Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera).

ABSTRACT: Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on host associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.) in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.

SUBMITTER: Ghanavi HR

PROVIDER: S-EPMC8718532 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Micro-CT imaging in species description: exploring beyond sclerotized structures in lichen moths (Lepidoptera: Erebidae, Arctiinae, Lithosiini).

Project description:X-ray micro-computed tomography imaging (micro-CT) is valuable for systematic research since it permits the non-destructive scanning and imaging of internal structures of very rare species and/or type specimens. Additionally, micro-CT allows to view the morphology and the functional anatomy of structures in their natural anatomical position, without deformations that typically occur using classical dissection protocols. In this study we provide the description of two new species of lichen moths (Lepidoptera: Erebidae, Lithosiini) from the Atlantic Forest in eastern Brazil: Nodozana heliae Moraes sp. nov. from Rio de Janeiro state and Epeiromulona pataxo Moraes & Aguiar sp. nov. from Bahia state. The male and female genitalia as well as the wing morphology were examined by means of non-destructive micro-CT, subsequent 3D model reconstruction, 360 degree spinning animations, 2D images from different angles, and those were compared against classical genitalia dissections from the same specimens. We conclude that techniques complement each other, micro-CT being particularly useful to study wing venation, sclerotized internal structures and muscles, while classical dissection is useful to study membranous structures, particularly in the female genitalia, abdominal skin and specialised scales on the male 8th sternite.

| S-EPMC10351509 | biostudies-literature

Phylogeny and evolution of pharmacophagy in tiger moths (Lepidoptera: Erebidae: Arctiinae).

Project description:The focus of this study was to reconstruct a phylogenetic hypothesis for the moth subfamily Arctiinae (tiger moths, woolly bears) to investigate the evolution of larval and adult pharmacophagy of pyrrolizidine alkaloids (PAs) and the pathway to PA chemical specialization in Arctiinae. Pharmacophagy, collection of chemicals for non-nutritive purposes, is well documented in many species, including the model species Utetheisa ornatrix L. A total of 86 exemplar ingroup species representing tiger moth tribes and subtribes (68 genera) and nine outgroup species were selected. Ingroup species included the most species-rich generic groups to represent the diversity of host-plant associations and pharmacophagous behaviors found throughout Arctiinae. Up to nine genetic markers were sequenced: one mitochondrial (COI barcode region), one nuclear rRNA (D2 region, 28S rRNA), and seven nuclear protein-coding gene fragments: elongation factor 1-α protein, wingless, ribosomal protein subunit S5, carbamoylphosphate synthase domain regions, glyceraldehyde-3-phosphate dehydrogenase, isocitrate dehydrogenase and cytosolic malate dehydrogenase. A total of 6984 bp was obtained for most species. These data were analyzed using model-based phylogenetic methods: maximum likelihood (ML) and Bayesian inference (BI). Ancestral pharmacophagous behaviors and obligate PA associations were reconstructed using the resulting Bayes topology and Reconstructing Ancestral States in Phylogenies (RASP) software. Our results corroborate earlier studies on the evolution of adult pharmacophagous behaviors, suggesting that this behavior arose multiple times and is concentrated in the phaegopterine-euchromiine-ctenuchine clade (PEC). Our results suggest that PA specialization may have arisen early in the phylogeny of the subfamily and that facultative larval pharmacophagous behaviors are the derived condition.

| S-EPMC4103773 | biostudies-literature

Synopsis of fruit-piercing moths of the genus Eudocima (Lepidoptera, Erebidae) from Colombia.

Project description:In order to provide information about the diversity and distribution of Eudocima species in Colombia, 261 specimens deposited in entomological collections were examined and identified. We found seven of the eight species of Eudocima recorded in the Neotropics: E. anguina, E. colubra, E. collusoria, E. memorans and E. serpentifera, all being recorded for the first time from the country. We provide a list of the species, comments on the biology and distribution data, illustrations of the adults, and keys for species identification.

| S-EPMC7398947 | biostudies-literature

Changes in Species Richness and Composition of Tiger Moths (Lepidoptera: Erebidae: Arctiinae) among Three Neotropical Ecoregions.

