Hereditas最新文献

{"title":"The complete mitogenome of <i>Orcula dolium</i> (Draparnaud, 1801); ultra-deep sequencing from a single long-range PCR using the Ion-Torrent PGM.","authors":"D S J Groenenberg, J Harl, E Duijm, E Gittenberger","doi":"10.1186/s41065-017-0028-2","DOIUrl":"10.1186/s41065-017-0028-2","url":null,"abstract":"<p><strong>Background: </strong>With the increasing capacity of present-day next-generation sequencers the field of mitogenomics is rapidly changing. Enrichment of the mitochondrial fraction, is no longer necessary for obtaining mitogenomic data. Despite the benefits, shotgun sequencing approaches also have disadvantages. They do not guarantee obtaining the <i>complete</i> mitogenome, generally require larger amounts of input DNA and coverage is low compared to sequencing with enrichment strategies. If the mitogenome could be amplified in a single amplification, additional time and costs for sample preparation might outweigh these disadvantages.</p><p><strong>Results: </strong>A sequence of the complete mitochondrial genome of the pupilloid landsnail <i>Orcula dolium</i> is presented. The mitogenome was amplified in a single long-range (LR) PCR and sequenced on an Ion Torrent PGM (Life Technologies). The length is 14,063 nt and the average depth of coverage is 1112 X. This is the first published mitogenome for a member of the family Orculidae. It has the typical metazoan makeup of 13 protein coding genes (PCGs), 2 ribosomal RNAs (12S and 16S) and 22 transfer RNAs (tRNAs). <i>Orcula</i> is positioned between <i>Pupilla</i> and the Vertiginidae as the sister-group of <i>Gastrocopta</i> and <i>Vertigo</i>, together. An ancestral gene order reconstruction shows that Orthurethra in contrast to other Stylommatophora, have tRNA-H before tRNA-G and that the gene order in the 'non-achatinoid' clade is identical to that of closely related non-stylommatophoran taxa.</p><p><strong>Conclusions: </strong>We show it is feasible to ultra-deep sequence a mitogenome from a single LR-PCR. This approach is particularly relevant to studies that have low concentrations of input DNA. It results in a more efficient use of NGS capacity (only the targeted fraction is sequenced) and is an effective selection against nuclear mitochondrial inserts (NUMTS). In contrast to previous studies based in particular on 28S, our results indicate that phylogeny reconstructions based on complete mitogenomes might be more suitable to resolve deep relationships within Stylommatophora. Ancestral gene order reconstructions reveal rearrangements that characterize systematic groups.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2017-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5379511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34901923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Psychomotor retardation with a 1q42.11-q42.12 deletion.","authors":"Jialing He,&nbsp;Yingjun Xie,&nbsp;Shu Kong,&nbsp;Wenjun Qiu,&nbsp;Xiaoman Wang,&nbsp;Ding Wang,&nbsp;Xiaofang Sun,&nbsp;Deming Sun","doi":"10.1186/s41065-016-0022-0","DOIUrl":"https://doi.org/10.1186/s41065-016-0022-0","url":null,"abstract":"<p><p>A 1q42 deletion is a rare structure variation that commonly harbours various deletion breakpoints along with diversified phenotypes. In our study, we found a <i>de novo</i> 1q42 deletion in a boy who did not have a cleft palate or a congenital diaphragmatic hernia but presented with psychomotor retardation. A 1.9 Mb deletion located within 1q42.11-q42.12 was validated at the molecular cytogenetic level. This is the first report of a 1q42.11-q42.12 deletion in a patient with onlypsychomotor retardation. The precise break points could facilitate the discovery of potential causative genes, such as <i>LBR, EPHX1</i>, etc. The correlation between the psychomotor retardation and the underlying genetic factors could not only shed light on the diagnosis of psychomotor retardation at the genetic level but also provide potential therapeutic targets.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2017-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0022-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34805853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association study of rust traits in orchardgrass using SLAF-seq technology.","authors":"Bing Zeng,&nbsp;Haidong Yan,&nbsp;Xinchun Liu,&nbsp;Wenjing Zang,&nbsp;Ailing Zhang,&nbsp;Sifan Zhou,&nbsp;Linkai Huang,&nbsp;Jinping Liu","doi":"10.1186/s41065-017-0027-3","DOIUrl":"https://doi.org/10.1186/s41065-017-0027-3","url":null,"abstract":"<p><strong>Background: </strong>While orchardgrass (<i>Dactylis glomerata</i> L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass.</p><p><strong>Results: </strong>In this study, a genome-wide association study (GWAS) was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in orchardgrass. A total of 2,334,889 SLAF tags were generated to produce 2,309,777 SNPs. ADMIXTURE analysis revealed unstructured subpopulations for 33 accessions, indicating that this orchardgrass population could be used for association analysis. Linkage disequilibrium (LD) analysis revealed an average r² of 0.4 across all SNP pairs, indicating a high extent of LD in these samples. Through GWAS, a total of 4,604 SNPs were found to be significantly (<i>P</i> < 0.01) associated with the rust trait. The bulk analysis discovered a number of 5,211 SNPs related to rust trait. Two candidate genes, including cytochrome P450, and prolamin were implicated in disease resistance through prediction of functional genes surrounding each high-quality SNP (<i>P</i> < 0.01) associated with rust traits based on GWAS analysis and bulk analysis.