Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The first mitochondrial genome for caddisfly (insecta: Trichoptera) with phylogenetic implications.

ABSTRACT: The Trichoptera (caddisflies) is a holometabolous insect order with 14,300 described species forming the second most species-rich monophyletic group of animals in freshwater. Hitherto, there is no mitochondrial genome reported of this order. Herein, we describe the complete mitochondrial (mt) genome of a caddisfly species, Eubasilissa regina (McLachlan, 1871). A phylogenomic analysis was carried out based on the mt genomic sequences of 13 mt protein coding genes (PCGs) and two rRNA genes of 24 species belonging to eight holometabolous orders. Both maximum likelihood and Bayesian inference analyses highly support the sister relationship between Trichoptera and Lepidoptera.

SUBMITTER: Wang Y

PROVIDER: S-EPMC3879591 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The first mitochondrial genome for caddisfly (insecta: Trichoptera) with phylogenetic implications.

Wang Yuyu Y Liu Xingyue X Yang Ding D

International journal of biological sciences 20131213 1

The Trichoptera (caddisflies) is a holometabolous insect order with 14,300 described species forming the second most species-rich monophyletic group of animals in freshwater. Hitherto, there is no mitochondrial genome reported of this order. Herein, we describe the complete mitochondrial (mt) genome of a caddisfly species, Eubasilissa regina (McLachlan, 1871). A phylogenomic analysis was carried out based on the mt genomic sequences of 13 mt protein coding genes (PCGs) and two rRNA genes of 24 s ...[more]

PMID: 24391451

Similar Datasets

The complete mitochondrial genome of the long-horned caddisfly Triaenodes tardus (Insecta: Trichoptera: Leptoceridae).

Project description:The long-horned caddisfly Triaenodes tardus Milne, 1934 (Leptoceridae), is a widespread herbivorous North American caddisfly found in both lentic and lotic habitats. Whole genome Illumina sequencing allowed the assembly of a complete circular mitogenome of 14,963?bp from T. tardus consisting of 73.4% AT nucleotides, 22 tRNAs, 13 protein-coding genes, two rRNAs and a control region in the ancestral insect gene order. Triaenodes tardus COX1 features an atypical TTG start codon as in some lepdioptera and prokaryotes. Phylogenetic reconstruction places T. tardus as sister to Sericostoma personatum (Sericostomatidae) within a monophyletic Order Trichoptera, which is consistent with previous phylogenetic hypotheses.

| S-EPMC7800763 | biostudies-literature

The complete mitochondrial genome of the giant casemaker caddisfly Phryganea cinerea (Insecta: Trichoptera: Phryganeidae).

Project description:The rush sedge caddisfly Phryganea cinerea Walker, 1852 (Phryganeidae, the giant casemakers), is a widespread and adaptable North American caddisfly. Genome skimming by Illumina sequencing permitted the assembly of a complete 15,043?bp circular mitogenome from P. cinerea consisting of 78.2% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the ancestral insect gene order. Phryganea cinerea COX1 features an atypical CGA start codon and COX1, NAD1, NAD4, and NAD5 exhibit incomplete stop codons completed by the addition of 3' A residues to the mRNA. Phylogenetic reconstruction reveals a monophyletic Order Trichoptera and Family Phyrganeidae.

| S-EPMC7800077 | biostudies-literature

The complete mitochondrial genome of the North American caddisfly Anabolia bimaculata (Insecta: Trichoptera: Limnephilidae).

Project description:The caddisfly Anabolia bimaculata, is a rapidly-maturing caddisfly found in temporary ponds across western North America. Whole genome Illumina sequencing facilitated the assembly of a complete circular mitochondrial genome of 15,048?bp from A. bimaculata consisting of 78.2% AT nucleotides, 22 tRNAs, 13 protein-coding genes, two rRNAs and a control region arranged in the canonical and ancestral gene order found in insects. This gene order is consistent with the gene order found in most other caddisfly species. Maximum likelihood phylogenetic reconstruction places A. bimaculata within a monophyletic Order Trichoptera and sister to the primitive lepidopteran Micropterix calthella (Micropterigidae).

| S-EPMC7799544 | biostudies-literature

The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera).

Project description:Caddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera. They are the most diverse (>16,000 species) of the strictly aquatic insect orders and are widely employed as bio-indicators in water quality assessment and monitoring. Among the numerous adaptations to aquatic habitats, caddisfly larvae use silk and materials from the environment (e.g., stones, sticks, leaf matter) to build composite structures such as fixed retreats and portable cases. Understanding how caddisflies have adapted to aquatic habitats will help explain the evolution and subsequent diversification of the group. We sequenced a retreat-builder caddisfly Stenopsyche tienmushanensis Hwang and assembled a high-quality genome from both Illumina and Pacific Biosciences (PacBio) sequencing. In total, 601.2 M Illumina reads (90.2 Gb) and 16.9 M PacBio subreads (89.0 Gb) were generated. The 451.5 Mb assembled genome has a contig N50 of 1.29 M, has a longest contig of 4.76 Mb, and covers 97.65% of the 1,658 insect single-copy genes as assessed by Benchmarking Universal Single-Copy Orthologs. The genome comprises 36.76% repetitive elements. A total of 14,672 predicted protein-coding genes were identified. The genome revealed gene expansions in specific groups of the cytochrome P450 family and olfactory binding proteins, suggesting potential genomic features associated with pollutant tolerance and mate finding. In addition, the complete gene complex of the highly repetitive H-fibroin, the major protein component of caddisfly larval silk, was assembled. We report the draft genome of Stenopsyche tienmushanensis, the highest-quality caddisfly genome so far. The genome information will be an important resource for the study of caddisflies and may shed light on the evolution of aquatic insects.

| S-EPMC6302954 | biostudies-literature

Complete mitochondrial genome and phylogenetic analysis of the caddisfly Neucentropus mandjuricus (Trichoptera: Polycentropodidae).

