DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes最新文献_第10页

Diet alters both the structure and taxonomy of the ovine gut microbial ecosystem. 饮食改变了羊肠道微生物生态系统的结构和分类。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2014-01-01 Epub Date: 2013-10-29 DOI: 10.1093/dnares/dst044

Melinda J Ellison, Gavin C Conant, Rebecca R Cockrum, Kathy J Austin, Huan Truong, Michela Becchi, William R Lamberson, Kristi M Cammack

{"title":"Diet alters both the structure and taxonomy of the ovine gut microbial ecosystem.","authors":"Melinda J Ellison, Gavin C Conant, Rebecca R Cockrum, Kathy J Austin, Huan Truong, Michela Becchi, William R Lamberson, Kristi M Cammack","doi":"10.1093/dnares/dst044","DOIUrl":"https://doi.org/10.1093/dnares/dst044","url":null,"abstract":"We surveyed the ruminal metagenomes of 16 sheep under two different diets using Illumina pair-end DNA sequencing of raw microbial DNA extracted from rumen samples. The resulting sequence data were bioinformatically mapped to known prokaryotic 16S rDNA sequences to identify the taxa present in the samples and then analysed for the presence of potentially new taxa. Strikingly, the majority of the microbial individuals found did not map to known taxa from 16S sequence databases. We used a novel statistical modelling approach to compare the taxonomic distributions between animals fed a forage-based diet and those fed concentrated grains. With this model, we found significant differences between the two groups both in the dominant taxa present in the rumen and in the overall shape of the taxa abundance curves. In general, forage-fed animals have a more diverse microbial ecosystem, whereas the concentrate-fed animals have ruminal systems more heavily dominated by a few taxa. As expected, organisms from methanogenic groups are more prevalent in forage-fed animals. Finally, all of these differences appear to be grounded in an underlying common input of new microbial individuals into the rumen environment, with common organisms from one feed group being present in the other, but at much lower abundance. ","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"115-25"},"PeriodicalIF":4.1,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dst044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40276834","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: 42

Development and characterization of cDNA resources for the common marmoset: one of the experimental primate models. 普通狨猴cDNA资源的开发与鉴定:一种实验性灵长类动物模型。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2013-06-01 Epub Date: 2013-03-29 DOI: 10.1093/dnares/dst007

Shoji Tatsumoto, Naoki Adati, Yasushi Tohtoki, Yoshiyuki Sakaki, Thorsten Boroviak, Sonoko Habu, Hideyuki Okano, Hiroshi Suemizu, Erika Sasaki, Masanobu Satake

{"title":"Development and characterization of cDNA resources for the common marmoset: one of the experimental primate models.","authors":"Shoji Tatsumoto, Naoki Adati, Yasushi Tohtoki, Yoshiyuki Sakaki, Thorsten Boroviak, Sonoko Habu, Hideyuki Okano, Hiroshi Suemizu, Erika Sasaki, Masanobu Satake","doi":"10.1093/dnares/dst007","DOIUrl":"https://doi.org/10.1093/dnares/dst007","url":null,"abstract":"The common marmoset is a new world monkey, which has become a valuable experimental animal for biomedical research. This study developed cDNA libraries for the common marmoset from five different tissues. A total of 290 426 high-quality EST sequences were obtained, where 251 587 sequences (86.5%) had homology (1E(-100)) with the Refseqs of six different primate species, including human and marmoset. In parallel, 270 673 sequences (93.2%) were aligned to the human genome. When 247 090 sequences were assembled into 17 232 contigs, most of the sequences (218 857 or 15 089 contigs) were located in exonic regions, indicating that these genes are expressed in human and marmoset. The other 5578 sequences (or 808 contigs) mapping to the human genome were not located in exonic regions, suggesting that they are not expressed in human. Furthermore, a different set of 118 potential coding sequences were not similar to any Refseqs in any species, and, thus, may represent unknown genes. The cDNA libraries developed in this study are available through RIKEN Bio Resource Center. A Web server for the marmoset cDNAs is available at http://marmoset.nig.ac.jp/index.html, where each marmoset EST sequence has been annotated by reference to the human genome. These new libraries will be a useful genetic resource to facilitate research in the common marmoset.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"255-62"},"PeriodicalIF":4.1,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dst007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40237026","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: 11

