Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Chromosome-level Genome Assembly and Evolution Analysis of Andrena camellia (Hymenoptera: Andrenidae).

ABSTRACT: Andrena camellia, an effective pollinator of the economicallysignificant crop Camellia oleifera, can withstand the toxic pollen of C. oleifera, making A. camellia a crucial for resource conservation and cultivation of C. oleifera. In this study, the whole genome of A. camellia was sequenced on the Oxford Nanopore platform. The assembled genome size was 340.73 Mb including 50 scaffolds (N50=47.435 Mb) and 131 contigs (N50=17.2 Mb). A total of 11, 258 protein-coding genes were annotated, in addition, 1,104 non-coding RNAs were identified. Further analysis that some chromosomes of A. camellia have a high level of synteny with those of Apis mellifera, Osmia bicornis and Andrena minutula. Thus, our reported genome of A. camellia serves as a valuable resource for studying species evolution, behavioral biology, and adaption to toxic pollen of C. oleifera.

SUBMITTER: Zhao K

PROVIDER: S-EPMC10210616 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A Chromosome-level Genome Assembly and Evolution Analysis of Andrena camellia (Hymenoptera: Andrenidae).

Zhao Kaixuan K Luo Arong A Zhou Qingsong Q Wei Wei W Liu Wenping W Zhu Chaodong C Niu Zeqing Z Zhou Zeyang Z Huang Dunyuan D

Genome biology and evolution 20230512

Andrena camellia, an effective pollinator of the economicallysignificant crop Camellia oleifera, can withstand the toxic pollen of C. oleifera, making A. camellia a crucial for resource conservation and cultivation of C. oleifera. In this study, the whole genome of A. camellia was sequenced on the Oxford Nanopore platform. The assembled genome size was 340.73 Mb including 50 scaffolds (N50=47.435 Mb) and 131 contigs (N50=17.2 Mb). A total of 11, 258 protein-coding genes were annotated, in additi ...[more]

PMID: 37170910

Similar Datasets

A chromosome-level genome assembly of Meteorus pulchricornis Wesmael (Hymenoptera: Braconidae).

Project description:Meteorus pulchricornis Wesmael (Hymenoptera: Braconidae) is an important parasitoid of lepidopteran insects. So far, only three scaffold-level genomes have been published for the genus Meteorus. In this study, we present a high-quality, chromosome-level genome assembly of M. pulchricornis, characterized by high accuracy and contiguity. This assembly was achieved using Oxford Nanopore Technologies long-read, MGI-SEQ short-read, and Hi-C sequencing methods. The final assembly was 158.5 Mb in genome size, with 153.8 Mb (97.03%) assigned to ten pseudochromosomes. The scaffold N50 length reached 17.51 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 99.3%. The genome contains 28.29 Mb of repetitive elements, accounting for 18.39% of the total genome size. We identified 12,342 protein-coding genes, of which 12,308 genes were annotated functionally. Our investigation into gene family evolution in M. pulchricornis showed that 563 gene families expanded, 1,739 contracted, and 58 underwent rapid evolution. The high-quality genome assembly we report here is advantageous for further research on parasitoid wasps and provides a foundational data resource for natural enemy studies.

| S-EPMC11751096 | biostudies-literature

Chromosome-level genome assembly of Microplitis manilae Ashmead, 1904 (Hymenoptera: Braconidae).

Project description:Microplitis manilae Ashmead (Hymenoptera: Braconidae) is an important parasitoid of agricultural pests in lepidopteran species. So far, two extant genome assembles from the genus Microplitis are fragmented. Here, we offered a high-quality genome assembly of M. manilae at the chromosome level with high accuracy and contiguity, assembled by ONT long-read, MGI-SEQ short-read, and Hi-C sequencing methods. The final assembled genome size was 282.85 Mb, with 268.17 Mb assigned to 11 pseudochromosomes. The scaffold N50 length was 25.23 Mb, and the complete BUSCO score was 98.61%. The genome contained 152.37 Mb of repetitive elements, representing 53.87% of the total genome size. We predicted 15,689 protein-coding genes, of which 13,580 genes were annotated functionally. Gene family evolution investigations of M. manilae revealed 615 expanded and 635 contracted gene families. The high-quality genome of M. manilae reported in this paper will be a useful genomic resource for research on parasitoid wasps in the future.

| S-EPMC10172384 | biostudies-literature

Rediscovered parasitism of Andrena savignyi Spinola (Hymenoptera, Andrenidae) by Stylops (Strepsiptera, Stylopidae) and revised taxonomic status of the parasite.

