Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Ricania speculum (Walker, 1851) (Hemiptera: Ricaniidae): investigation of intraspecific variations on mitochondrial genome.

ABSTRACT: We have determined a mitochondrial genome of Ricania speculum (Walker, 1851) collected in Jeollabuk-do, Republic of Korea. The circular mitogenome of R. speculum is 15,530 bp long which is shorter than that of the previous mitogenome of R. speculum by 199 bp. It includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs. Intraspecific variation between two mitogenome of R. speculum was investigated: 171 SNPs and 18 INDELs were identified, presenting a high level of intraspecific variations on mitochondrial genome.

SUBMITTER: Lee H

PROVIDER: S-EPMC7682737 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of Ricania speculum (Walker, 1851) (Hemiptera: Ricaniidae): investigation of intraspecific variations on mitochondrial genome.

Lee Hyobin H Park Jonghyun J Xi Hong H Lee Gwan-Seok GS Kim Iksoo I Park Jongsun J Lee Wonhoon W

Mitochondrial DNA. Part B, Resources 20201120 3

We have determined a mitochondrial genome of Ricania speculum (Walker, 1851) collected in Jeollabuk-do, Republic of Korea. The circular mitogenome of R. speculum is 15,530 bp long which is shorter than that of the previous mitogenome of R. speculum by 199 bp. It includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs. Intraspecific variation between two mitogenome of R. speculum was investigated: 171 SNPs and 18 INDELs were identified, presenti ...[more]

PMID: 33367111

Similar Datasets

Sperm ultrastructure of Pochazia shantungensis (Chou & Lu) and Ricania speculum (Walker) (Hemiptera, Ricaniidae) with phylogenetic implications.

Project description:The sperm ultrastructure of two ricaniid species, Pochazia shantungensis (Chou & Lu) and Ricania speculum (Walker), was investigated using light and transmission electron microscopy. Both species have monoflagellate sperm, the shape and ultrastructure of the mature spermatozoon of these two species are similar in morphology, and 128 spermatozoa are organized into sperm bundles with their heads embedded in a homogenous matrix forming the spermatodesmata. The individual sperm is filiform and includes the head, neck and flagellum. The head is needle-like, with a bilayer acrosome and an inferior elongated nucleus which is formed of homogeneously compact and electron-dense chromatin. The neck region is indistinct and is comprised of the centriole and centriole adjunct with a homogeneous dense substance. The long flagellum has the typical 9 + 9 + 2 axoneme microtubule pattern and two symmetrical mitochondrial derivatives with an orderly array of cristae flanking both sides, and a pair of well-developed fishhook-shaped accessory bodies. Current evidence shows that ricaniid species have D-shaped mitochondrial derivatives in cross-section and a serrated electron-dense region. The phylogenetic relationship of Fulgoroidea with other superfamilies in Auchenorrhyncha is briefly discussed.

| S-EPMC6803357 | biostudies-literature

The complete mitochondrial genome of Ricania shantungensis (Hemiptera: Ricaniidae) in Korea.

Project description:In this study, we have sequenced and annotated the complete mitochondrial genome of Ricania shantungensis (Hemiptera: Ricaniidae) for the first time. The circular mitogenome of R. shantungensis was 15,789 bp, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single control region of 1,363 bp. Its AT ratio was 74.6%. According to the phylogenetic tree, R. shantungensis was clustered with the genus Ricania.

| S-EPMC7759257 | biostudies-literature

Complete mitochondrial genome of Ricania shantungensis Chou & Lu, 1977 (Hemiptera: Ricaniidae).

Project description:Ricania shantungensis Chou & Lu, 1977 (Hemiptera: Ricaniidae), is an invasive pest that attacks forest as well as agricultural trees. We sequenced the 15,358 bp long complete mitochondrial genome (mitogenome) of this species; it consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one major non-coding AT-rich region. The orientation and gene order of the R. shantungensis mitogenome are identical to that of the ancestral type found in majority of the insects. Bayesian inference (BI) phylogeny placed the R. shantungensis examined in our study, together with Ricania spp. in a group with the highest nodal support, forming the family Ricaniidae to which R. shantungensis belongs.

| S-EPMC8530477 | biostudies-literature

Determination of an optimum sampling unit of Ricania shantungensis (Hemiptera: Ricaniidae) eggs in persimmons.

Project description:Even though the optimum sampling methods for invasive pests are very important in newly invaded areas, the standard sampling unit of Ricania shantungensis is still undeveloped in persimmons. Among all developmental stages of R. shantungensis, the egg has close relationship between its density and subsequent tree damage. Thus, this study was conducted to suggest an optimum sampling unit for R. shantungensis eggs in persimmons based on characteristics of its within-tree distribution pattern. The within-tree distribution pattern was characterized with 60 persimmon trees by cutting 12 branches at three vertical levels (low, middle, and high) in four horizontal criteria (east, west, south, and north) per tree. The sampling units were determined based on coefficient of variation (CV) and coefficient of determination (r2) calculated from egg mass numbers per 10 cm from the tip within a branch. In numbers of R. shantungensis egg masses, there was no significant difference (P > 0.05) horizontally, but significant (P < 0.05) difference vertically. More R. shantungensis eggs were found on terminal branches of each trunk. The 60 cm from the tip of branches in the terminal positions of each trunk was selected as the optimum sampling unit for R. shantungensis in persimmons because this unit has the lowest CV value and more than 0.9 of r2 value. Even though the optimum sample number per tree should be determined field-specifically, it would be acceptable to sample two or three branches by considering this pests' recognizable damage level. This small sampling unit could make the sampling of R. shantungensis become more economical, precise, and consistent in persimmon fields.

| S-EPMC8906605 | biostudies-literature

Ricania speculum

Project description:Hemipteroid Insect Assembling the Tree of Life Project

| PRJNA357442 | ENA

Ricania speculum

Project description:Ricania speculum overview

| PRJNA492582 | ENA

Describe the morphology and mitochondrial genome of Mecidea indica Dallas, 1851 (Hemiptera, Pentatomidae), with its phylogenetic position.