Functions of the Hha and YdgT proteins in transcriptional silencing by the nucleoid proteins, H-NS and StpA, in Escherichia coli. Hha和YdgT蛋白在大肠杆菌类核蛋白H-NS和StpA转录沉默中的作用

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2013-06-01 Epub Date: 2013-03-29 DOI: 10.1093/dnares/dst008

Takeshi Ueda, Hiroki Takahashi, Ebru Uyar, Shu Ishikawa, Naotake Ogasawara, Taku Oshima

{"title":"Functions of the Hha and YdgT proteins in transcriptional silencing by the nucleoid proteins, H-NS and StpA, in Escherichia coli.","authors":"Takeshi Ueda, Hiroki Takahashi, Ebru Uyar, Shu Ishikawa, Naotake Ogasawara, Taku Oshima","doi":"10.1093/dnares/dst008","DOIUrl":"https://doi.org/10.1093/dnares/dst008","url":null,"abstract":"The Hha and YdgT proteins are suggested to modulate the expression of horizontally acquired genes by interacting with H-NS and StpA, which play central roles in the transcriptional silencing of such genes. However, it is also possible that Hha/YdgT repress gene expression independently of H-NS/StpA, as we have not fully understood the molecular mechanism through which Hha/YdgT modulate H-NS/StpA activity. To gain further insight into the basic functions of Hha/YdgT, we analysed the impact of hha/ydgT double inactivation on the transcriptome profile of Escherichia coli K-12, and compared the effects with that of hns/stpA double inactivation. In addition, we examined the effects of hha/ydgT inactivation on the chromosomal binding of H-NS, and conversely the effects of hns/stpA inactivation on the chromosomal binding of Hha. Our results demonstrated that the chromosomal binding of Hha requires H-NS/StpA, and is necessary for the repression of a subset of genes in the H-NS/StpA regulon. Furthermore, the distribution of H-NS binding around Hha/YdgT-dependent and -independent genes suggests that Hha/YdgT proteins modulate formation of the H-NS/StpA-DNA complex.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"263-71"},"PeriodicalIF":4.1,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dst008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40237025","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: 44

ChloroMitoSSRDB: open source repository of perfect and imperfect repeats in organelle genomes for evolutionary genomics. ChloroMitoSSRDB:用于进化基因组学的细胞器基因组完美和不完美重复序列的开源存储库。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2013-04-01 Epub Date: 2013-01-02 DOI: 10.1093/dnares/dss038

Gaurav Sablok, Suresh B Mudunuri, Sujan Patnana, Martina Popova, Mario A Fares, Nicola La Porta

{"title":"ChloroMitoSSRDB: open source repository of perfect and imperfect repeats in organelle genomes for evolutionary genomics.","authors":"Gaurav Sablok, Suresh B Mudunuri, Sujan Patnana, Martina Popova, Mario A Fares, Nicola La Porta","doi":"10.1093/dnares/dss038","DOIUrl":"https://doi.org/10.1093/dnares/dss038","url":null,"abstract":"Microsatellites or simple sequence repeats (SSRs) are repetitive stretches of nucleotides (A, T, G, C) that are distributed either as single base pair stretches or as a combination of two- to six-nucleotides units that are non-randomly distributed within coding and in non-coding regions of the genome. ChloroMitoSSRDB is a complete curated web-oriented relational database of perfect and imperfect repeats in organelle genomes. The present version of the database contains perfect and imperfect SSRs of 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes). We detected a total of 5838 chloroplast perfect SSRs, 37 297 chloroplast imperfect SSRs, 5898 mitochondrial perfect SSRs and 50 355 mitochondrial imperfect SSRs across these genomes. The repeats have been further hyperlinked to the annotated gene regions (coding or non-coding) and a link to the corresponding gene record in National Center for Biotechnology Information(www.ncbi.nlm.nih.gov/) to identify and understand the positional relationship of the repetitive tracts. ChloroMitoSSRDB is connected to a user-friendly web interface that provides useful information associated with the location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, etc. ChloroMitoSSRDB will serve as a repository for developing functional markers for molecular phylogenetics, estimating molecular variation across species. Database URL: ChloroMitoSSRDB can be accessed as an open source repository at www.mcr.org.in/chloromitossrdb.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"127-33"},"PeriodicalIF":4.1,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dss038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40206099","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: 21