Project description:Parasitism of Andrena (Suandrena) savignyi Spinola (Hymenoptera: Andrenidae) by Stylops Kirby (Strepsiptera: Stylopidae) has been recorded only once, and from an individual collected in Egypt almost a century ago, with the parasite described as Stylops savignyi Hofeneder. The recent rediscovery of this Stylops from an individual of Andrena savignyi permits a reinterpretation of the species and its affinities among other Stylops. The bee was collected at flowers of Zilla spinosa (Turra) Prantl. (Brassicaceae) in Amariah, Riyadh, Kingdom of Saudi Arabia. Based on DNA barcode sequences from material sampled across Africa, Asia, and Europe, it is apparent that Stylops savignyi is conspecific with Stylops nassonowi Pierce, and we accordingly synonymize this name (syn. n.), with the latter representing the senior and valid name for the species. A differential diagnosis is provided for Stylops nassonowi and the morphology of the female is described, as well as the first instars.

| S-EPMC4591606 | biostudies-literature

A bee's-eye view of landscape change: differences in diet of 2 Andrena species (Hymenoptera: Andrenidae) between 1943 and 2021.

Project description:Declines in pollinating insects have been linked to changes in land cover, affecting the availability of nesting sites and floral resources. Our study is the first analysis of changes in pollen load composition of 2 mining bees, Andrena barbilabris (Kirby) and Andrena flavipes (Panzer) (Hymenoptera: Andrenidae), at the same sites in central England, over 75 years. This provides a unique opportunity to remove spatial variation and review temporal changes in pollen diet within the context of landscape change. We analyzed modern-day pollen load composition for these species and compared it with historical data from the same sites. We then examined potential links between land-use change and the bees' diets. Both bees showed dietary flexibility and lower diet breadth for A. barbilabris, and the bees' foraging strategies appear to have changed. Andrena flavipes collected more pollen taxa in a single load, while A. barbilabris appeared to source pollen from greater distances. Landscape changes at the studied sites have affected the nutritional environment for these bees. Our findings are supported by an existing assessment of floral resources, which found floral diversity has decreased overall in both the habitats used by these bees. However, more research is needed on the nutritional content of pollens used by these bees, both now and historically, to estimate how pollen diversity has changed. The bee's-eye view underlines the importance of understanding how species respond to local changes so that effective conservation strategies can be developed.

| S-EPMC11441578 | biostudies-literature

Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini).

Project description:Anthidiini, a large bee tribe characterized by light-colored maculations, represents nearly 1,000 pollinator species, but no genomes are yet available for this tribe. Here, we report a chromosome-level genome assembly of Anthidium xuezhongi collected from the Tibetan Plateau. Using PacBio long reads and Hi-C data, we assembled a genome of 189.14 Mb with 99.94% of the assembly located in 16 chromosomes. Our assembly contains 23 scaffolds, with the scaffold N50 length of 12.53 Mb, and BUSCO completeness of 98.70% (n = 1,367). We masked 25.98 Mb (13.74%) of the assembly as repetitive elements, identified 385 noncoding RNAs, and predicted 10,820 protein-coding genes (99.20% BUSCO completeness). Gene family evolution analyses identified 9,251 gene families, of which 31 gene families experienced rapid evolution. Interspecific chromosomal variation among A. xuezhongi, Bombus terrestris, and Apis mellifera showed strong chromosomal syntenic relationships. This high-quality genome assembly is a valuable resource for evolutionary and comparative genomic analyses of bees.

| S-EPMC8850706 | biostudies-literature

Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution.

Project description:BACKGROUND:Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. RESULTS:Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. CONCLUSIONS:We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution.

| S-EPMC6898958 | biostudies-literature

A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae).

Project description:Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae) is a wasp capable of parasitizing a variety of lepidopteran pests at the "egg-larval" stage which distributes throughout Taiwan, Guangdong, Zhejiang, and Hainan provinces of China. This wasp has been successfully used to control pests such as Spodoptera litura Fabricius, 1775, Spodoptera frugiperda (JE Smith, 1797), Spodoptera exigua (Hübner, 1808), and Helicoverpa armigera (Hübner, 1808). So far, there is only one genome assembled from the Chelonus genus [Chelonus insularis (Cresson, 1865)] and it is fragmented with 455 scaffolds. Here, we report a chromosome-level genome assembly of C. formosanus, which was sequenced using PacBio, Illumina, and Hi-C technologies. The long reads were 35.4 Gb (∼150× coverage) with an average length of 15.23 kb. The size of the genome assembly was 139.59 Mb. More than 99.46% of the assembled sequences were anchored to seven pseudochromosomes (138.84 Mb). The Benchmarking University Single-Copy Orthologs (BUSCO) assessment results showed 99.0% of the 1,367 genes (insect_odb10 database) were completely present. We annotated 11,242 protein-coding genes including 98.6% of BUSCO complete genes that were recovered. Nearly one-fourth of the genome assembly (22.25%) was annotated as repetitive sequences and 324 noncoding RNAs were predicted. There were 58 gene families found with significant expansion including allelopathic families (odorant receptors and ionotropic receptors), which may play a crucial role in efficiently locating a wide range of hosts. This high-quality genome assembly and annotation could provide a highly valuable resource of parasitic wasp for the biological control of Lepidoptera pest.

