DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes最新文献_第3页

The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. 古近系遗迹树Bretschneidera sinensis的基因组:基因家族进化、人口统计学历史和适应性snp权衡的见解。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-01-28 DOI: 10.1093/dnares/dsac003

Hai-Lin Liu, A J Harris, Zheng-Feng Wang, Hong-Feng Chen, Zhi-An Li, Xiao Wei

{"title":"The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs.","authors":"Hai-Lin Liu, A J Harris, Zheng-Feng Wang, Hong-Feng Chen, Zhi-An Li, Xiao Wei","doi":"10.1093/dnares/dsac003","DOIUrl":"https://doi.org/10.1093/dnares/dsac003","url":null,"abstract":"Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene-Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8825261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39902119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species. 雌雄异株野生芦笋雌雄系染色体单倍型阶段基因组组合。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-01-28 DOI: 10.1093/dnares/dsac002

Kenta Shirasawa, Saki Ueta, Kyoko Murakami, Mostafa Abdelrahman, Akira Kanno, Sachiko Isobe

{"title":"Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species.","authors":"Kenta Shirasawa, Saki Ueta, Kyoko Murakami, Mostafa Abdelrahman, Akira Kanno, Sachiko Isobe","doi":"10.1093/dnares/dsac002","DOIUrl":"https://doi.org/10.1093/dnares/dsac002","url":null,"abstract":"Asparagus kiusianus is a disease-resistant dioecious plant species and a wild relative of garden asparagus (Asparagus officinalis). To enhance A. kiusianus genomic resources, advance plant science, and facilitate asparagus breeding, we determined the genome sequences of the male and female lines of A. kiusianus. Genome sequence reads obtained with a linked-read technology were assembled into four haplotype-phased contig sequences (∼1.6 Gb each) for the male and female lines. The contig sequences were aligned onto the chromosome sequences of garden asparagus to construct pseudomolecule sequences. Approximately 55,000 potential protein-encoding genes were predicted in each genome assembly, and ∼70% of the genome sequence was annotated as repetitive. Comparative analysis of the genomes of the two species revealed structural and sequence variants between the two species as well as between the male and female lines of each species. Genes with high sequence similarity with the male-specific sex determinant gene in A. officinalis, MSE1/AoMYB35/AspTDF1, were presented in the genomes of the male line but absent from the female genome assemblies. Overall, the genome sequence assemblies, gene sequences, and structural and sequence variants determined in this study will reveal the genetic mechanisms underlying sexual differentiation in plants, and will accelerate disease-resistance breeding in garden asparagus.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8826022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39829464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids. 板栗(Castanea crenata Sieb)染色体水平基因组组装。et Zucc.)揭示了木本棒状体中保守的染色体片段。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2021-09-13 DOI: 10.1093/dnares/dsab016

Kenta Shirasawa, Sogo Nishio, Shingo Terakami, Roberto Botta, Daniela Torello Marinoni, Sachiko Isobe

{"title":"Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids.","authors":"Kenta Shirasawa, Sogo Nishio, Shingo Terakami, Roberto Botta, Daniela Torello Marinoni, Sachiko Isobe","doi":"10.1093/dnares/dsab016","DOIUrl":"https://doi.org/10.1093/dnares/dsab016","url":null,"abstract":"Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2021-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/10/97/dsab016.PMC8435554.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39338653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis. 绞股蓝染色体水平的基因组组装为绞股蓝皂苷的生物合成提供了见解。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2021-09-13 DOI: 10.1093/dnares/dsab018

Ding Huang, Ruhong Ming, Shiqiang Xu, Jihua Wang, Shaochang Yao, Liangbo Li, Rongshao Huang, Yong Tan