Project description:Paraná, Yungas and Chaco Serrano ecoregions are among the most species-rich terrestrial habitats at higher latitude. However, the information for tiger moths, one of the most speciose groups of moths, is unknown in these ecoregions. In this study, we assess their species richness and composition in all three of these ecoregions. Also we investigated whether the species composition of tiger moths is influenced by climatic factors and altitude. Tiger moth species were obtained with samples from 71 sites using standardized protocols (21 sites were in Yungas, 19 in Paraná and 31 in Chaco Serrano). Rarefaction-extrapolation curves, non-parametric estimators for incidence and sample coverage indices were performed to assess species richness in the ecoregions studied. Non metric multidimensional scaling and adonis tests were performed to compare the species composition of tiger moths among ecoregions. Permutest analysis and Pearson correlation were used to evaluate the relationship among species composition and annual mean temperature, annual temperature range, annual precipitation, precipitation seasonality and altitude. Among ecoregions Paraná was the richest with 125 species, followed by Yungas with 63 species and Chaco Serrano with 24 species. Species composition differed among these ecoregions, although Yungas and Chaco Serrano were more similar than Paraná. Species composition was significantly influenced by climatic factors and altitude. This study showed that species richness and species composition of tiger moths differed among the three ecoregions assessed. Furthermore, not only climatic factors and altitude influence the species composition of tiger moths among ecoregions, but also climatic seasonality at higher latitude in Neotropical South America becomes an important factor.

| S-EPMC5040457 | biostudies-literature

Complete mitochondrial genome of Eilema ussiricum (Lepidoptera: Erebidae).

Project description:The Eilema ussiricum belongs to Erebidae in Lepidoptera. The complete mitogenome of E. ussiricum was described in this study, which is typically circular duplex molecules and 15,344 bp in length, containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an A + T-rich region. All the inferred tRNA secondary structures show the common cloverleaf pattern, with the exception of tRNA-Ser(AGN) which lacks the DHU arm. Except for cox1 started with CGA, all other PCGs started with the standard ATN codons. All of the PCGs terminated with the stop codon TAA. The phylogenetic tree showed that the species of subfamily Arctiinae include E. ussiricum are clustered into a clade.

| S-EPMC7748757 | biostudies-literature

Molecular Detection and Genetic Diversity of Casuarina Moth, Lymantria xylina (Lepidoptera: Erebidae).

Project description:The casuarina moth, Lymantria xylina Swinhoe (Lepidoptera: Erebidae), is an important pest in the Australian pine tree, Casuarina equisetifolia, forest in the coastal area of South China. At the same time, as a closely related species of Lymantria dispar L. (Lepidoptera: Erebidae), it is also a potential quarantine pest. In the present study, specific primers were designed for identification of L. xylina based on the COI barcoding sequence between L. xylina and four other common forest pests. A 569-bp fragment was successfully amplified from 40 L. xylina from five geographical populations in four Chinese provinces. In addition, even through the analysis came from five highly diverse populations of L. xylina, the genetic distances ranged from 0.001 to 0.031. The neighbor-joining tree showed that the species from Hubei and Chongqing were clustered within a distinct group.

| S-EPMC6007311 | biostudies-literature

Diversity of Akanthomyces on moths (Lepidoptera) in Thailand.

