Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Complete Mitochondrial Genome of Lepidotrigona flavibasis (Hymenoptera: Meliponini) and High Gene Rearrangement in Lepidotrigona Mitogenomes.

ABSTRACT: We reported the sequence and characteristics of the complete mitochondrial genome of an ecologically important stingless bee, Lepidotrigona flavibasis (Hymenoptera: Meliponini), that has suffered serious population declines in recent years. A phylogenetic analysis based on complete mitogenomes indicated that L. flavibasis was first clustered with another Lepidotrigona species (L. terminata) and then joined with the other two Melipona (Hymenoptera: Meliponini) stingless bees (M. scutellaris and M. bicolor), forming a single clade of stingless bees. The stingless bee clade has a closer relationship with bumblebees (Bombus) (Hymenoptera: Apidae) than with honeybees (Apis) (Hymenoptera: Apidae). Extremely high gene rearrangements involving tRNAs, rRNAs, D-loop regions, and protein-coding genes were observed in the Lepidotrigona mitogenomes, suggesting an overactive evolutionary status in Lepidotrigona species. These mitogenomic organization variations could provide a good system with which to understand the evolutionary history of Meliponini.

SUBMITTER: Wang CY

PROVIDER: S-EPMC8174572 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications.

Project description:The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable "backbone" of relationships among families.

| S-EPMC8707279 | biostudies-literature

The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world's largest frogs.

Project description:The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr , tRNAPro , tRNAPhe , tRNAVal , tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).

| S-EPMC6709665 | biostudies-literature

Massive gene rearrangement in mitogenomes of phytoseiid mites.

Project description:Mitochondrial (mt) gene sequences have been widely used to infer phylogeny in animals. The relative order of mt genes in the mitogenome can also be a useful marker for evolution, but the propensity of mt gene rearrangements vary tremendously among taxa. Ticks and mites in Acari exemplify this trend as some families retain the ancestral arthropod gene order, while others show highly divergent gene orders. Mites in Phytoseiidae, many of which are effective biological control agents, show some of the most divergent gene orders. However, the diversity of mitogenome order within this family is little known. We thus sequenced three mt genomes of phytoseiid mites from two of the most speciose genera: Amblyseius swirskii (Athias-Henriot), Amblyseius tsugawai (Ehara) and Neoseiulus womersleyi (Schicha). We find differences in mt GC skew and nucleotide composition, especially between N. womersleyi and the two Amblyseius species. Each species within Phytoseiidae (including three previously available sequences) present a unique gene order. Phytoseiid mitogenomes show some of the highest numbers of breakpoints when compared to the ancestral arthropod order (up to 33), as well as high numbers of breakpoints within the family (14-30). This suggests a history of massive, ongoing mitogenome rearrangements in the family. Phylogenetic analyses of mt sequences confirm that the degree of gene rearrangements follows phylogenetic relatedness. We discuss possible causes for the high degree of mt gene rearrangement within phytoseiid mites as well as selection in the mt and nuclear genome tied to the independent evolution of many diverse feeding strategies in the family. Finally, we suggest N. womersleyi should be used instead of the synonym Amblyseius pseudolongispinosus.

| S-EPMC9093193 | biostudies-literature

The complete mitochondrial genome of Engyodontium album and comparative analyses with Ascomycota mitogenomes.

Project description:Engyodontium album is a widespread pathogen that causes different kinds of dermatoses and respiratory tract diseases in humans and animals. In spite of its perniciousness, the basic genetic and molecular background of this species remains poorly understood. In this study, the mitochondrial genome sequence of E. album was determined using a high-throughput sequencing platform. The circular mitogenome was found to be 28,081 nucleotides in length and comprised of 17 protein-coding genes, 24 tRNA genes, and 2 rRNA genes. The nucleotide composition of the genome was A+T-biased (74.13%). Group-II introns were found in the nad1, nad5, and cob genes. The most frequently used codon of protein-coding genes was UAU. Isoleucine was identified as the most common amino acid, while proline was the least common amino acid in protein-coding genes. The gene-arrangement order is nearly the same when compared with other Ascomycota mitogenomes. Phylogenetic relationships based on the shared protein-coding genes revealed that E. album is closely related to the Cordycipitaceae family, with a high-confidence support value (100%). The availability of the mitogenome of E. album will shed light on the molecular systematic and genetic differentiation of this species.

| S-EPMC5738615 | biostudies-literature

Complete mitochondrial genome of Bombus breviceps (Hymenoptera: Apidae).

Project description:The complete mitochondrial genome of Bombus breviceps, which belongs to the subgenus of Alpigenobombus in Bombus genus, was sequenced. This circular mitogenome is 16,743 bp (83.5% AT) in length, with two rRNA genes, 22 tRNA genes, and 13 protein-coding genes. All protein-coding genes are initiated with the common invertebrate initiation codon except TTA for ND2, and terminated by the typical stop codon TAA or TAG. tRNA-Ser (TCT) lacks a dihydrouridine (DHU) arm while other tRNA genes form a cloverleaf structure. Phylogenetic analysis shows that genus Bombus has a closer relationship with genus Melipona than any other genera in Apidae family, and B. breviceps clusters closer to B. lapidarius than any other bumblebees with sequenced mitogenome.

| S-EPMC7800184 | biostudies-literature

Complete mitochondrial genome of Bombus consobrinus (Hymenoptera: Apidae).