Polygenic molecular architecture underlying non-sexual cell aggregation in budding yeast. 芽殖酵母中无性细胞聚集的多基因分子结构。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2013-02-01 Epub Date: 2013-01-02 DOI: 10.1093/dnares/dss033

Jiarui Li, Lin Wang, Xiaoping Wu, Ou Fang, Luwen Wang, Chenqi Lu, Shengjie Yang, Xiaohua Hu, Zewei Luo

{"title":"Polygenic molecular architecture underlying non-sexual cell aggregation in budding yeast.","authors":"Jiarui Li, Lin Wang, Xiaoping Wu, Ou Fang, Luwen Wang, Chenqi Lu, Shengjie Yang, Xiaohua Hu, Zewei Luo","doi":"10.1093/dnares/dss033","DOIUrl":"https://doi.org/10.1093/dnares/dss033","url":null,"abstract":"Cell aggregation in unicellular organisms, induced by either cell non-sexual adhesion to yield flocs and biofilm, or pheromone-driving sexual conjugation is of great significance in cellular stress response, medicine, and brewing industries. Most current literatures have focused on one form of cell aggregation termed flocculation and its major molecular determinants, the flocculation (FLO) family genes. Here, we implemented a map-based approach for dissecting the molecular basis of non-sexual cell aggregation in Saccharomyces cerevisiae. Genome-wide mapping has identified four major quantitative trait loci (QTL) underlying nature variation in the cell aggregation phenotype. High-resolution mapping following up with knockout and allele replacement experiments resolved the QTL into the underlying genes (AMN1, RGA1, FLO1, and FLO8) or even into the causative nucleotide. Genetic variation in the QTL genes can explain up to 46% of phenotypic variation of this trait. Of these genes, AMN1 plays the leading role, differing from the FLO family members, in regulating expression of cell clumping phenotype through inducing cell segregation defect. These findings provide novel insights into the molecular mechanism of how cell aggregation is regulated in budding yeast, and the data will be directly implicated to understand the molecular basis and evolutionary implications of cell aggregation in other fungus species.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"55-66"},"PeriodicalIF":4.1,"publicationDate":"2013-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dss033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40206098","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: 25

De novo assembly and functional annotation of the olive (Olea europaea) transcriptome. 橄榄转录组的从头组装和功能注释。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2013-02-01 Epub Date: 2013-01-07 DOI: 10.1093/dnares/dss036

Antonio Muñoz-Mérida, Juan José González-Plaza, Andrés Cañada, Ana María Blanco, Maria del Carmen García-López, José Manuel Rodríguez, Laia Pedrola, M Dolores Sicardo, M Luisa Hernández, Raúl De la Rosa, Angjelina Belaj, Mayte Gil-Borja, Francisco Luque, José Manuel Martínez-Rivas, David G Pisano, Oswaldo Trelles, Victoriano Valpuesta, Carmen R Beuzón

