DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes最新文献_第2页

MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.) MIG-seq是小麦(Triticum spp.)高通量基因分型的有效方法。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-04-01 DOI: 10.1093/dnares/dsac011

Kazusa Nishimura, Koichi Motoki, Akira Yamazaki, Rihito Takisawa, Y. Yasui, T. Kawai, K. Ushijima, R. Nakano, T. Nakazaki

{"title":"MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.)","authors":"Kazusa Nishimura, Koichi Motoki, Akira Yamazaki, Rihito Takisawa, Y. Yasui, T. Kawai, K. Ushijima, R. Nakano, T. Nakazaki","doi":"10.1093/dnares/dsac011","DOIUrl":"https://doi.org/10.1093/dnares/dsac011","url":null,"abstract":"Abstract MIG-seq (Multiplexed inter-simple sequence repeats genotyping by sequencing) has been developed as a low cost genotyping technology, although the number of polymorphisms obtained is assumed to be minimal, resulting in the low application of this technique to analyses of agricultural plants. We applied MIG-seq to 12 plant species that include various crops and investigated the relationship between genome size and the number of bases that can be stably sequenced. The genome size and the number of loci, which can be sequenced by MIG-seq, are positively correlated. This is due to the linkage between genome size and the number of simple sequence repeats (SSRs) through the genome. The applicability of MIG-seq to population structure analysis, linkage mapping, and quantitative trait loci (QTL) analysis in wheat, which has a relatively large genome, was further evaluated. The results of population structure analysis for tetraploid wheat showed the differences among collection sites and subspecies, which agreed with previous findings. Additionally, in wheat biparental mapping populations, over 3,000 SNPs/indels with low deficiency were detected using MIG-seq, and the QTL analysis was able to detect recognized flowering-related genes. These results revealed the effectiveness of MIG-seq for genomic analysis of agricultural plants with large genomes, including wheat.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83159232","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: 2

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

The genome of Populus alba x Populus tremula var. glandulosa clone 84K 白杨与白杨(Populus tremula var. glandulosa)克隆84K的基因组

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-10-01 DOI: 10.1093/dnares/dsz020

Deyou Qiu, Shenglong Bai, Jianchao Ma, Lisha Zhang, Fenjuan Shao, Kaikai Zhang, Yanfang Yang, Ting Sun, Jinling Huang, Yun Zhou, D. Galbraith, Zhaoshan Wang, Guiling Sun

{"title":"The genome of Populus alba x Populus tremula var. glandulosa clone 84K","authors":"Deyou Qiu, Shenglong Bai, Jianchao Ma, Lisha Zhang, Fenjuan Shao, Kaikai Zhang, Yanfang Yang, Ting Sun, Jinling Huang, Yun Zhou, D. Galbraith, Zhaoshan Wang, Guiling Sun","doi":"10.1093/dnares/dsz020","DOIUrl":"https://doi.org/10.1093/dnares/dsz020","url":null,"abstract":"Abstract Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"76 1","pages":"423 - 431"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86624216","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: 42

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

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-09-20 DOI: 10.1093/dnares/dsz022

M. Kumagai, Daiki Nishikawa, Y. Kawahara, Hironobu Wakimoto, Ryutaro Itoh, Norio Tabei, Tsuyoshi Tanaka, T. Itoh

{"title":"TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data","authors":"M. Kumagai, Daiki Nishikawa, Y. Kawahara, Hironobu Wakimoto, Ryutaro Itoh, Norio Tabei, Tsuyoshi Tanaka, T. Itoh","doi":"10.1093/dnares/dsz022","DOIUrl":"https://doi.org/10.1093/dnares/dsz022","url":null,"abstract":"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+ (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 collaborators 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":"11 1","pages":"445 - 452"},"PeriodicalIF":0.0,"publicationDate":"2019-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87330330","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: 17

Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato 通过数量性状位点分析和全基因组关联研究，开发甘薯对隐性丝瓜病抗性相关分子标记

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-08-03 DOI: 10.1093/dnares/dsz018

Rumi Sasai, Hiroaki Tabuchi, K. Shirasawa, Kazuki Kishimoto, Shusei Sato, Y. Okada, Akihide Kuramoto, A. Kobâyashi, S. Isobe, M. Tahara, Y. Monden

{"title":"Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato","authors":"Rumi Sasai, Hiroaki Tabuchi, K. Shirasawa, Kazuki Kishimoto, Shusei Sato, Y. Okada, Akihide Kuramoto, A. Kobâyashi, S. Isobe, M. Tahara, Y. Monden","doi":"10.1093/dnares/dsz018","DOIUrl":"https://doi.org/10.1093/dnares/dsz018","url":null,"abstract":"Abstract The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"94 1","pages":"399 - 409"},"PeriodicalIF":0.0,"publicationDate":"2019-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91331078","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

Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes 细菌基因组和宏基因组Illumina测序现有文库制备试剂盒的测序偏倚比较

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-07-31 DOI: 10.1093/dnares/dsz017

Mitsuhiko P. Sato, Yoshitoshi Ogura, Keiji Nakamura, Ruriko Nishida, Yasuhiro Gotoh, Masahiro Hayashi, Junzo Hisatsune, M. Sugai, Itoh Takehiko, Tetsuya Hayashi

