DNA Research最新文献_第8页

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain). 巴利阿里群岛（西班牙）利尔福德壁蜥 Podarcis lilfordi (Günther, 1874) 染色体级基因组组装。

IF 3.9 2区生物学

DNA Research Pub Date : 2023-06-01 DOI: 10.1093/dnares/dsad008

Jessica Gomez-Garrido, Fernando Cruz, Tyler S Alioto, Nathalie Feiner, Tobias Uller, Marta Gut, Ignacio Sanchez Escudero, Giacomo Tavecchia, Andreu Rotger, Katherin Eliana Otalora Acevedo, Laura Baldo

{"title":"Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).","authors":"Jessica Gomez-Garrido, Fernando Cruz, Tyler S Alioto, Nathalie Feiner, Tobias Uller, Marta Gut, Ignacio Sanchez Escudero, Giacomo Tavecchia, Andreu Rotger, Katherin Eliana Otalora Acevedo, Laura Baldo","doi":"10.1093/dnares/dsad008","DOIUrl":"10.1093/dnares/dsad008","url":null,"abstract":"The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 3","pages":""},"PeriodicalIF":3.9,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10214862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9604292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome sequence and salinity adaptation of the desert shrub Nitraria sibirica (Nitrariaceae, Sapindales). 荒漠灌木西伯利亚白刺(Nitraria sibirica)基因组序列与盐度适应。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-05-11 DOI: 10.1093/dnares/dsad011

Xiaohui Ma, Dafu Ru, Diego F Morales-Briones, Fengyuan Mei, Jingjing Wu, Jianquan Liu, Shengdan Wu

{"title":"Genome sequence and salinity adaptation of the desert shrub Nitraria sibirica (Nitrariaceae, Sapindales).","authors":"Xiaohui Ma, Dafu Ru, Diego F Morales-Briones, Fengyuan Mei, Jingjing Wu, Jianquan Liu, Shengdan Wu","doi":"10.1093/dnares/dsad011","DOIUrl":"https://doi.org/10.1093/dnares/dsad011","url":null,"abstract":"The genetic bases of halophytes for salinity tolerance are crucial for genetically breeding salt-tolerant crops. All natural Nitrariaceae species that exclusively occur in arid environments are highly tolerant to salt stress, but the underlying genomic bases to this adaptation remain unknown. Here we present a high-quality, chromosome-level genome sequence of Nitraria sibirica, with an assembled size of 456.66 Mb and 23,365 annotated genes. Phylogenomic analyses confirmed N. sibirica as the sister to all other sampled representatives from other families in Sapindales, and no lineage-specific whole-genome duplication was found except the gamma triplication event. Still, we found that the genes involved in K + retention, energy supply, and Fe absorption expanded greatly in N. sibirica. Deep transcriptome analyses showed that leaf photosynthesis and cuticular wax formation in roots were enhanced under salt treatments. Furthermore, many transcription factors involved in salt tolerance changed their expressions significantly and displayed tissue- and concentration-dependent signaling in response to salt stress. Additionally, we found vacuolar Na + compartmentalization is an ongoing process under salt treatment, while Na + exclusion tends to function at high salt concentrations. These genomic and transcriptomic changes conferred salt tolerance in N. sibirica and pave the way for future breeding of salt-tolerant crops.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2b/78/dsad011.PMC10211498.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9894892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Detection of tandem repeats in the Capsicum annuum genome. 辣椒基因组串联重复序列的检测。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-04-25 DOI: 10.1093/dnares/dsad007

Valentina Rudenko, Eugene Korotkov

{"title":"Detection of tandem repeats in the Capsicum annuum genome.","authors":"Valentina Rudenko, Eugene Korotkov","doi":"10.1093/dnares/dsad007","DOIUrl":"https://doi.org/10.1093/dnares/dsad007","url":null,"abstract":"In this study, we modified the multiple alignment method based on the generation of random position weight matrices (RPWM) and used it to search for tandem repeats (TRs) in the Capsicum annuum genome. The application of the modified (m)RPWM method, which considers the correlation of adjusting nucleotides, resulted in the identification of 908,072 TR regions with repeat lengths from 2 to 200 bp in the C. annuum genome, where they occupied ~29%. The most common TRs were 2 and 3 bp long followed by those of 21, 4, and 15 bp. We performed clustering analysis of TRs with repeat lengths of 2 and 21 bp and created position-weight matrices (PWMs) for each group; these templates could be used to search for TRs of a given length in any nucleotide sequence. All detected TRs can be accessed through publicly available database (http : //victoria.biengi.ac.ru/capsicum_tr/). Comparison of mRPWM with other TR search methods such as Tandem Repeat Finder, T-REKS, and XSTREAM indicated that mRPWM could detect significantly more TRs at similar false discovery rates, indicating its superior performance. The developed mRPWM method can be successfully applied to the identification of highly divergent TRs, which is important for functional analysis of genomes and evolutionary studies.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10211496/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9528783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake). 松茸(Tricholoma matsutake)端粒-端粒基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-04-25 DOI: 10.1093/dnares/dsad006

