Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis.

ABSTRACT:

Background

The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences.

Methods

Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups.

Results

The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.

SUBMITTER: Chen D

PROVIDER: S-EPMC6925956 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterisation of the complete mitochondrial genome of Lucanus chengyuani (Coleoptera: Lucanidae).

Project description:We sequenced and assembled the complete mitochondrial genome of Lucanus chengyuani, from the Alishan, Chiayi County, Taiwan. The length of the complete mitogenome of L. chengyuani is 16,926 bp and the mitogenome contains 13 protein-coding, 22 tRNA, and 2 rDNA genes. Nucleotide compositions of the whole mitogenome of L. chengyuani are 38.37% for A, 27.96% for T, 23.03% for C, and 10.637% for G. The AT and GC skewness of mitogenome sequence are 0.157 and -0.368, showing the A-skew and C-skew. The reconstructed phylogenetic relationships of 9 Lucanidae species based on 13 mitochondrial protein-coding genes are highly supported. The clade including Neolucanus maximus and Odontolabis cuvera is sister to the rest of the stag beetle clades, which contains L. chengyuani and L. mazama. Mitogenomic data from this study will provide useful information for further studies for the population genetics, speciation, biogeography, and conservation of L. chengyuani in the future.

| S-EPMC7707321 | biostudies-literature

Distribution and habitat preferences of the stag beetle Lucanus cervus (L.) in forested areas of Poland.

Project description:The incorporation of Lucanus cervus (L.) in Annex 2 of the EU Habitats Directive imposed on EU member countries the obligation to prepare protection plans and undertake adequate measures aimed at the preservation of this species. A necessary precondition for their implementation was connected with the identification of current localities of L. cervus. This paper presents the distribution of L. cervus localities in Poland, identified on the basis of a survey conducted in the areas administered by the State Forests. Habitat preferences for the selection of biotopes by stag beetles were evaluated in terms of forest-site types. This will facilitate effective protection of L. cervus by indicating potential biotopes for this species, particularly in areas with high abundance. The survey showed the presence of L. cervus in 176 localities distributed in 47 forest districts. Most of them were found in three main areas comprising forests in the areas of Zielona Góra, Wrocław and the Świętokrzyskie Mts. They constitute large-scale refuges. In 98% of cases the development of L. cervus was associated with oaks Quercus robur and Quercus petraea. Other host plants included Fagus sylvatica and Acer pseudoplatanus. The age of trees colonised by stag beetles ranged from 70 to 248 years, 134 years on average. Lucanus cervus was most frequently found in deciduous mesic forest sites (41% of localities) and deciduous mixed mesic forest sites (24% of localities). Over 90% of recorded localities are situated in forested areas, understood to include stands, residual trees and stumps, as well as localities at forest edges and along roads in the vicinity of forests.

| S-EPMC6978315 | biostudies-literature

Allometry and Fighting Behaviour of a Dimorphic Stag Beetle Cyclommatus mniszechi (Coleoptera: Lucanidae).

Project description:Male stag beetles (Coleoptera: Lucanidae) use their mandibles as weapons to compete for resources and reproduction. Mandible size in stag beetles can be associated with different behaviours and the outcome of male contests. We investigated the allometric relationship between mandible and body size in males of the stag beetle Cyclommatus mniszechi to uncover distinct morphs. The results divided male C. mniszechi into majors and minors with the switch point of mandible length at 14.01 mm. The allometric slope of mandibles was positive for both morphs but was steeper for the minors. We also characterised the fighting behaviour of the different morphs in size-matched contests using sequential analyses. Males matched each other's behaviour in contests with many physical contacts, no injury and a progression from low towards high aggression and rare de-escalation. Major and minor males employed the same behavioural elements in contests, but major males were more likely to escalate directly into more aggressive phases and minor males tended to stay within phases. This finding suggests that major males may compete more aggressively than minor males in contests.

| S-EPMC7074643 | biostudies-literature

The European Stag Beetle (Lucanus cervus) Monitoring Network: International Citizen Science Cooperation Reveals Regional Differences in Phenology and Temperature Response.

Project description:To address the decline in biodiversity, international cooperation in monitoring of threatened species is needed. Citizen science can play a crucial role in achieving this challenging goal, but most citizen science projects have been established at national or regional scales. Here we report on the establishment and initial findings of the European Stag Beetle Monitoring Network (ESBMN), an international network of stag beetle (Lucanus cervus) monitoring schemes using the same protocol. The network, started in 2016, currently includes 14 countries (see results) but with a strong variation in output regarding the number of transects (148 successful transects in total) and transect walks (1735). We found differences across European regions in the number of stag beetles recorded, related to phenology and temperature, but not for time of transect start. Furthermore, the initial experiences of the ESBMN regarding international cooperation, citizen science approach, and drop-out of volunteers is discussed. An international standardised protocol that allows some local variation is essential for international collaboration and data management, and analysis is best performed at the international level, whereas recruiting, training, and maintaining volunteers is best organised locally. In conclusion, we appeal for more joint international citizen science-based monitoring initiatives assisting international red-listing and conservation actions.

| S-EPMC8466357 | biostudies-literature

Divergence in Gut Bacterial Community Among Life Stages of the Rainbow Stag Beetle Phalacrognathus muelleri (Coleoptera: Lucanidae).

