The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora

Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth’s most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes.

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

10.21203/rs.3.rs-25479/v2 ◽

2021 ◽

Author(s):

Lina Yang ◽

Ruru Chen ◽

Rui Zhang ◽

Andreas C. Dimitriou ◽

Jianmei An

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Nuclear Genome ◽

Nuclear Data ◽

Sister Group ◽

Structural Features ◽

Rrna Genes ◽

Sister Group Relationship ◽

Trna Genes ◽

Protein Coding

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.

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The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications

ZooKeys ◽

10.3897/zookeys.1061.70176 ◽

2021 ◽

Vol 1061 ◽

pp. 57-73

Author(s):

Renyi Zhang ◽

Qian Tang ◽

Lei Deng

Keyword(s):

Complete Mitochondrial Genome ◽

Genetic Material ◽

Start Codon ◽

Trna Genes ◽

Protein Coding ◽

Simple Loop ◽

Stop Codons ◽

Phylogenetic Implications ◽

Complete Mitogenome ◽

Rna Genes

Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobio elongatus (Yao & Yang, 1977). The mitogenome of M. elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M. elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNASer(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M. elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

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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.

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Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

International Journal of Molecular Sciences ◽

10.3390/ijms21134685 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4685

Author(s):

Zhenhai Li ◽

Min Li ◽

Shannan Xu ◽

Li Liu ◽

Zuozhi Chen ◽

...

Keyword(s):

Divergence Time ◽

Rrna Genes ◽

12S Rrna ◽

Trna Genes ◽

Coding Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Gc Skew ◽

The Family ◽

Conserved Genes

Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

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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.

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The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses

Scientific Reports ◽

10.1038/s41598-020-77661-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Wenbin Xu ◽

Boshun Xia ◽

Xinwei Li

Keyword(s):

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Distinct Species ◽

The Other ◽

Trna Genes ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Noncoding Sequences ◽

Chloroplast Genomes ◽

Rna Genes

AbstractThe six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.

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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.

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Mitochondrial Genomes of Hestina persimilis and Hestinalis nama (Lepidoptera, Nymphalidae): Genome Description and Phylogenetic Implications

Insects ◽

10.3390/insects12080754 ◽

2021 ◽

Vol 12 (8) ◽

pp. 754

Author(s):

Yupeng Wu ◽

Hui Fang ◽

Jiping Wen ◽

Juping Wang ◽

Tianwen Cao ◽

...

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Mitochondrial Genomes ◽

Comparative Genomic ◽

Trna Genes ◽

Cox1 Gene ◽

Protein Coding ◽

Phylogenetic Implications ◽

Typical Composition

In this study, the complete mitochondrial genomes (mitogenomes) of Hestina persimilis and Hestinalis nama (Nymphalidae: Apaturinae)were acquired. The mitogenomes of H. persimilis and H. nama are 15,252 bp and 15,208 bp in length, respectively. These two mitogenomes have the typical composition, including 37 genes and a control region. The start codons of the protein-coding genes (PCGs) in the two mitogenomes are the typical codon pattern ATN, exceptCGA in the cox1 gene. Twenty-one tRNA genes show a typical clover leaf structure, however, trnS1(AGN) lacks the dihydrouridine (DHU) stem. The secondary structures of rrnL and rrnS of two species were predicted, and there are several new stem loops near the 5’ of rrnL secondary structure. Based on comparative genomic analysis, four similar conservative structures can be found in the control regions of these two mitogenomes. The phylogenetic analyses were performed on mitogenomes of Nymphalidae. The phylogenetic trees show that the relationships among Nymphalidae are generally identical to previous studies, as follows: Libytheinae\Danainae + ((Calinaginae + Satyrinae) + Danainae\Libytheinae + ((Heliconiinae + Limenitidinae) + (Nymphalinae + (Apaturinae + Biblidinae)))). Hestinalisnama isapart fromHestina, andclosely related to Apatura, forming monophyly.

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The complete mitochondrial genome of Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

PeerJ ◽

10.7717/peerj.8762 ◽

2020 ◽

Vol 8 ◽

pp. e8762

Author(s):

Yue Shen ◽

Yu-Zhou Du

Keyword(s):

Mitochondrial Genome ◽

Northern Hemisphere ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Trna Genes ◽

Protein Coding ◽

The Family ◽

Maximum Likelihood Methods ◽

Rna Genes

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

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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.

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