Project description:We have sequenced and annotated the complete mitogenome of Neucentropus mandjuricus Martynov, 1907, a monotypic genus of Polycentropodidae with controversial taxonomic status. The complete mitogenome of N. mandjuricus is 15,020 bp in length, including 13 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and a non-coding control region. The maximum-likelihood and Bayesian's inference trees based on 13 protein-coding genes of 23 trichopteran species show that N. mandjuricus clusters together with the other polycentropodid Plectrocnemia sp. with high support value. This study provides a basis for further study on mitogenome and phylogenetics of the Polycentropodidae.

| S-EPMC9754035 | biostudies-literature

Tools for instar determination of European caddisfly larvae (Insecta: Trichoptera).

Project description:The paper explores the adult-forewing-length to larval-head-width relationship as a basis for instar determination of final instar caddisfly larvae on a family level. In addition, reference data from published sources were used to extract series of percentage-head-width increments and factors-of-increase for penultimate to first instars. This material provides estimates for head widths of earlier instars on the family level.

| S-EPMC7116636 | biostudies-literature

Larval cases of caddisfly (Insecta: Trichoptera) affinity in Early Permian marine environments of Gondwana.

Project description:Caddisflies (Trichoptera) are small, cosmopolitan insects closely related to the Lepidoptera (moths and butterflies). Most caddisflies construct protective cases during their larval development. Although the earliest recognisable caddisflies date back to the early Mesozoic (Early and Middle Triassic), being particularly numerous and diverse during the Late Jurassic and Early Cretaceous, the first records of their larval case constructions are known exclusively from much younger, Early to Middle Jurassic non-marine deposits in the northern hemisphere. Here we present fossils from the Early Permian (Asselian-Sakmarian) marine deposits of Brazil which have strong morphological and compositional similarity to larval cases of caddisflies. If they are, which is very probable, these finds not only push back the fossil record of true caddisflies, but also indicate that their larvae constructed cases at the very beginning of their evolution in marine environments. Since modern caddisflies that construct larval cases in marine environments are only known from eastern Australia and New Zealand, we suggest that this marine ecology may have first evolved in western Gondwana during the Early Permian and later spread across southern Pangea.

| S-EPMC4725916 | biostudies-literature

Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera).

Project description:Members of the speciose insect order Trichoptera (caddisflies) provide important ecosystem services, for example, nutrient cycling through breaking down of organic matter. They are also of industrial interest due to their larval silk secretions. These form the basis for their diverse case-making behavior that allows them to exploit a wide range of ecological niches. Only five genomes of this order have been published thus far, with variable qualities regarding contiguity and completeness. A low-cost sequencing strategy, that is, using a single Oxford Nanopore flow cell per individual along with Illumina sequence reads was successfully used to generate high-quality genomes of two Trichoptera species, Plectrocnemia conspersa and Hydropsyche tenuis. Of the de novo assembly methods compared, assembly of low coverage Nanopore reads (∼18×) and subsequent polishing with long reads followed by Illumina short reads (∼80-170× coverage) yielded the highest genome quality both in terms of contiguity and BUSCO completeness. The presented genomes are the shortest to date and extend our knowledge of genome size across caddisfly families. The genomic region that encodes for light (L)-chain fibroin, a protein component of larval caddisfly silk was identified and compared with existing L-fibroin gene clusters. The new genomic resources presented in this paper are among the highest quality Trichoptera genomes and will increase the knowledge of this important insect order by serving as the basis for phylogenomic and comparative genomic studies.

| S-EPMC6916706 | biostudies-literature

First Complete Mitochondrial Genome of Melyridae (Coleoptera, Cleroidea): Genome Description and Phylogenetic Implications.

Project description:To explore the characteristics of the mitogenome of Melyridae and reveal phylogenetic relationships, the mitogenome of Cordylepherus sp. was sequenced and annotated. This is the first time a complete mitochondrial genome has beengenerated in this family. Consistent with previous observations of Cleroidea species, the mitogenome of Cordylepherus sp. is highly conserved in gene size, organization and codon usage, and secondary structures oftRNAs. All protein-coding genes(PCGs) initiate withthe standard start codon ATN,except ND1, which starts with TTG, and terminate with the complete stop codons of TAA and TAG, or incomplete forms, TA- and T-. MosttRNAs have the typical clover-leaf structure, except trnS1 (Ser, AGN), whose dihydrouridine (DHU) armis reduced. In the A+T-rich region, three types of tandem repeat sequence units are found, including a 115 bp sequence tandemly repeated twice, a 16 bp sequence tandemly repeated three timeswith a partial third repeat and a 10 bp sequence tandemly repeated seven times. Phylogenetic analyses based on 13 protein-coding genes by both Bayesian inference (BI) and maximum likelihood (ML) methods suggest that Melyridae sensu lato is polyphyletic, and Dasytinae and Malchiinae are supported as independent families.

| S-EPMC7909412 | biostudies-literature

First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications.

Project description:Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.

| S-EPMC9860506 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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