Hiroyuki Kurokochi, Naoyuki Tajima, Mitsuhiko P Sato, Kazutoshi Yoshitake, Shuichi Asakawa, Sachiko Isobe, Kenta Shirasawa

引用次数: 0

Chromosome-level genome assembly of Phrynocephalus forsythii using third-generation DNA sequencing and Hi-C analysis. 利用第三代DNA测序和Hi-C分析的连翘蕨染色体水平基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-04-01 DOI: 10.1093/dnares/dsad003

Yue Qi, Wei Zhao, Yangyang Zhao, Chenkai Niu, Shuhui Cao, Yingmei Zhang

{"title":"Chromosome-level genome assembly of Phrynocephalus forsythii using third-generation DNA sequencing and Hi-C analysis.","authors":"Yue Qi, Wei Zhao, Yangyang Zhao, Chenkai Niu, Shuhui Cao, Yingmei Zhang","doi":"10.1093/dnares/dsad003","DOIUrl":"https://doi.org/10.1093/dnares/dsad003","url":null,"abstract":"Phrynocephalus forsythii is a viviparous sand lizard that is endemic to the Tarim Basin with a broad altitudinal range of 872-3,100 m. Such variation in altitude and ecological variables can offer an opportunity to uncover genetic mechanisms of ectothermic adaptation to extreme environments at high- and low-altitude. Furthermore, the evolutionary relationship of karyotype with two different chromosome numbers (2n = 46 or 2n = 48) in the Chinese Phrynocephalus is unclear. In this study, a chromosome-level reference genome of P. forsythii was assembled. The genome assembly size was 1.82 Gb with a contig N50 length of 46.22 Mb, 20,194 protein-coding genes were predicted and 95.50% of these genes were annotated in functional public databases. After cluster contigs into chromosome level using Hi-C paired-end reads, we found that two chromosomes of P. forsythii were originated from one ancestral chromosome of species with 46 chromosomes. Comparative genomic analysis revealed that numerous characteristics associated with high- or low-altitude adaptation, including energy metabolism pathways, hypoxic adaptation, and immune, exhibit rapid changes or show signals of positive selection in the P. forsythii genome. This genome provides an excellent genome resource for the study of the karyotype evolution and ecological genomics of Phrynocephalus.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 2","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10113879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9330727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The genome sequence and demographic history of Przewalskia tangutica (Solanaceae), an endangered alpine plant on the Qinghai-Tibet Plateau. 青藏高原濒危高山植物白喉普氏原羚(Przewalskia tangutica)的基因组序列与种群历史