{"title":"Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes","authors":"Mitsuhiko P. Sato, Yoshitoshi Ogura, Keiji Nakamura, Ruriko Nishida, Yasuhiro Gotoh, Masahiro Hayashi, Junzo Hisatsune, M. Sugai, Itoh Takehiko, Tetsuya Hayashi","doi":"10.1093/dnares/dsz017","DOIUrl":"https://doi.org/10.1093/dnares/dsz017","url":null,"abstract":"Abstract In bacterial genome and metagenome sequencing, Illumina sequencers are most frequently used due to their high throughput capacity, and multiple library preparation kits have been developed for Illumina platforms. Here, we systematically analysed and compared the sequencing bias generated by currently available library preparation kits for Illumina sequencing. Our analyses revealed that a strong sequencing bias is introduced in low-GC regions by the Nextera XT kit. The level of bias introduced is dependent on the level of GC content; stronger bias is generated as the GC content decreases. Other analysed kits did not introduce this strong sequencing bias. The GC content-associated sequencing bias introduced by Nextera XT was more remarkable in metagenome sequencing of a mock bacterial community and seriously affected estimation of the relative abundance of low-GC species. The results of our analyses highlight the importance of selecting proper library preparation kits according to the purposes and targets of sequencing, particularly in metagenome sequencing, where a wide range of microbial species with various degrees of GC content is present. Our data also indicate that special attention should be paid to which library preparation kit was used when analysing and interpreting publicly available metagenomic data.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"35 1","pages":"391 - 398"},"PeriodicalIF":0.0,"publicationDate":"2019-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82765153","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: 74

Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model 用新的机器学习模型揭示小鼠嗅觉长非编码转录组

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-07-18 DOI: 10.1093/dnares/dsz015

Antonio P. Camargo, T. S. Nakahara, L. E. Firmino, P. H. Netto, João B. P. do Nascimento, Elisa R. Donnard, P. Galante, M. Carazzolle, B. Malnic, F. Papes

{"title":"Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model","authors":"Antonio P. Camargo, T. S. Nakahara, L. E. Firmino, P. H. Netto, João B. P. do Nascimento, Elisa R. Donnard, P. Galante, M. Carazzolle, B. Malnic, F. Papes","doi":"10.1093/dnares/dsz015","DOIUrl":"https://doi.org/10.1093/dnares/dsz015","url":null,"abstract":"Abstract Very little is known about long non-coding RNAs (lncRNAs) in the mammalian olfactory sensory epithelia. Deciphering the non-coding transcriptome in olfaction is relevant because these RNAs have been shown to play a role in chromatin modification and nuclear architecture reorganization, processes that accompany olfactory differentiation and olfactory receptor gene choice, one of the most poorly understood gene regulatory processes in mammals. In this study, we used a combination of in silico and ex vivo approaches to uncover a comprehensive catalogue of olfactory lncRNAs and to investigate their expression in the mouse olfactory organs. Initially, we used a novel machine-learning lncRNA classifier to discover hundreds of annotated and unannotated lncRNAs, some of which were predicted to be preferentially expressed in the main olfactory epithelium and the vomeronasal organ, the most important olfactory structures in the mouse. Moreover, we used whole-tissue and single-cell RNA sequencing data to discover lncRNAs expressed in mature sensory neurons of the main epithelium. Candidate lncRNAs were further validated by in situ hybridization and RT-PCR, leading to the identification of lncRNAs found throughout the olfactory epithelia, as well as others exquisitely expressed in subsets of mature olfactory neurons or progenitor cells.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"33 1","pages":"365 - 378"},"PeriodicalIF":0.0,"publicationDate":"2019-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88287853","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: 7

Phased genome sequence of an interspecific hybrid flowering cherry, ‘Somei-Yoshino’ (Cerasus × yedoensis) 种间杂交开花樱桃‘Somei-Yoshino’(Cerasus × yedoensis)的阶段性基因组序列

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2019-03-12 DOI: 10.1093/dnares/dsz016

K. Shirasawa, T. Esumi, H. Hirakawa, Hideyuki Tanaka, A. Itai, A. Ghelfi, Hideki Nagasaki, S. Isobe

{"title":"Phased genome sequence of an interspecific hybrid flowering cherry, ‘Somei-Yoshino’ (Cerasus × yedoensis)","authors":"K. Shirasawa, T. Esumi, H. Hirakawa, Hideyuki Tanaka, A. Itai, A. Ghelfi, Hideki Nagasaki, S. Isobe","doi":"10.1093/dnares/dsz016","DOIUrl":"https://doi.org/10.1093/dnares/dsz016","url":null,"abstract":"We report the phased genome sequence of an interspecific hybrid, the flowering cherry Somei-Yoshino (Cerasus × yedoensis). The sequence was determined by single-molecule real-time sequencing technology and assembled using a trio-binning strategy in which allelic variation was resolved to obtain phased sequences. The resultant assembly consisting of two haplotype genomes spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between two genome sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherry varieties suggested that Somei-Yoshino is derived from a cross between C. spachiana and either C. speciose or its derivative. Transcriptome data for flowering date revealed comprehensive changes in gene expression in floral bud development toward flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"27 1","pages":"379 - 389"},"PeriodicalIF":0.0,"publicationDate":"2019-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75738736","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: 39