DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes最新文献_第4页

A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits. 具有显著完整性的菠菜基因组组装，及其用于农艺性状候选基因的快速鉴定。

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/dsab004

Hideki Hirakawa, Atsushi Toyoda, Takehiko Itoh, Yutaka Suzuki, Atsushi J Nagano, Suguru Sugiyama, Yasuyuki Onodera

{"title":"A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits.","authors":"Hideki Hirakawa, Atsushi Toyoda, Takehiko Itoh, Yutaka Suzuki, Atsushi J Nagano, Suguru Sugiyama, Yasuyuki Onodera","doi":"10.1093/dnares/dsab004","DOIUrl":"https://doi.org/10.1093/dnares/dsab004","url":null,"abstract":"Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N50 = 11.3 Mb) with a low proportion of undetermined nucleotides (Ns = 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing ∼73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.","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://www.ncbi.nlm.nih.gov/pmc/articles/PMC8231376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39249499","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: 7

Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq. 利用单分子长读测序和RNA-seq分析裸鱼转录组的特征和复杂性。

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/dsab005

Xindan Li, Jinming Wu, Xinping Xiao, Yifeng Rong, Haile Yang, Junyi Li, Qiong Zhou, Weiguo Zhou, Jianquan Shi, Hongfang Qi, Hao Du

{"title":"Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq.","authors":"Xindan Li, Jinming Wu, Xinping Xiao, Yifeng Rong, Haile Yang, Junyi Li, Qiong Zhou, Weiguo Zhou, Jianquan Shi, Hongfang Qi, Hao Du","doi":"10.1093/dnares/dsab005","DOIUrl":"https://doi.org/10.1093/dnares/dsab005","url":null,"abstract":"The Tibetan Schizothoracinae fish Gymnocypris przewalskii has the ability to adapt to the extreme plateau environment, making it an ideal biological material for evolutionary biology research. However, the lack of well-annotated reference genomes has limited the study of the molecular genetics of G. przewalskii. To characterize its transcriptome features, we first used long-read sequencing technology in combination with RNA-seq for transcriptomic analysis. A total of 159,053 full-length (FL) transcripts were captured by Iso-Seq, having a mean length of 3,445 bp with N50 value of 4,348. Of all FL transcripts, 145,169 were well-annotated in the public database and 134,537 contained complete open reading frames. There were 4,149 pairs of alternative splicing events, of which three randomly selected were defined by RT-PCR and sequencing, and 13,293 long non-coding RNAs detected, based on all-vs.-all BLAST. A total of 118,185 perfect simple sequence repeats were identified from FL transcripts. The FL transcriptome might provide basis for further research of G. przewalskii.","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://sci-hub-pdf.com/10.1093/dnares/dsab005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38994006","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: 3

Low-level expression of the Type II restriction-modification system confers potent bacteriophage resistance in Escherichia coli. II型限制性修饰系统的低水平表达赋予大肠杆菌强有力的噬菌体抗性。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2020-02-01 DOI: 10.1093/dnares/dsaa003

Karolina Wilkowska, Iwona Mruk, Beata Furmanek-Blaszk, Marian Sektas

{"title":"Low-level expression of the Type II restriction-modification system confers potent bacteriophage resistance in Escherichia coli.","authors":"Karolina Wilkowska, Iwona Mruk, Beata Furmanek-Blaszk, Marian Sektas","doi":"10.1093/dnares/dsaa003","DOIUrl":"https://doi.org/10.1093/dnares/dsaa003","url":null,"abstract":"Abstract Restriction–modification systems (R–M) are one of the antiviral defense tools used by bacteria, and those of the Type II family are composed of a restriction endonuclease (REase) and a DNA methyltransferase (MTase). Most entering DNA molecules are usually cleaved by the REase before they can be methylated by MTase, although the observed level of fragmented DNA may vary significantly. Using a model EcoRI R–M system, we report that the balance between DNA methylation and cleavage may be severely affected by transcriptional signals coming from outside the R–M operon. By modulating the activity of the promoter, we obtained a broad range of restriction phenotypes for the EcoRI R–M system that differed by up to 4 orders of magnitude in our biological assays. Surprisingly, we found that high expression levels of the R–M proteins were associated with reduced restriction of invading bacteriophage DNA. Our results suggested that the regulatory balance of cleavage and methylation was highly sensitive to fluctuations in transcriptional signals both up- and downstream of the R–M operon. Our data provided further insights into Type II R–M system maintenance and the potential conflict within the host bacterium.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2020-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dsaa003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37734573","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: 6

Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors. 海星从变态发育到高度衍生的五体形体的转录组学分析，重点是神经转录因子。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2020-02-01 DOI: 10.1093/dnares/dsaa007

Maria Byrne, Demian Koop, Dario Strbenac, Paula Cisternas, Regina Balogh, Jean Yee Hwa Yang, Phillip L Davidson, Gregory Wray

{"title":"Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors.","authors":"Maria Byrne, Demian Koop, Dario Strbenac, Paula Cisternas, Regina Balogh, Jean Yee Hwa Yang, Phillip L Davidson, Gregory Wray","doi":"10.1093/dnares/dsaa007","DOIUrl":"https://doi.org/10.1093/dnares/dsaa007","url":null,"abstract":"The Echinodermata is characterized by a secondarily evolved pentameral body plan. While the evolutionary origin of this body plan has been the subject of debate, the molecular mechanisms underlying its development are poorly understood. We assembled a de novo developmental transcriptome from the embryo through metamorphosis in the sea star Parvulastra exigua. We use the asteroid model as it represents the basal-type echinoderm body architecture. Global variation in gene expression distinguished the gastrula profile and showed that metamorphic and juvenile stages were more similar to each other than to the pre-metamorphic stages, pointing to the marked changes that occur during metamorphosis. Differential expression and gene ontology (GO) analyses revealed dynamic changes in gene expression throughout development and the transition to pentamery. Many GO terms enriched during late metamorphosis were related to neurogenesis and signalling. Neural transcription factor genes exhibited clusters with distinct expression patterns. A suite of these genes was up-regulated during metamorphosis (e.g. Pax6, Eya, Hey, NeuroD, FoxD, Mbx, and Otp). In situ hybridization showed expression of neural genes in the CNS and sensory structures. Our results provide a foundation to understand the metamorphic transition in echinoderms and the genes involved in development and evolution of pentamery.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2020-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dsaa007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37876036","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

Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions. 地理上不同萝卜品种全基因组单核苷酸多态性的鉴定。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2020-02-01 DOI: 10.1093/dnares/dsaa001

Hiroto Kobayashi, Kenta Shirasawa, Nobuko Fukino, Hideki Hirakawa, Takashi Akanuma, Hiroyasu Kitashiba

{"title":"Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions.","authors":"Hiroto Kobayashi, Kenta Shirasawa, Nobuko Fukino, Hideki Hirakawa, Takashi Akanuma, Hiroyasu Kitashiba","doi":"10.1093/dnares/dsaa001","DOIUrl":"https://doi.org/10.1093/dnares/dsaa001","url":null,"abstract":"Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2020-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dsaa001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37650177","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

TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data. TASUKE+:一个基于网络的平台，用于探索GWAS结果和大规模重测序数据。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2020-02-01 DOI: 10.1093/dnares/dsaa002

Masahiko Kumagai, Daiki Nishikawa, Yoshihiro Kawahara, Hironobu Wakimoto, Ryutaro Itoh, Norio Tabei, Tsuyoshi Tanaka, Takeshi Itoh