| S-EPMC8808538 | biostudies-literature

The bees of the genus <i>Andrena</i> Fabricius, 1775 (Hymenoptera, Andrenidae) described by Ferdinand Morawitz from the collection of Aleksey Fedtschenko.

Project description:The type specimens of the genus Andrena Fabricius, 1775, described by Ferdinand Morawitz from the collection of Aleksey Fedtschenko deposited in the Zoological Museum of the Moscow State University and in the Zoological Institute, Russian Academy of Sciences, St. Petersburg (Russia), are critically reviewed. Precise information with illustrations of types for 52 taxa is provided; of these 39 species are valid and thirteen are invalid (ten synonyms and three homonyms). Lectotypes are here designated for the following 24 nominal taxa: Andrenaacutilabris Morawitz, 1876, A.aulica Morawitz, 1876, A.bicarinata Morawitz, 1876, A.combusta Morawitz, 1876, A.comparata Morawitz, 1876, A.corallina Morawitz, 1876, A.discophora Morawitz, 1876, A.fedtschenkoi Morawitz, 1876, A.initialis Morawitz, 1876, A.laeviventris Morawitz, 1876, A.leucorhina Morawitz, 1876, A.mucorea Morawitz, 1876, A.nitidicollis Morawitz, 1876, A.oralis Morawitz, 1876, A.planirostris Morawitz, 1876, A.ravicollis Morawitz, 1876, A.rufilabris Morawitz, 1876, A.sarta Morawitz, 1876, A.smaragdina Morawitz, 1876, A.sogdiana Morawitz, 1876, A.subaenescens Morawitz, 1876, A.tuberculiventris Morawitz, 1876, A.turkestanica Morawitz, 1876, and A.virescens Morawitz, 1876.

| S-EPMC9848645 | biostudies-literature

Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution.

Project description:The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Here we report a chromosome-level genome assembly for the mangrove horseshoe crab (Carcinoscorpius rotundicauda) using PacBio reads and Hi-C data. The assembly spans 1.67 Gb with contig N50 of 7.8 Mb and 98% of the genome assigned to 16 chromosomes. The genome contains five Hox clusters with 34 Hox genes, the highest number reported in any invertebrate. Detailed analysis of the genome provides evidence that suggests three rounds of whole-genome duplication (WGD), raising questions about the relationship between WGD and species radiation. Several gene families, particularly those involved in innate immunity, have undergone extensive tandem duplication. These expanded gene families may be important components of the innate immune system of horseshoe crabs, whose amebocyte lysate is a sensitive agent for detecting endotoxin contamination.

| S-EPMC7210998 | biostudies-literature

A chromosome-level genome assembly of the gall maker pest inquiline, Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae).

Project description:Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae) is an inquiline of gall maker Aiolomorphus rhopaloides Walker (Hymenoptera: Eurytomidae). They are of significant economic significance and predominantly inhabit bamboo forest. So far, only four scaffold-level genomes have been published for the family Torymidae. In this study, we present a high-quality genome assembly of D. aiolomorphi at the chromosome level, achieved through the integration of Nanopore (ONT) long-read, Illumina pair-end DNA short-read, and High-through Chromosome Conformation Capture (Hi-C) sequencing methods. The final assembly was 1,084.56 Mb in genome size, with 1,083.41 Mb (99.89%) assigned to five pseudochromosomes. The scaffold N50 length reached 224.87 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 97.3%. The genome contained 762.12 Mb of repetitive elements, accounting for 70.27% of the total genome size. A total of 18,011 protein-coding genes were predicted, with 17,829 genes being functionally annotated. The high-quality genome assembly of D. aiolomorphi presented in this study will serve as a valuable genomic resource for future research on parasitoid wasps. The results of this study may also contribute to the development of biological control strategies for pest management in bamboo forests, enhancing ecological balance and economic sustainability.

| S-EPMC11362566 | 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