IF 4.1 2区生物学

DNA Research Pub Date : 2023-04-01 DOI: 10.1093/dnares/dsad005

Ying Wu, Jiao Yang, Yongzhi Yang, Jianquan Liu

{"title":"The genome sequence and demographic history of Przewalskia tangutica (Solanaceae), an endangered alpine plant on the Qinghai-Tibet Plateau.","authors":"Ying Wu, Jiao Yang, Yongzhi Yang, Jianquan Liu","doi":"10.1093/dnares/dsad005","DOIUrl":"https://doi.org/10.1093/dnares/dsad005","url":null,"abstract":"To adapt to high-altitude habitats, many alpine plants develop self-compatible breeding systems from outcrossing. The genetic bases for this shift and the resulting demographic consequences remain largely unexplored. Here, we present a high-quality, chromosome-level genome assembly of the monotypic and endangered alpine perennial Przewalskia tangutica (Solanaceae) occurring on the Qinghai-Tibet Plateau (QTP). Our assembled genome is approximately 3 Gb, with a contig N50 size of 17 Mb, and we identified one lineage-specific whole-genome duplication. We found that the gametophytic self-incompatibility (GSI) syntenic locus to the other obligate outcrossing Solanaceae species was broken by the inserted the long terminal repeats, and changes in the flower-specific expression of the homologous genes, and the linked GSI genes in this species. Such changes may have led to its self-compatibility. We identified three deeply diverged lineages in the central distribution of this species, and the gene flow between them was weak but continuous. All three lineages diverged and decreased their population sizes since the largest glaciations occurred in the QTP approximately 720-500 thousand years ago. In addition, we identified one obvious hybrid population between two lineages, suggesting that genetic exchanges between and within lineages still occur. Our results provide insights into evolutionary adaptation through facultative self-pollination and demographic consequences of this alpine rare species in arid habitats.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 2","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10119639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9338183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level genome assembly of the endangered plant Tetraena mongolica. 濒危植物蒙古四叶草染色体水平的基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-04-01 DOI: 10.1093/dnares/dsad004

Bingru Liu, Xiaoyu Zhao, Ziyin Wang, Huili Liu, Xueshuang Huang, Peng Yang

{"title":"Chromosome-level genome assembly of the endangered plant Tetraena mongolica.","authors":"Bingru Liu, Xiaoyu Zhao, Ziyin Wang, Huili Liu, Xueshuang Huang, Peng Yang","doi":"10.1093/dnares/dsad004","DOIUrl":"https://doi.org/10.1093/dnares/dsad004","url":null,"abstract":"Tetraena mongolica is an endangered xerophytic shrub with high ecological value for the restoration of desert vegetation because of its high tolerance to drought and heat stress. Here, we generated a high-quality chromosome-level reference genome of T. mongolica by combining PacBio HiFi data and Hi-C sequencing technologies, which was approximately 1.12 Gb (contig N50 of 25.5 Mb) in size and contained 61,888 protein-coding genes; repetitive sequences comprised 44.8% of the genome. This genome of T. mongolica is the first published genome sequence of a member of the order Zygophyllales. Genome analysis showed that T. mongolica has undergone a recent whole genome duplication event, and a recent burst of long terminal repeat insertions afterward, which may be responsible for its genome size expansion and drought adaptation. We also conducted searches for gene homologues and identified terpene synthase (TPS) gene families and candidate genes involved in triacylglycerol biosynthesis. The T. mongolica genome sequence could aid future studies aimed at functional gene identification, germplasm resource management, molecular breeding efforts, as well as evolutionary studies of Fabids and angiosperm taxa.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 2","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10113878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9329957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau. 青藏高原矮嵩草(Kobresia myosuroides)染色体尺度基因组揭示了青藏高原一个优势草本类群的核型进化和近期多样化。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsac049

Yu Ning, Yang Li, Shu Bin Dong, Hong Guo Yang, Chun Yi Li, Biao Xiong, Jun Yang, Yu Kun Hu, Xian Yun Mu, Xiao Fei Xia

{"title":"The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau.","authors":"Yu Ning, Yang Li, Shu Bin Dong, Hong Guo Yang, Chun Yi Li, Biao Xiong, Jun Yang, Yu Kun Hu, Xian Yun Mu, Xiao Fei Xia","doi":"10.1093/dnares/dsac049","DOIUrl":"https://doi.org/10.1093/dnares/dsac049","url":null,"abstract":"Kobresia species are common in meadows on the Qinghai-Tibet Plateau. They are important food resources for local livestock, and serve a critical foundation for ecosystem integration. Genetic resources of Kobresia species are scarce. Here, we generated a chromosome-level genome assembly for K. myosuroides (Cyperaceae), using PacBio long-reads, Illumina short-reads, and Hi-C technology. The final assembly had a total size of 399.9 Mb with a contig N50 value of 11.9 Mb. The Hi-C result supported a 29 pseudomolecules model which was in consistent with cytological results. A total of 185.5 Mb (44.89% of the genome) transposable elements were detected, and 26,748 protein-coding genes were predicted. Comparative analysis revealed that Kobresia plants have experienced recent diversification events during the late Miocene to Pliocene. Karyotypes analysis indicated that the fission and fusion of chromosomes have been a major driver of speciation, which complied with the lack of whole-genome duplication (WGD) in K. myosuroides genome. Generally, this high-quality reference genome provides insights into the evolution of alpine sedges, and may be helpful to endemic forage improvement and alpine ecosystem preservation.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10537969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes. Lyophyllum shimeji的基因组为外生菌根真菌基因组的初始进化提供了见解。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsac053

