The 431 bp AT-rich region includes the motif ATAGA followed by a 23 bp poly-T stretch, short tandem repeats (STRs) of TC and TA, two copies of a 28 bp repeat ‘ATTAAATTAATAAATTAA TATATTAATA’ and a poly-A element. Phylogenetic analyses within Sphingidae confirmed that T.japonica belongs to the Macroglossinae and showed that the phylogenetic relationship of T.japonica is closer to Ampelophagarubiginosa than Daphnisnerii. Phylogenetic analyses within Theretra demonstrate that T.japonica, T.jugurtha, T.suffusa, and T.capensis are clustered into one clade.

Download Full-text