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

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.

Download Full-text

Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects

Scientific Reports ◽

10.1038/s41598-021-82561-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yu Sun ◽

Hua Huang ◽

Yudong Liu ◽

Shanshan Liu ◽

Jun Xia ◽

...

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Mitochondrial Genomes ◽

Base Pairs ◽

Rich Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Lepidopteran Insects

AbstractIn this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.

Download Full-text

The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp., and Dicyema japonicum

10.1101/282285 ◽

2018 ◽

Author(s):

Helen. E. Robertson ◽

Philipp. H. Schiffer ◽

Maximilian. J. Telford

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Complete Mitochondrial Genome ◽

Mitochondrial Protein ◽

Small Subunit ◽

Mitochondrial Genomes ◽

List Type ◽

Protein Coding ◽

Protein Coding Genes ◽

Cell Layers

AbstractThe Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a divergent gene order compared to other metazoans. The data we present from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical across the Metazoa. The cox1 gene from dicyemid species has a series of conserved in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.Key FindingsWe report the first almost-complete mitochondrial genome from an orthonectid parasite, Intoshia linei, including 12 protein-coding genes; 20 tRNAs and putative sequences for large and small subunit rRNAs. We find that the I. linei mitochondrial genome is exceptionally AT-rich and has a novel gene order compared to other published metazoan mitochondrial genomes. These findings are indicative of the rapid rate of evolution that has occurred in the I. linei mitochondrial genome.We also report nine and eight protein-coding genes, respectively, from the dicyemid species Dicyema sp. and Dicyema japonicum, and use the cox1 genes from both species for phylogenetic inference of the internal phylogeny of the dicyemids.We find that the cox1 gene from dicyemids has a series of four conserved in-frame deletions which appear to be unique to this group.

Download Full-text

Complete Mitochondrial Genomes of Three Mangifera Species, Their Genomic Structure And Gene Transfer From Chloroplast Genomes

10.21203/rs.3.rs-1059761/v1 ◽

2021 ◽

Author(s):

Yingfeng Niu ◽

Chengwen Gao ◽

Jin Liu

Keyword(s):

Mitochondrial Genome ◽

Genomic Structure ◽

Mangifera Indica ◽

Gene Content ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes

Abstract BackgroundAmong the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species. Results Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63-69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24-27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7-10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407-6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value. ConclusionsWe sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content of Mangifera mitochondrial genomes is similar across various species. Gene transferred from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

Download Full-text

Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)

PeerJ ◽

10.7717/peerj.6866 ◽

2019 ◽

Vol 7 ◽

pp. e6866 ◽

Cited By ~ 3

Author(s):

Gengyun Niu ◽

Yaoyao Zhang ◽

Zhenyi Li ◽

Meicai Wei

Keyword(s):

Mitochondrial Genome ◽

New Genus ◽

Complete Mitochondrial Genome ◽

Sister Group ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Protein Coding Genes ◽

A New Species ◽

High Support

A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.

Download Full-text

The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum

Parasitology Open ◽

10.1017/pao.2018.12 ◽

2018 ◽

Vol 4 ◽

Cited By ~ 1

Author(s):

Helen E. Robertson ◽

Philipp H. Schiffer ◽

Maximilian J. Telford

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Complete Mitochondrial Genome ◽

Mitochondrial Protein ◽

Mitochondrial Genes ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Protein Coding Genes ◽

Limited Support ◽

Cell Layers

Download Full-text

Mitochondrial genome organization and vertebrate phylogenetics

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000400008 ◽

2000 ◽

Vol 23 (4) ◽

pp. 745-752 ◽

Cited By ~ 57

Author(s):

Sérgio Luiz Pereira

Keyword(s):

Mitochondrial Genome ◽

Genome Organization ◽

Tandem Duplication ◽

Probable Mechanism ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Protein Coding Genes ◽

Use Of Data ◽

New Gene ◽

Conserved Gene

With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.

Download Full-text

Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes): evolutionary relationships and a repetitive element in the Control Region (D-loop)

10.1101/2020.10.26.355867 ◽

2020 ◽

Author(s):

Rubens Pasa ◽

Fabiano Bezerra Menegídio ◽

Igor Henrique Rodrigues-Oliveira ◽

Iuri Batista da Silva ◽

Matheus Lewi Cruz Bonaccorsi de Campos ◽

...

Keyword(s):

Neotropical Region ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Raw Data ◽

Protein Coding ◽

Protein Coding Genes ◽

Species Complexes ◽

D Loop ◽

Complete Mitochondrial Genomes

AbstractWe are presenting the complete mitogenomes of eight fish species/cytotypes from Neotropical region belonging to the Astyanax and Psalidodon genus: A. aeneus, A. altiparanae, P. fasciatus (from two locations - Upper Paraná and São Francisco river basins), A. lacustris, P. rivularis (two cytotypes) and P. rioparanaibano. We perform the whole-genome sequencing for six of these species in a Novaseq 6000 - by Illumina, meanwhile two genomes were assembled from raw data available in databases. Plus, we reassembled and annotated the mitochondrial genomes for A. mexicanus and P. paranae, both already described and with raw data available online. All the genomes presented the same organization, with 13 protein-coding genes, 22 tRNA genes and two rRNA genes. Aiming to contribute to the understanding of the several cryptic species complexes and phylogeny of the genus, we perform Bayesian analysis using the 13 protein-coding genes from these species, plus Deuterodon giton and using a Brycon species as outgroup.

Download Full-text

Mitochondrial Genome Sequence of Phytophthora sansomeana and Comparative Analysis of Phytophthora Mitochondrial Genomes

10.1101/2020.03.23.003319 ◽

2020 ◽

Author(s):

Guohong Cai ◽

Steven R. Scofield

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Proteins ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Phylogenomic Analysis ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Circular Molecule

ABSTRACTPhytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthetase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3’ truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.

Download Full-text

Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

Genes ◽

10.3390/genes10080563 ◽

2019 ◽

Vol 10 (8) ◽

pp. 563 ◽

Cited By ~ 2

Author(s):

Hu Li

Keyword(s):

Mitochondrial Genome ◽

Stop Codon ◽

Complete Mitochondrial Genome ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Future Studies ◽

Protein Coding Genes ◽

Phylogenetic Implications ◽

Paraphyletic Group ◽

Complete Mitochondrial Genomes

In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.

Download Full-text

Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae)

Journal of Insect Science ◽

10.1093/jisesa/ieaa090 ◽

2020 ◽

Vol 20 (5) ◽

Author(s):

Jungmo Lee ◽

Jonghyun Park ◽

Hong Xi ◽

Jongsun Park

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Complete Mitochondrial Genome ◽

Mitochondrial Gene ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Transfer Rnas ◽

Mitochondrial Gene Order ◽

Rna Genes ◽

Simple Sequence

Abstract Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.

Download Full-text