</p><p><strong>Conclusions: </strong>The large number of SNPs associated with rust traits and these two candidate genes may provide the basis for further research on rust resistance mechanisms and marker-assisted selection (MAS) for rust-resistant lineages.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2017-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-017-0027-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34775831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed","authors":"C. Rochus, A. Johansson","doi":"10.1186/s41065-017-0026-4","DOIUrl":"https://doi.org/10.1186/s41065-017-0026-4","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2017-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-017-0026-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A replication study of schizophrenia-related rare copy number variations in a Han Southern Chinese population","authors":"Jianmin Yuan, Jianlinhu Hu, Zhiqiang Li, Fuquan Zhang, Dexiang Zhou, Chunhui Jin","doi":"10.1186/s41065-016-0025-x","DOIUrl":"https://doi.org/10.1186/s41065-016-0025-x","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2017-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0025-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42926485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular breeding of a novel orange-brown tomato fruit with enhanced beta-carotene and chlorophyll accumulation.","authors":"Ranjith Kumar Manoharan, Hee-Jeong Jung, Indeok Hwang, Namhee Jeong, Kang Hee Kho, Mi-Young Chung, Ill-Sup Nou","doi":"10.1186/s41065-016-0023-z","DOIUrl":"10.1186/s41065-016-0023-z","url":null,"abstract":"<p><strong>Background: </strong>Tomatoes provide a significant dietary source of the carotenoids, lycopene and β-carotene. During ripening, carotenoid accumulation determines the fruit colors while chlorophyll degradation. These traits have been, and continue to be, a significant focus for plant breeding efforts. Previous work has found strong evidence for a relationship between <i>CYC-B</i> gene expression and the orange color of fleshy fruit. Other work has identified a point mutation in <i>SGR</i> that impedes chlorophyll degradation and causes brown flesh color to be retained in some tomato varieties.</p><p><strong>Methods: </strong>We crossed two inbred lines, KNY2 (orange) and KNB1 (brown) and evaluated the relationship between these genes for their effect on fruit color. Phenotypes of F2 generation plants were analyzed and a novel 'orange-brown' fruit color was identified.</p><p><strong>Results: </strong>We confirm two SNPs, one in <i>CYC-B</i> and another in <i>SGR</i> gene sequence, associated with segregation of 'orange-brown' fruit color in F2 generation. The carotenoid and chlorophyll content of a fleshy fruit was assessed across the different phenotypes and showed a strong correlation with expression pattern of carotenoid biosynthesis genes and SGR function. The orange-brown fruit has high β-carotene and chlorophyll. Our results provide valuable information for breeders to develop tomato fruit of a novel color using molecular markers.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2017-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5226094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48977105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis of genes involved in anthocyanins biosynthesis and transport in berries of black and white spine grapes (Vitis davidii)","authors":"Lei Sun, X. Fan, Ying Zhang, Jianfu Jiang, Haisheng Sun, Chonghuai Liu","doi":"10.1186/s41065-016-0021-1","DOIUrl":"https://doi.org/10.1186/s41065-016-0021-1","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0021-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill)","authors":"Sakshi Chaudhary, Bharat Kumar Mishra, Thiruvettai Vivek, S. Magadum, J. K. Yasin","doi":"10.1186/s41065-016-0019-8","DOIUrl":"https://doi.org/10.1186/s41065-016-0019-8","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0019-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Negative frequency dependent selection on sympatric mtDNA haplotypes in Drosophila subobscura","authors":"G. Arnqvist, Z. K. Novicic, J. Castro, A. Sayadi","doi":"10.1186/s41065-016-0020-2","DOIUrl":"https://doi.org/10.1186/s41065-016-0020-2","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0020-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A C-banded karyotype of mitotic chromosomes in diploid purple coneflower (Echinacea purpurea L.)","authors":"Wei-zhen Jiang, Qing-ling Li, Xiao-lu Chen, Yi Ren, Rong Chen, Hong Wu, Yue-Cheng Yang","doi":"10.1186/s41065-016-0016-y","DOIUrl":"https://doi.org/10.1186/s41065-016-0016-y","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0016-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}