Project description:The complete mitochondrial genome of Bombus consobrinus was sequenced. This circular mitogenome is 17,966 bp (86.7% of AT) in length, which contains 22 tRNA genes, 13 protein-coding genes and two rRNA genes. All protein-coding genes are initiated with the typical ATN codon and terminated by TAA codon except an incomplete stop codon T for ND4 gene. tRNA-Ser (AGN) lacks a dihydrouridine (DHU) arm while other tRNA genes form a typical cloverleaf structure. The complete mitochondrial genome of B. consobrinus will be useful to understand the inter-species relationship and genetic diversity of bumblebees.

| S-EPMC7800586 | biostudies-literature

Evolutionary dynamics of the mitochondrial genome in the evaniomorpha (hymenoptera)—a group with an intermediate rate of gene rearrangement.

Project description:We determined the complete mitochondrial (mt) genomes of three evaniomorph species, Ceraphron sp. (Ceraphronoidea), Gasteruption sp. (Evanioidea), and Orthogonalys pulchella (Trigonalyoidea) as well as the nearly complete mt genome from another evaniomorph species, Megalyra sp. (Megalyroidea). Each of them possesses dramatic gene rearrangements, including protein-coding or rRNA genes. Gene inversions were identified in all of these mt genomes; for example, the two rRNA genes have inverted and moved into the nad2-cox1 junction in the Megalyra sp. mt genome. In addition, we found two copies of a 10-bp complementary repeat at the beginning of rrnS and at the end of trnL(2) in the Gasteruption sp. mt genome, consistent with recombination as the possible mechanism for gene inversion and long-range movement. Although each of the genomes contains a number of repeats of varying size, there was no consistent association of the size or number of repeats with the extent or type of gene rearrangement. The breakpoint distance analysis showed the Evaniomorpha has an intermediate rate of gene rearrangement. Sequence-based phylogenetic analyses of 13 protein-coding and 2 rRNA genes in 22 hymenopteran taxa recovered a paraphyletic Evaniomorpha with the Aculeata nested within it. Within the Evaniomorpha, our analyses confirmed the Trigonalyoidea + Megalyroidea as the sister group to the Aculeata and recovered a novel clade, Ceraphronoidea + Evanioidea. In contrast to previous hymenopteran phylogenetic studies, the internal relationships of the Evaniomorpha were highly supported and robust to the variation of alignment approach and phylogenetic inference approach.

| S-EPMC4122943 | biostudies-literature

The complete mitochondrial genome of Trichopria drosophilae (Hymenoptera: Diapriidae).

Project description:Trichopria drosophilae (Hymenoptera: Diapriidae) is an important pupal endoparasitoid of Drosophila species, which has been found to be an ideal biocontrol agent to D. suzukii. In this study, the complete mitochondrial genome of T. drosophilae (GeneBank accession number: MN966974) was sequenced using Illumina HiSeq X Ten system. The mitochondrial genome is 16,375 bp long and comprises 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. Among them, 24 genes are in majority strand, while the others are in minority strand. The nucleotide composition of A, G, C, T is 44.9%, 6.4%, 5.6%, 43.2% respectively. We also performed a phylogenetic analysis with other known mitochondrial genomes within four families that have been shown to parasitize drosophilid species. The result shows that T. drosophilae is closely related to Ismarus sp.

| S-EPMC7782102 | biostudies-literature

The complete mitochondrial genome of Leptopilina syphax (Hymenoptera: Figitidae).

Project description:Leptopilina syphax (Hymenoptera: Figitidae) is a newly recorded species of parasitic wasp, and it attacks the larval stage of Drosophilidae, mainly the Drosophila species. Few works have been done in the basic study of L. syphax, including the data of mitochondrial genome. In this study, the complete mitochondrial genome of L. syphax (GeneBank accession number: MT649407) was sequenced using Illumina HiSeq X Ten system. The mitochondrial genome is 15,882bp long and comprises 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. Meanwhile, 26 genes are in majority strand, and the remaining 11 genes are in minority strand. The overall base composition is 41.7% for A, 6.0% for G, 13.6% for C, and 38.7% for T, with an A + T content of 80.4%, respectively. We also performed a phylogenetic analysis with other known mitochondrial genomes of some parasitic wasps. The results show that L. syphax is closely related to L. boulardi, which is another Drosophila parasitoid.

| S-EPMC7801089 | biostudies-literature

The complete mitochondrial genome of Cerceris bucculata (Hymenoptera: Crabronidae).

Project description:The complete mitochondrial genome of the Cerceris bucculata (A. Costa, 1860) (Hymenoptera: Crabronidae) was obtained via next-generation sequencing. This mitochondrial genome is 16178 bp in length with 37 classical eukaryotic mitochondrial genes and an A + T-rich region. All the 13 PCGs begin with typical ATN codons. Among them, eleven PCG genes terminate with TAA, two with T--. All of the 22 tRNA genes, ranging from 58 to 72 bp with typical cloverleaf structure except for trnS1, whose dihydrouridine (DHU) arm forms a simple loop. Phylogenetic analysis highly supported Crabronidae shown as sister group of anthophila bees.

| S-EPMC8204971 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data