{"title":"De novo assembly and functional annotation of the olive (Olea europaea) transcriptome.","authors":"Antonio Muñoz-Mérida, Juan José González-Plaza, Andrés Cañada, Ana María Blanco, Maria del Carmen García-López, José Manuel Rodríguez, Laia Pedrola, M Dolores Sicardo, M Luisa Hernández, Raúl De la Rosa, Angjelina Belaj, Mayte Gil-Borja, Francisco Luque, José Manuel Martínez-Rivas, David G Pisano, Oswaldo Trelles, Victoriano Valpuesta, Carmen R Beuzón","doi":"10.1093/dnares/dss036","DOIUrl":"https://doi.org/10.1093/dnares/dss036","url":null,"abstract":"Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"93-108"},"PeriodicalIF":4.1,"publicationDate":"2013-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dss036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40218393","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: 82

Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species. 米曲霉(Aspergillus oryzae)菌株间的基因组比较分析揭示了突变定位位点与高度分化基因区域之间的密切关系。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2012-10-01 Epub Date: 2012-08-21 DOI: 10.1093/dnares/dss019

Myco Umemura, Hideaki Koike, Noriko Yamane, Yoshinori Koyama, Yuki Satou, Ikuya Kikuzato, Morimi Teruya, Masatoshi Tsukahara, Yumi Imada, Youji Wachi, Yukino Miwa, Shuichi Yano, Koichi Tamano, Yutaka Kawarabayasi, Kazuhiro E Fujimori, Masayuki Machida, Takashi Hirano

{"title":"Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species.","authors":"Myco Umemura, Hideaki Koike, Noriko Yamane, Yoshinori Koyama, Yuki Satou, Ikuya Kikuzato, Morimi Teruya, Masatoshi Tsukahara, Yumi Imada, Youji Wachi, Yukino Miwa, Shuichi Yano, Koichi Tamano, Yutaka Kawarabayasi, Kazuhiro E Fujimori, Masayuki Machida, Takashi Hirano","doi":"10.1093/dnares/dss019","DOIUrl":"https://doi.org/10.1093/dnares/dss019","url":null,"abstract":"Aspergillus oryzae has been utilized for over 1000 years in Japan for the production of various traditional foods, and a large number of A. oryzae strains have been isolated and/or selected for the effective fermentation of food ingredients. Characteristics of genetic alterations among the strains used are of particular interest in studies of A. oryzae. Here, we have sequenced the whole genome of an industrial fungal isolate, A. oryzae RIB326, by using a next-generation sequencing system and compared the data with those of A. oryzae RIB40, a wild-type strain sequenced in 2005. The aim of this study was to evaluate the mutation pressure on the non-syntenic blocks (NSBs) of the genome, which were previously identified through comparative genomic analysis of A. oryzae, Aspergillus fumigatus, and Aspergillus nidulans. We found that genes within the NSBs of RIB326 accumulate mutations more frequently than those within the SBs, regardless of their distance from the telomeres or of their expression level. Our findings suggest that the high mutation frequency of NSBs might contribute to maintaining the diversity of the A. oryzae genome.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"375-82"},"PeriodicalIF":4.1,"publicationDate":"2012-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dss019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30850440","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: 21

Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus. 聚磷微月状放线菌基因组的破译。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2012-10-01 Epub Date: 2012-08-23 DOI: 10.1093/dnares/dss020

Akatsuki Kawakoshi, Hidekazu Nakazawa, Junji Fukada, Machi Sasagawa, Yoko Katano, Sanae Nakamura, Akira Hosoyama, Hiroki Sasaki, Natsuko Ichikawa, Satoshi Hanada, Yoichi Kamagata, Kazunori Nakamura, Shuji Yamazaki, Nobuyuki Fujita