Project description:Akanthomyces is a genus of invertebrate-pathogenic fungi from the family Cordycipitaceae (Ascomycota, Hypocreales). Its species occurs on two different types of hosts, spiders and insects, and in the latter case specifically Lepidoptera adults. Three new species of Akanthomyces, A. noctuidarum, A. pyralidarum, and A. tortricidarum occurring on adult moths from Thailand are proposed based on the differences of their morphological characteristics and molecular data. Phylogenetic analyses using a combined dataset, including the internal transcribed spacer regions, the large subunit of the ribosomal DNA, translation elongation factor 1-α, the largest subunit of RNA polymerase II, and the second largest subunit of RNA polymerase II, support the delimitation of these new species in Akanthomyces.

| S-EPMC7410849 | biostudies-literature

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads.

Project description:Unmapped reads are often discarded from the analysis of whole-genome re-sequencing, but new biological information and insights can be uncovered through their analysis. In this paper, we investigate unmapped reads from the re-sequencing data of 33 pea aphid genomes from individuals specialized on different host plants. The unmapped reads for each individual were retrieved following mapping to the Acyrthosiphon pisum reference genome and its mitochondrial and symbiont genomes. These sets of unmapped reads were then cross-compared, revealing that a significant number of these unmapped sequences were conserved across individuals. Interestingly, sequences were most commonly shared between individuals adapted to the same host plant, suggesting that these sequences may contribute to the divergence between host plant specialized biotypes. Analysis of the contigs obtained from assembling the unmapped reads pooled by biotype allowed us to recover some divergent genomic regions previously excluded from analysis and to discover putative novel sequences of A. pisum and its symbionts. In conclusion, this study emphasizes the interest of the unmapped component of re-sequencing data sets and the potential loss of important information. We here propose strategies to aid the capture and interpretation of this information.

| S-EPMC4815510 | biostudies-literature

Exploring the diversity of Arcobacter butzleri from cattle in the UK using MLST and whole genome sequencing.

Project description:Arcobacter butzleri is considered to be an emerging human foodborne pathogen. The completion of an A. butzleri genome sequence along with microarray analysis of 13 isolates in 2007 revealed a surprising amount of diversity amongst A. butzleri isolates from humans, animals and food. In order to further investigate Arcobacter diversity, 792 faecal samples were collected from cattle on beef and dairy farms in the North West of England. Arcobacter was isolated from 42.5% of the samples and the diversity of the isolates was investigated using multilocus sequence typing. An A. butzleri whole genome sequence, obtained by 454 shotgun sequencing of an isolate from a clinically-healthy dairy cow, showed a number of differences when compared to the genome of a human-derived A. butzleri isolate. PCR-based prevalence assays for variable genes suggested some tentative evidence for source-related distributions. We also found evidence for phenotypic differences relating to growth capabilities between our representative human and cattle isolates. Our genotypic and phenotypic observations suggest that some level of niche adaptation may have occurred in A. butzleri.

| S-EPMC3566208 | biostudies-literature

Exploring the genetic diversity of the Japanese population: Insights from a large-scale whole genome sequencing analysis.

Project description:The Japanese archipelago is a terminal location for human migration, and the contemporary Japanese people represent a unique population whose genomic diversity has been shaped by multiple migrations from Eurasia. We analyzed the genomic characteristics that define the genetic makeup of the modern Japanese population from a population genetics perspective from the genomic data of 9,287 samples obtained by high-coverage whole-genome sequencing (WGS) by the National Center Biobank Network. The dataset comprised populations from the Ryukyu Islands and other parts of the Japanese archipelago (Hondo). The Hondo population underwent two episodes of population decline during the Jomon period, corresponding to the Late Neolithic, and the Edo period, corresponding to the Early Modern era, while the Ryukyu population experienced a population decline during the shell midden period of the Late Neolithic in this region. Haplotype analysis suggested increased allele frequencies for genes related to alcohol and fatty acid metabolism, which were reported as loci that had experienced positive natural selection. Two genes related to alcohol metabolism were found to be 12,500 years out of phase with the time when they began to increase in the allele frequency; this finding indicates that the genomic diversity of Japanese people has been shaped by events closely related to agriculture and food production.

| S-EPMC10703243 | 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