Yuuki Kobayashi, Tomoko F Shibata, Hideki Hirakawa, Tomoaki Nishiyama, Akiyoshi Yamada, Mitsuyasu Hasebe, Shuji Shigenobu, Masayoshi Kawaguchi

{"title":"The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes.","authors":"Yuuki Kobayashi, Tomoko F Shibata, Hideki Hirakawa, Tomoaki Nishiyama, Akiyoshi Yamada, Mitsuyasu Hasebe, Shuji Shigenobu, Masayoshi Kawaguchi","doi":"10.1093/dnares/dsac053","DOIUrl":"https://doi.org/10.1093/dnares/dsac053","url":null,"abstract":"Mycorrhizae are one of the most fundamental symbioses between plants and fungi, with ectomycorrhizae being the most widespread in boreal forest ecosystems. Ectomycorrhizal fungi are hypothesized to have evolved convergently from saprotrophic ancestors in several fungal clades, especially members of the subdivision Agaricomycotina. Studies on fungal genomes have identified several typical characteristics of mycorrhizal fungi, such as genome size expansion and decreases in plant cell-wall degrading enzymes (PCWDEs). However, genomic changes concerning the evolutionary transition to the ectomycorrhizal lifestyle are largely unknown. In this study, we sequenced the genome of Lyophyllum shimeji, an ectomycorrhizal fungus that is phylogenetically related to saprotrophic species and retains some saprotroph-like traits. We found that the genome of Ly. shimeji strain AT787 lacks both incremental increases in genome size and reduced numbers of PCWDEs. Our findings suggest that the previously reported common genomic traits of mycorrhizal fungi are not essential for the ectomycorrhizal lifestyle, but are a result of abolishing saprotrophic activity. Since Ly. shimeji is commercially consumed as an edible mushroom, the newly available genomic information may also impact research designed to enhance the cultivation of this mushroom.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/24/22/dsac053.PMC9896470.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10649995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A chromosome-level genome assembly of the Henosepilachna vigintioctomaculata provides insights into the evolution of ladybird beetles. 一个染色体水平的基因组组装的Henosepilachna vigintioctomaculata提供洞察瓢虫甲虫的进化。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsad001

Wenbo Zhu, Shengqi Chi, Yanchun Wang, Haorong Li, Zhongkai Wang, Songdong Gu, Ting Sun, Hui Xiang, Ping You, Yandong Ren

{"title":"A chromosome-level genome assembly of the Henosepilachna vigintioctomaculata provides insights into the evolution of ladybird beetles.","authors":"Wenbo Zhu, Shengqi Chi, Yanchun Wang, Haorong Li, Zhongkai Wang, Songdong Gu, Ting Sun, Hui Xiang, Ping You, Yandong Ren","doi":"10.1093/dnares/dsad001","DOIUrl":"https://doi.org/10.1093/dnares/dsad001","url":null,"abstract":"The ladybird beetle Henosepilachna vigintioctomaculata is an economically significant oligophagous pest that induces damage to many Solanaceae crops. An increasing number of studies have examined the population and phenotype diversity of ladybird beetles. However, few comparative genome analyses of ladybird beetle species have been conducted. Here, we obtained a high-quality chromosome-level genome assembly of H. vigintioctomaculata using various sequencing technologies, and the chromosome-level genome assembly was ~581.63 Mb, with 11 chromosomes successfully assembled. The phylogenetic analysis showed that H. vigintioctomaculata is a more ancient lineage than the other three sequenced ladybird beetles, Harmonia axyridis, Propylea japonica, and Coccinella septempunctata. We also compared positively selected genes (PSGs), transposable elements (TEs) ratios and insertion times, and key gene families associated with environmental adaptation among these ladybird beetles. The pattern of TEs evolution of H. vigintioctomaculata differs from the other three ladybird beetles. The PSGs were associated with ladybird beetles development. However, the key gene families associated with environmental adaptation in ladybird beetles varied. Overall, the high-quality draft genome sequence of H. vigintioctomaculata provides a useful resource for studies of beetle biology, especially for the invasive biology of ladybird beetles.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/4f/4d/dsad001.PMC9936504.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10807136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1