{"title":"Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis.","authors":"Ding Huang, Ruhong Ming, Shiqiang Xu, Jihua Wang, Shaochang Yao, Liangbo Li, Rongshao Huang, Yong Tan","doi":"10.1093/dnares/dsab018","DOIUrl":"https://doi.org/10.1093/dnares/dsab018","url":null,"abstract":"Gynostemma pentaphyllum (Thunb.) Makino is an economically valuable medicinal plant belonging to the Cucurbitaceae family that produces the bioactive compound gypenoside. Despite several transcriptomes having been generated for G. pentaphyllum, a reference genome is still unavailable, which has limited the understanding of the gypenoside biosynthesis and regulatory mechanism. Here, we report a high-quality G. pentaphyllum genome with a total length of 582 Mb comprising 1,232 contigs and a scaffold N50 of 50.78 Mb. The G. pentaphyllum genome comprised 59.14% repetitive sequences and 25,285 protein-coding genes. Comparative genome analysis revealed that G. pentaphyllum was related to Siraitia grosvenorii, with an estimated divergence time dating to the Paleogene (∼48 million years ago). By combining transcriptome data from seven tissues, we reconstructed the gypenoside biosynthetic pathway and potential regulatory network using tissue-specific gene co-expression network analysis. Four UDP-glucuronosyltransferases (UGTs), belonging to the UGT85 subfamily and forming a gene cluster, were involved in catalyzing glycosylation in leaf-specific gypenoside biosynthesis. Furthermore, candidate biosynthetic genes and transcription factors involved in the gypenoside regulatory network were identified. The genetic information obtained in this study provides insights into gypenoside biosynthesis and lays the foundation for further exploration of the gypenoside regulatory mechanism.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2021-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a7/85/dsab018.PMC8476931.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39400106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Understanding small ORF diversity through a comprehensive transcription feature classification. 通过全面的转录特征分类了解小ORF多样性。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2021-09-13 DOI: 10.1093/dnares/dsab007

Diego Guerra-Almeida, Diogo Antonio Tschoeke, Rodrigo Nunes-da-Fonseca

{"title":"Understanding small ORF diversity through a comprehensive transcription feature classification.","authors":"Diego Guerra-Almeida, Diogo Antonio Tschoeke, Rodrigo Nunes-da-Fonseca","doi":"10.1093/dnares/dsab007","DOIUrl":"https://doi.org/10.1093/dnares/dsab007","url":null,"abstract":"Small open reading frames (small ORFs/sORFs/smORFs) are potentially coding sequences smaller than 100 codons that have historically been considered junk DNA by gene prediction software and in annotation screening; however, the advent of next-generation sequencing has contributed to the deeper investigation of junk DNA regions and their transcription products, resulting in the emergence of smORFs as a new focus of interest in systems biology. Several smORF peptides were recently reported in non-canonical mRNAs as new players in numerous biological contexts; however, their relevance is still overlooked in coding potential analysis. Hence, this review proposes a smORF classification based on transcriptional features, discussing the most promising approaches to investigate smORFs based on their different characteristics. First, smORFs were divided into non-expressed (intergenic) and expressed (genic) smORFs. Second, genic smORFs were classified as smORFs located in non-coding RNAs (ncRNAs) or canonical mRNAs. Finally, smORFs in ncRNAs were further subdivided into sequences located in small or long RNAs, whereas smORFs located in canonical mRNAs were subdivided into several specific classes depending on their localization along the gene. We hope that this review provides new insights into large-scale annotations and reinforces the role of smORFs as essential components of a hidden coding DNA world.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2021-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/18/a6/dsab007.PMC8435553.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39166636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

A high-quality chromosome-level genome of wild Rosa rugosa. 野生蔷薇的高质量染色体水平基因组。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2021-09-13 DOI: 10.1093/dnares/dsab017

Fengqi Zang, Yan Ma, Xiaolong Tu, Ping Huang, Qichao Wu, Zhimin Li, Tao Liu, Furong Lin, Surui Pei, Dekui Zang, Xuemei Zhang, Yongqi Zheng, Yunyan Yu