{"title":"Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus.","authors":"Akatsuki Kawakoshi, Hidekazu Nakazawa, Junji Fukada, Machi Sasagawa, Yoko Katano, Sanae Nakamura, Akira Hosoyama, Hiroki Sasaki, Natsuko Ichikawa, Satoshi Hanada, Yoichi Kamagata, Kazunori Nakamura, Shuji Yamazaki, Nobuyuki Fujita","doi":"10.1093/dnares/dss020","DOIUrl":"https://doi.org/10.1093/dnares/dss020","url":null,"abstract":"Polyphosphate accumulating organisms (PAOs) belong mostly to Proteobacteria and Actinobacteria and are quite divergent. Under aerobic conditions, they accumulate intracellular polyphosphate (polyP), while they typically synthesize polyhydroxyalkanoates (PHAs) under anaerobic conditions. Many ecological, physiological, and genomic analyses have been performed with proteobacterial PAOs, but few with actinobacterial PAOs. In this study, the whole genome sequence of an actinobacterial PAO, Microlunatus phosphovorus NM-1(T) (NBRC 101784(T)), was determined. The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits). In contrast, it harbours only a single ppx gene for exopolyphosphatase, although two copies of ppx are generally present in other actinobacteria. Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H(+) symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs. Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"383-94"},"PeriodicalIF":4.1,"publicationDate":"2012-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dss020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30859687","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: 42

High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). 鹰嘴豆(Cicer arietinum L.)饱和连锁图谱的高通量SNP发现及基因分型

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2012-10-01 Epub Date: 2012-08-03 DOI: 10.1093/dnares/dss018

Rashmi Gaur, Sarwar Azam, Ganga Jeena, Aamir Waseem Khan, Shalu Choudhary, Mukesh Jain, Gitanjali Yadav, Akhilesh K Tyagi, Debasis Chattopadhyay, Sabhyata Bhatia

{"title":"High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.).","authors":"Rashmi Gaur, Sarwar Azam, Ganga Jeena, Aamir Waseem Khan, Shalu Choudhary, Mukesh Jain, Gitanjali Yadav, Akhilesh K Tyagi, Debasis Chattopadhyay, Sabhyata Bhatia","doi":"10.1093/dnares/dss018","DOIUrl":"https://doi.org/10.1093/dnares/dss018","url":null,"abstract":"The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"357-73"},"PeriodicalIF":4.1,"publicationDate":"2012-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dss018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30812020","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: 129

Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, Florida endemic plant. 美国佛罗里达州一种高度濒危的特有种植物——紫豆科植物(Ziziphus celata) 454个花转录组序列的组装、基因注释和标记开发

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2012-01-01 Epub Date: 2011-10-27 DOI: 10.1093/dnares/dsr037

Christine E Edwards, Thomas L Parchman, Carl W Weekley

{"title":"Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, Florida endemic plant.","authors":"Christine E Edwards, Thomas L Parchman, Carl W Weekley","doi":"10.1093/dnares/dsr037","DOIUrl":"https://doi.org/10.1093/dnares/dsr037","url":null,"abstract":"Large-scale DNA sequence data may enable development of genetic resources in endangered species, thereby facilitating conservation efforts. Ziziphus celata, a federally endangered, self-incompatible plant species occurring in Florida, USA, is one species for which genetic resources are necessary to facilitate new introductions and augmentations essential for recovery of the species. We used 454 pyrosequencing of a Z. celata normalized floral cDNA library to create a genomic resource for gene and marker discovery. A half-plate GS-FLX Titanium run yielded 655 337 reads averaging 250 bp. A total of 474 025 reads were assembled de novo into 84 645 contigs averaging 408 bp, while 181 312 reads remained unassembled. Forty-seven and 43% of contig consensus sequences had BLAST matches to known proteins in the Uniref50 and TAIR9 annotated protein databases, respectively; many contigs fully represented orthologous proteins in TAIR9. A total of 22 707 unique genes were sequenced, indicating substantial coverage of the Z. celata transcriptome. We detected single-nucleotide polymorphisms and simple sequence repeats (SSRs) and developed thousands of SSR primers for use in future genetic studies. As a first step towards understanding self-incompatibility in Z. celata, we identified sequences belonging to the gene family encoding self-incompatibility. This study demonstrates the efficacy of 454 transcriptome sequencing for rapid gene and marker discovery in an endangered plant.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":"1-9"},"PeriodicalIF":4.1,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/dnares/dsr037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40115711","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: 39