Project description:Although stag beetles are popular saprophytic insects, there are few studies about their gut bacterial community. This study focused on the gut bacterial community structure of the rainbow stag beetle (i.e., Phalacrognathus muelleri) in its larvae (three instars) and adult stages, using high throughput sequencing (Illumina Miseq). Our aim was to compare the gut bacterial community structure among different life stages. The results revealed that bacterial alpha diversity increased from the 1st instar to the 3rd instar larvae. Adults showed the lowest gut bacterial alpha diversity. Bacterial community composition was significantly different between larvae and adults (p = 0.001), and 1st instar larvae (early instar) had significant differences with the 2nd (p= 0.007) and 3rd (p = 0.001) instar larvae (final instar). However, there was little difference in the bacterial community composition between the 2nd and 3rd instar larvae (p = 0.059). Our study demonstrated dramatic shifts in gut bacterial community structure between larvae and adults. Larvae fed on decaying wood and adults fed on beetle jelly, suggesting that diet is a crucial factor shaping the gut bacterial community structure. There were significant differences in bacterial community structure between early instar and final instars larvae, suggesting that certain life stages are associated with a defined gut bacterial community.

| S-EPMC7589407 | biostudies-literature

Characterization of a population of Pelodera strongyloides (Nematoda: Rhabditidae) associated with the beetle Lucanus ibericus (Coleoptera: Lucanidae) from Georgia.

Project description:During a field survey for entomopathogenic nematodes in Georgia, in the territory of Borjomi-Kharagauli, a nematode population was isolated from the body of single dead beetle of Lucanus ibericus Motschulsky 1845 (Coleoptera: Lucanidae). Based on morphological characters and molecular analyses, the nematode species is identical to Pelodera strongyloides (Schneider, 1860, 1866), being the first record of this species in Georgia. Morphometrics of the Georgian population agree with the original description, and females differ from males by very few characters. The Georgian population of P. strongyloides was molecularly characterized by sequencing the D2 to D3 expansion domains of the 28S rRNA gene and two new molecular markers as the ITS and the mitochondrial COI gene. Phylogenetic analyses revealed that all P. strongyloides sequences grouped together along with all other Pelodera species.

| S-EPMC8015381 | biostudies-literature

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

Project description: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.

| S-EPMC7583265 | biostudies-literature

The complete mitochondrial genome of Korean indigenous stag beetle, Dorcus koreanus.

Project description:In this study, the mitogenome sequences of Korean indigenous stag beetle, Dorcus koreanus, was completely determined by next-generation sequencing analysis. The complete mitogenome of D. koreanus has 15,421 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one control region. The gene orders and content were identical with previously recorded mitogenomes of Lucanidae species. Phylogenetic analysis based on mitogenome dataset, consisting PCGs was revealed the taxonomical position in the family Lucanidae.

| S-EPMC7671679 | biostudies-literature

Testing the performance of a fragment of the COI gene to identify western Palaearctic stag beetle species (Coleoptera, Lucanidae).

Project description:The taxonomy of stag beetles (coleopteraLucanidae) remains challenging, mainly due to the sexual dimorphism and the strong allometry in males. Such conjecture confounds taxonomic based conservation efforts that are urgently needed due to numerous threats to stag beetle biodiversity. Molecular tools could help solve the problem of identification of the different recognized taxa in the "Lucanus cervus complex" and in some related Palaearctic species. We investigated the potential use of a 670 bp region at the 3' end of the mitochondrial cytochrome c oxidase subunit I gene (COI) for barcoding purposes (different from the standard COI barcoding region). Well resolved species and subspecies were L. tetraodon, L. cervusakbesianus, L. c. laticornis, as well as the two eastern Asian outgroup taxa L. formosanus and L. hermani. Conversely, certain taxa could not be distinguished from each other based on K2P-distances and tree topologies: L. c. fabiani / L. (P.) barbarossa, L. c. judaicus / an unknown Lucanus species, L. c. cervus / L. c. turcicus / L. c. pentaphyllus / L. (P.) macrophyllus / L. ibericus. The relative roles of phenotypic plasticity, recurrent hybridisation and incomplete lineage sorting underlying taxonomic and phylogenetic discordances are discussed.

| S-EPMC3890674 | biostudies-literature

The first complete mitochondrial genome of the genus Homoderus and insights into phylogeny of Lucanidae (Coleoptera: Lucanidae).

Project description:Homoderus mellyi belongs to the Lucanidae family of Coleoptera. The first complete mitogenome of Homoderus is reported in this paper. The genome is 16,807 bp in length and contains the typical 37 genes with 22 transfer RNA genes, 13 protein coding genes, and 2 ribosomal RNA genes. The gene order is conserved across the lineage. The average base composition of the mitogenome is 36.6% for A, 20.8% for C, 11.6% for G, and 31.1% for T. The percentage of GC is 32.3%. The genome organization, nucleotide composition, and codon usage are similar to other beetles. Phylogenetic analysis shows that Lucanidae is monophyletic, and all subfamilies are monophyletic, respectively. The phylogenetic position of H. mellyi is consistent with other research.

| S-EPMC11299458 | 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