{"title":"TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data.","authors":"Masahiko Kumagai, Daiki Nishikawa, Yoshihiro Kawahara, Hironobu Wakimoto, Ryutaro Itoh, Norio Tabei, Tsuyoshi Tanaka, Takeshi Itoh","doi":"10.1093/dnares/dsaa002","DOIUrl":"https://doi.org/10.1093/dnares/dsaa002","url":null,"abstract":"Recent revolutionary advancements in sequencing technologies have made it possible to obtain mass quantities of genome-scale sequence data in a cost-effective manner and have drastically altered molecular biological studies. To utilize these sequence data, genome-wide association studies (GWASs) have become increasingly important. Hence, there is an urgent need to develop a visualization tool that enables efficient data retrieval, integration of GWAS results with diverse information and rapid public release of such large-scale genotypic and phenotypic data. We developed a web-based genome browser TASUKE þ (https://tasuke.dna.affrc.go.jp/), which is equipped with the following functions: (i) interactive GWAS results visualization with genome resequencing data and annotation information, (ii) PCR primer design, (iii) phylogenetic tree reconstruction and (iv) data sharing via the web. GWAS results can be displayed in parallel with polymorphism data, read depths and annotation information in an interactive and scalable manner. Users can design PCR primers for polymorphic sites of interest. In addition, a molecular phylogenetic tree of any region can be reconstructed so that the overall relationship among the examined genomes can be understood intuitively at a glance. All functions are implemented through user-friendly web-based interfaces so that researchers can easily share data with collab-orators in remote places without extensive bioinformatics knowledge.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2020-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dsaa002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37683585","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: 5

Genome-wide analysis of short interspersed nuclear elements provides insight into gene and genome evolution in citrus. 对柑橘短穿插核元件的全基因组分析为柑橘基因和基因组进化提供了新的思路。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2020-02-01 DOI: 10.1093/dnares/dsaa004

Haijun Meng, Jiancan Feng, Tuanhui Bai, Zaihai Jian, Yanhui Chen, Guoliang Wu

{"title":"Genome-wide analysis of short interspersed nuclear elements provides insight into gene and genome evolution in citrus.","authors":"Haijun Meng, Jiancan Feng, Tuanhui Bai, Zaihai Jian, Yanhui Chen, Guoliang Wu","doi":"10.1093/dnares/dsaa004","DOIUrl":"https://doi.org/10.1093/dnares/dsaa004","url":null,"abstract":"Short interspersed nuclear elements (SINEs) are non-autonomous retrotransposons that are highly abundant, but not well annotated, in plant genomes. In this study, we identified 41,573 copies of SINEs in seven citrus genomes, including 11,275 full-length copies. The citrus SINEs were distributed among 12 families, with an average full-length rate of 0.27, and were dispersed throughout the chromosomes, preferentially in AT-rich areas. Approximately 18.4% of citrus SINEs were found in close proximity (≤1 kb upstream) to genes, indicating a significant enrichment of SINEs in promoter regions. Citrus SINEs promote gene and genome evolution by offering exons as well as splice sites and start and stop codons, creating novel genes and forming tandem and dispersed repeat structures. Comparative analysis of unique homologous SINE-containing loci (HSCLs) revealed chromosome rearrangements in sweet orange, pummelo, and mandarin, suggesting that unique HSCLs might be valuable for understanding chromosomal abnormalities. This study of SINEs provides us with new perspectives and new avenues by which to understand the evolution of citrus genes and genomes.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2020-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dsaa004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37817910","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

Evolution of Aspergillus oryzae before and after domestication inferred by large-scale comparative genomic analysis 大规模比较基因组分析推断米曲霉驯化前后的进化

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-11-22 DOI: 10.1093/dnares/dsz024

N. Watarai, Nozomi Yamamoto, Kazunori Sawada, Takuji Yamada

{"title":"Evolution of Aspergillus oryzae before and after domestication inferred by large-scale comparative genomic analysis","authors":"N. Watarai, Nozomi Yamamoto, Kazunori Sawada, Takuji Yamada","doi":"10.1093/dnares/dsz024","DOIUrl":"https://doi.org/10.1093/dnares/dsz024","url":null,"abstract":"Abstract Aspergillus oryzae is an industrially useful species, of which various strains have been identified; however, their genetic relationships remain unclear. A. oryzae was previously thought to be asexual and unable to undergo crossbreeding. However, recent studies revealed the sexual reproduction of Aspergillus flavus, a species closely related to A. oryzae. To investigate potential sexual reproduction in A. oryzae and evolutionary history among A. oryzae and A. flavus strains, we assembled 82 draft genomes of A. oryzae strains used practically. The phylogenetic tree of concatenated genes confirmed that A. oryzae was monophyletic and nested in one of the clades of A. flavus but formed several clades with different genomic structures. Our results suggest that A. oryzae strains have undergone multiple inter-genomic recombination events between A. oryzae ancestors, although sexual recombination among domesticated species did not appear to have occurred during the domestication process, at least in the past few decades. Through inter- and intra-cladal comparative analysis, we found that evolutionary pressure induced by the domestication of A. oryzae appears to selectively cause non-synonymous and gap mutations in genes involved in fermentation characteristics, as well as intra-genomic rearrangements, with the conservation of industrially useful catalytic enzyme-encoding genes.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"25 1","pages":"465 - 472"},"PeriodicalIF":0.0,"publicationDate":"2019-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74820909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 26