Project description:We here describe the external morphology and complete mitochondrial genome characteristics of Mecidea indica Dallas, 1851, and clarify the evolutionary rate and divergence time. The M. indica mitochondrial genome length is 15,670 bp, and it exhibits a typical high A+T-skew (76.31%). The sequence shows strong synteny with the original gene arrangement of Drosophila yakuba Burla, 1954 without rearrangement. The M. indica mitochondrial genome characteristics were analyzed, and phylogenetic trees of Pentatomidae were reconstructed using Bayesian methods based on different datasets of the mitochondrial genome datasets. Phylogenetic analysis shows that M. indica belongs to Pentaotominae and form a sister-group with Anaxilaus musgravei Gross, 1976, and Asopinae is highly supported as monophyletic. Molecular clock analysis estimates a divergence time of Pentatomidae of 122.75 Mya (95% HPD: 98.76-145.43 Mya), within the Mesozoic Cretaceous; the divergence time of M. indica and A. musgravii was no later than 50.50 Mya (95% HPD: 37.20-64.80 Mya). In addition, the divergence time of Asopinae was 62.32 Mya (95% HPD: 47.08-78.23 Mya), which was in the Paleogene of the Cenozoic era. This study is of great significance for reconstructing the phylogeny of Pentatomidae and providing insights into its evolutionary history.

| S-EPMC10977800 | biostudies-literature

Damage analysis of Pochazia shantungensis (Hemiptera: Ricaniidae) in persimmons

Project description: Not available

| S-EPMC11020831 | biostudies-literature

Chromosomal-Level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae).

Project description:The true bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae), is a fascinating insect with prolonged diapause and medicinal properties but also a notorious pest. However, because of the lack of genomic resources, an in-depth understanding of its biological characteristics is lacking. Here, we report the first genome assembly of A. chinensis anchored to 10 pseudochromosomes, which was achieved by combining PacBio long reads and Hi-C sequencing data. This chromosome-level genome assembly was 1.55 Gb in size with a scaffold N50 of 156 Mb. The benchmarking universal single-copy ortholog (BUSCO) analysis of the assembly captured 96.6% of the BUSCO genes. A total of 686,888,052 bp of repeat sequences, 18,511 protein-coding genes, and 1,749 noncoding RNAs were annotated. By comparing the A. chinensis genome with that of 8 homologous insects and 2 model organisms, 213 rapidly evolving gene families were identified, including 83 expanded and 130 contracted gene families. The functional enrichment of Gene Ontology and KEGG pathways showed that the significantly expanded gene families were primarily involved in metabolism, immunity, detoxification, and DNA/RNA replication associated with stress responses. The data reported here shed light on the ecological adaptation of A. chinensis and further expanded our understanding of true bug evolution in general.

| S-EPMC8557641 | biostudies-literature

Comparative Analysis of the Complete Mitochondrial Genomes of Five Species of Ricaniidae (Hemiptera: Fulgoromorpha) and Phylogenetic Implications.

Project description:Ricaniidae is a relatively small planthopper family with about 69 genera and 442 species worldwide. Members of this family occur throughout the warm temperate and tropical regions. Some species cause devastating damage to major agricultural and economic plants. However, the relationship between Ricaniidae and other families of Fulgoroidea needs to be further explored. The morphological definitions of the two biggest genera, Pochazia Amyot & Serville, 1843 and Ricania Germar, 1818 (the type genus of Ricaniidae) remain controversial. In this study, mitogenomes of five representatives in these two genera were decoded using the next-generation sequence method and genome assembly. Results showed that their complete mitogenomes are circular DNA molecules with 15,457 to 16,411 bp. All protein-coding genes (PCGs) begin with the start codon ATN, GTG or TTG and end with TAA, TAG, an incomplete stop codon single T or an incomplete stop codon single A. A lost DHU arm was discovered in the trnS gene of the five mitogenomes and the trnV gene within Pochaziaconfusa, Pochazia guttifera and Ricania simulans. The remnant tRNAs folded into clover-leaf structures. The sliding window, genetic distance, and Ka/Ks analyses indicated that the cox1 gene is the slowest evolving and is relatively conserved. The phylogenetic tree topologies support (Delphacidae + (((Issidae + (Lophopidae + Caliscelidae)) + (Flatidae + Ricaniidae)) + (Achilidae + (Dictyopharidae + Fulgoridae)))) as the best topology, as recognized by both PhyloBayes, RAxML and MrBayes based on four data sets (PCG, PCGRNA, PCG12, PCG12RNA). The monophyly of Ricaniidae and the sister group status of two families Flatidae and Ricaniidae are supported, but all analyses failed to support the monophyly of Pochazia and Ricania. The diagnoses between these two genera cannot be resolved until more evidence is acquired.

| S-EPMC8772989 | biostudies-literature