{"title":"A high-quality chromosome-level genome of wild Rosa rugosa.","authors":"Fengqi Zang, Yan Ma, Xiaolong Tu, Ping Huang, Qichao Wu, Zhimin Li, Tao Liu, Furong Lin, Surui Pei, Dekui Zang, Xuemei Zhang, Yongqi Zheng, Yunyan Yu","doi":"10.1093/dnares/dsab017","DOIUrl":"https://doi.org/10.1093/dnares/dsab017","url":null,"abstract":"Rosa rugosa is an important shrub with economic, ecological, and pharmaceutical value. A high-quality chromosome-scale genome for R. rugosa sequences was assembled using PacBio and Hi-C technologies. The final assembly genome sequences size was about 407.1 Mb, the contig N50 size was 2.85 Mb, and the scaffold N50 size was 56.6 Mb. More than 98% of the assembled genome sequences were anchored to seven pseudochromosomes (402.9 Mb). The genome contained 37,512 protein-coding genes, with 37,016 genes (98.68%) that were functionally annotated, and 206.67 Mb (50.76%) of the assembled sequences are repetitive sequences. Phylogenetic analyses indicated that R. rugosa diverged from Rosa chinensis ∼6.6 million years ago, and no lineage-specific whole-genome duplication event occurred after divergence from R. chinensis. Chromosome synteny analysis demonstrated highly conserved synteny between R. rugosa and R. chinensis, between R. rugosa and Prunus persica as well. Comparative genome and transcriptome analysis revealed genes related to colour, scent, and environment adaptation. The chromosome-level reference genome provides important genomic resources for molecular-assisted breeding and horticultural comparative genomics research.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2021-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8435549/pdf/dsab017.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39397481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate. 整合全基因组关联研究和转录组学数据来预测影响甘蓝型油菜种子植酸的候选基因和有利单倍型。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2021-09-13 DOI: 10.1093/dnares/dsab011

Haijiang Liu, Xiaojuan Li, Qianwen Zhang, Pan Yuan, Lei Liu, Graham J King, Guangda Ding, Sheliang Wang, Hongmei Cai, Chuang Wang, Fangsen Xu, Lei Shi

{"title":"Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate.","authors":"Haijiang Liu, Xiaojuan Li, Qianwen Zhang, Pan Yuan, Lei Liu, Graham J King, Guangda Ding, Sheliang Wang, Hongmei Cai, Chuang Wang, Fangsen Xu, Lei Shi","doi":"10.1093/dnares/dsab011","DOIUrl":"https://doi.org/10.1093/dnares/dsab011","url":null,"abstract":"Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 × 106 single-nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27 kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low-phytate variety (LPA20) was significantly elevated compared with a high-phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favourable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2021-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c4/10/dsab011.PMC8435555.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39412998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Transcriptomes and DNA methylomes in apomictic cells delineate nucellar embryogenesis initiation in citrus. 柑橘无融合细胞的转录组和DNA甲基化组描述了柑桔核胚发生的起始。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2021-09-13 DOI: 10.1093/dnares/dsab014

Hui-Hui Jia, Yuan-Tao Xu, Zhao-Ping Yin, Xiao-Meng Wu, Mei Qing, Yan-Jie Fan, Xin Song, Kai-Dong Xie, Zong-Zhou Xie, Qiang Xu, Xiu-Xin Deng, Wen-Wu Guo

{"title":"Transcriptomes and DNA methylomes in apomictic cells delineate nucellar embryogenesis initiation in citrus.","authors":"Hui-Hui Jia, Yuan-Tao Xu, Zhao-Ping Yin, Xiao-Meng Wu, Mei Qing, Yan-Jie Fan, Xin Song, Kai-Dong Xie, Zong-Zhou Xie, Qiang Xu, Xiu-Xin Deng, Wen-Wu Guo","doi":"10.1093/dnares/dsab014","DOIUrl":"https://doi.org/10.1093/dnares/dsab014","url":null,"abstract":"Citrus nucellar poly-embryony (NPE) is a mode of sporophytic apomixis that asexual embryos formed in the seed through adventitious embryogenesis from the somatic nucellar cells. NPE allows clonal propagation of rootstocks, but it impedes citrus cross breeding. To understand the cellular processes involved in NPE initiation, we profiled the transcriptomes and DNA methylomes in laser microdissection captured citrus apomictic cells. In apomictic cells, ribosome biogenesis and protein degradation were activated, whereas auxin polar transport was repressed. Reactive oxygen species (ROS) accumulated in the poly-embryonic ovules, and response to oxidative stress was provoked. The global DNA methylation level, especially that of CHH context, was decreased, whereas the methylation level of the NPE-controlling key gene CitRWP was increased. A C2H2 domain-containing transcription factor gene and CitRWP co-expressed specifically in apomictic cells may coordinate to initiate NPE. The activated embryogenic development and callose deposition processes indicated embryogenic fate of nucellar embryo initial (NEI) cells. In our working model for citrus NPE initiation, DNA hyper-methylation may activate transcription of CitRWP, which increases C2H2 expression and ROS accumulation, triggers epigenetic regulation and regulates cell fate transition and NEI cell identity in the apomictic cells.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2021-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/dc/50/dsab014.PMC8476932.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39336649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense. 两种杜鹃花的全基因组测序与分析:成熟杜鹃花(Rhododendron ripense)和清水杜鹃花(Rhododendron kiyosumense)。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2021-09-13 DOI: 10.1093/dnares/dsab010