Sequencing of the black rockfish chromosomal genome provides insight into sperm storage in the female ovary 黑岩鱼染色体基因组测序提供了洞察精子储存在女性卵巢

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-11-11 DOI: 10.1093/dnares/dsz023

Qinghua Liu, Xueying Wang, Yongshuang Xiao, Haixia Zhao, Shihong Xu, Yanfeng Wang, Lele Wu, Li Zhou, Tengfei Du, Xuejiao Lv, Jun Li

{"title":"Sequencing of the black rockfish chromosomal genome provides insight into sperm storage in the female ovary","authors":"Qinghua Liu, Xueying Wang, Yongshuang Xiao, Haixia Zhao, Shihong Xu, Yanfeng Wang, Lele Wu, Li Zhou, Tengfei Du, Xuejiao Lv, Jun Li","doi":"10.1093/dnares/dsz023","DOIUrl":"https://doi.org/10.1093/dnares/dsz023","url":null,"abstract":"Abstract Black rockfish (Sebastes schlegelii) is an economically important viviparous marine teleost in Japan, Korea, and China. It is characterized by internal fertilization, long-term sperm storage in the female ovary, and a high abortion rate. For better understanding the mechanism of fertilization and gestation, it is essential to establish a reference genome for viviparous teleosts. Herein, we used a combination of Pacific Biosciences sequel, Illumina sequencing platforms, 10× Genomics, and Hi-C technology to obtain a genome assembly size of 848.31 Mb comprising 24 chromosomes, and contig and scaffold N50 lengths of 2.96 and 35.63 Mb, respectively. We predicted 39.98% repetitive elements, and 26,979 protein-coding genes. S. schlegelii diverged from Gasterosteus aculeatus ∼32.1-56.8 million years ago. Furthermore, sperm remained viable within the ovary for up to 6 months. The glucose transporter SLC2 showed significantly positive genomic selection, and carbohydrate metabolism-related KEGG pathways were significantly up-regulated in ovaries after copulation. In vitro suppression of glycolysis with sodium iodoacetate reduced sperm longevity significantly. The results indicated the importance of carbohydrates in maintaining sperm survivability. Decoding the S. schlegelii genome not only provides new insights into sperm storage; additionally, it is highly valuable for marine researchers and reproduction biologists.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"1 1","pages":"453 - 464"},"PeriodicalIF":0.0,"publicationDate":"2019-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90736234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 16

The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L. 组蛋白修饰H3赖氨酸27三甲基化在油菜三复制基因组中具有保守的基因调控作用。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-10-01 DOI: 10.1093/dnares/dsz021

A. Akter, S. Takahashi, Weiwei Deng, Daniel John Shea, Etsuko Itabashi, Motoki Shimizu, N. Miyaji, K. Osabe, Namiko Nishida, Yutaka Suzuki, C. Helliwell, M. Seki, W. Peacock, E. Dennis, R. Fujimoto

{"title":"The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L.","authors":"A. Akter, S. Takahashi, Weiwei Deng, Daniel John Shea, Etsuko Itabashi, Motoki Shimizu, N. Miyaji, K. Osabe, Namiko Nishida, Yutaka Suzuki, C. Helliwell, M. Seki, W. Peacock, E. Dennis, R. Fujimoto","doi":"10.1093/dnares/dsz021","DOIUrl":"https://doi.org/10.1093/dnares/dsz021","url":null,"abstract":"Abstract Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"40 1","pages":"433 - 443"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77377968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 18