Kenta Shirasawa, Nobuo Kobayashi, Akira Nakatsuka, Hideya Ohta, Sachiko Isobe

{"title":"Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense.","authors":"Kenta Shirasawa, Nobuo Kobayashi, Akira Nakatsuka, Hideya Ohta, Sachiko Isobe","doi":"10.1093/dnares/dsab010","DOIUrl":"https://doi.org/10.1093/dnares/dsab010","url":null,"abstract":"To enhance the genomics and genetics of azalea, the whole-genome sequences of two species of Rhododendron were determined and analysed in this study: Rhododendron ripense, the cytoplasmic donor and ancestral species of large-flowered and evergreen azalea cultivars; and Rhododendron kiyosumense, a native of Chiba prefecture (Japan) seldomly bred and cultivated. A chromosome-level genome sequence assembly of R. ripense was constructed by single-molecule real-time sequencing and genetic mapping, while the genome sequence of R. kiyosumense was assembled using the single-tube long fragment read sequencing technology. The R. ripense genome assembly contained 319 contigs (506.7 Mb; N50 length: 2.5 Mb) and was assigned to the genetic map to establish 13 pseudomolecule sequences. On the other hand, the genome of R. kiyosumense was assembled into 32,308 contigs (601.9 Mb; N50 length: 245.7 kb). A total of 34,606 genes were predicted in the R. ripense genome, while 35,785 flower and 48,041 leaf transcript isoforms were identified in R. kiyosumense through Iso-Seq analysis. Overall, the genome sequence information generated in this study enhances our understanding of genome evolution in the Ericales and reveals the phylogenetic relationship of closely related species. This information will also facilitate the development of phenotypically attractive azalea cultivars.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2021-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8435550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39205681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations. 苏氏念珠菌的基因组分析揭示了其杂交性质和双线粒体基因组构象。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2021-06-25 DOI: 10.1093/dnares/dsab006

Verónica Mixão, Eva Hegedűsová, Ester Saus, Leszek P Pryszcz, Andrea Cillingová, Jozef Nosek, Toni Gabaldón

{"title":"Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations.","authors":"Verónica Mixão, Eva Hegedűsová, Ester Saus, Leszek P Pryszcz, Andrea Cillingová, Jozef Nosek, Toni Gabaldón","doi":"10.1093/dnares/dsab006","DOIUrl":"https://doi.org/10.1093/dnares/dsab006","url":null,"abstract":"Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, C. subhashii was initially described as the causative agent of a case of peritonitis. Considering the relevance of whole-genome sequencing and analysis for our understanding of genome evolution and pathogenicity, we sequenced, assembled and annotated the genome of C. subhashii type strain. Our results show that C. subhashii presents a highly heterozygous genome and other signatures that point to a hybrid ancestry. The presence of functional pathways for assimilation of hydroxyaromatic compounds goes in line with the affiliation of this yeast with soil microbial communities involved in lignin decomposition. Furthermore, we observed that different clones of this strain may present circular or linear mitochondrial DNA. Re-sequencing and comparison of strains with differential mitochondrial genome topology revealed five candidate genes potentially associated with this conformational change: MSK1, SSZ1, ALG5, MRPL9 and OYE32.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2021-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c3/74/dsab006.PMC8311171.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39238079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10