Hereditas最新文献

{"title":"Analysis of differentially expressed genes and adaptive mechanisms of <i>Prunus triloba</i> Lindl. under alkaline stress.","authors":"Jia Liu,&nbsp;Yongqing Wang,&nbsp;Qingtian Li","doi":"10.1186/s41065-017-0031-7","DOIUrl":"https://doi.org/10.1186/s41065-017-0031-7","url":null,"abstract":"<p><strong>Background: </strong><i>Prunus triloba</i> Lindl. is a naturally salt-alkaline-tolerant plant with several unique characteristics, and it can be used as the rootstock of Chinese plum (<i>Prunus salicina</i> Lindl.) in saline-alkaline soils. To comprehensively investigate the alkaline acclimation mechanisms in <i>P. triloba</i>, a series of analyses were conducted under alkaline stress, including analyses of the kinetics of molecular and physiological changes, and leaf microstructure.</p><p><strong>Results: </strong>To understand the kinetics of molecular changes under short-term alkaline stress, we used Illumina HiSeq 2500 platform to identify alkaline stress-related differentially expressed genes (DEGs) in <i>P. triloba</i>. Approximately 53.0 million high-quality clean reads were generated from 59.6 million raw reads, and a total of 124,786 unigenes were obtained after <i>de novo</i> assembly of <i>P. triloba</i> transcriptome data. After alkaline stress treatment, a total of 8948 unigenes were identified as DEGs. Based on these DEGs, a Gene Ontology (GO) enrichment analysis was conducted, suggesting that 28 genes may play an important role in the early alkaline stress response. In addition, analysis of DEGs with the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that pathways were significant at different treatment time points. A significant positive correlation was found between the quantitative real-time PCR (qRT-PCR) results and the RNA-Seq data for seven alkaline-related genes, confirming the reliability of the RNA-Seq results. Based on physiological analysis of <i>P. triloba</i> in response to long-term alkaline stress, we found that the internal microstructures of the leaves of <i>P. triloba</i> changed to adapt to long-term alkaline stress. Various physiological indexes indicated that the degree of membrane injury increased with increasing duration of alkaline stress, affecting photosynthesis in <i>P. triloba</i> seedlings.</p><p><strong>Conclusions: </strong>This represents the first investigation into the physiology and transcriptome of <i>P. triloba</i> in response to alkaline stress. The results of this study can enrich the genomic resources available for <i>P. triloba</i>, as well as deepening our understanding of molecular and physiological alkaline tolerance mechanisms in <i>P. triloba</i>. This will also provide new insights into our understanding of alkaline acclimation mechanisms in Chinese plum (<i>Prunus salicina</i>) trees.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":"154 ","pages":"10"},"PeriodicalIF":2.7,"publicationDate":"2017-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-017-0031-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34979454","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":"Ancient role of <i>ten-m</i>/<i>odz</i> in segmentation and the transition from sequential to syncytial segmentation.","authors":"Axel Hunding,&nbsp;Stefan Baumgartner","doi":"10.1186/s41065-017-0029-1","DOIUrl":"https://doi.org/10.1186/s41065-017-0029-1","url":null,"abstract":"<p><strong>Background: </strong>Until recently, mechanisms of segmentation established for <i>Drosophila</i> served as a paradigm for arthropod segmentation. However, with the discovery of gene expression waves in vertebrate segmentation, another paradigm based on oscillations linked to axial growth was established. The <i>Notch</i> pathway and <i>hairy</i> delay oscillator are basic components of this mechanism, as is the <i>wnt</i> pathway. With the establishment of oscillations during segmentation of the beetle <i>Tribolium</i>, a common segmentation mechanism may have been present in the last common ancestor of vertebrates and arthropods. However, the <i>Notch</i> pathway is not involved in segmentation of the initial <i>Drosophila</i> embryo. In arthropods, the <i>engrailed</i>, <i>wingless</i> pair has a much more conserved function in segmentation than most of the hierarchy established for <i>Drosophila.</i></p><p><strong>Results: </strong>Here, we work backwards from this conserved pair by discussing possible mechanisms which could have taken over the role of the <i>Notch</i> pathway. We propose a pivotal role for the large transmembrane protein Ten-m/Odz. Ten-m/Odz may have had an ancient role in cell-cell communication, parallel to the <i>Notch</i> and <i>wnt</i> pathways. The Ten-m protein binds to the membrane with properties which resemble other membrane-based biochemical oscillators.</p><p><strong>Conclusion: </strong>We propose that such a simple transition could have formed the initial scaffold, on top of which the hierarchy, observed in the syncytium of dipterans, could have evolved.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":"154 ","pages":"8"},"PeriodicalIF":2.7,"publicationDate":"2017-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-017-0029-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34958215","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":"Genetic diversity and population structure analysis of Kala bhat (<i>Glycine max</i> (L.) Merrill) genotypes using SSR markers.","authors":"Yegappa Hipparagi, Rakesh Singh, Debjani Roy Choudhury, Veena Gupta","doi":"10.1186/s41065-017-0030-8","DOIUrl":"10.1186/s41065-017-0030-8","url":null,"abstract":"<p><strong>Background: </strong>Kala bhat (Black soybean) is an important legume crop in Uttarakhand state, India, due to its nutritional and medicinal properties. In the current study, the genetic variabilities present in Kala bhat were estimated using SSR markers and its variability was compared with other improved soybean varieties cultivated in Uttarakhand state, India.</p><p><strong>Results: </strong>Seventy-five genotypes cultivated in different districts of Uttarakhand were collected, and molecular analysis was done using 21 SSR markers. A total of 60 alleles were amplified with an average of 2.85 alleles per locus. The mean value of gene diversity and PIC was estimated to be 0.43 and 0.36, respectively. The unrooted phylogenetic tree grouped soybean genotypes into three major clusters, where, yellow seed coat (improved varieties) genotypes were grouped in one cluster, while reddish brown (improved varieties) and Kala bhat showed intermixing. Population structure divided the soybean genotypes into six different populations. AMOVA analysis showed 12% variance among the population, 66% variance among individual and 22% variance was observed within individuals. Principal Coordinate Analysis (PCoA) also showed that yellow seed coat genotypes were grouped in one cluster, whereas, the Kala bhat showed scattered distribution and few genotypes of Kala bhat showed grouping with red and yellow genotypes.</p><p><strong>Conclusions: </strong>The different genetic diversity parameters used in the present study indicate that Kala bhat genotypes were more diverse than the yellow seed coat and brown seed coat colour genotypes. Therefore, Kala bhat genotypes can be a good source for the soybean breeding programme due to its better genetic diversity as well as its medicinal properties.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":"154 ","pages":"9"},"PeriodicalIF":2.7,"publicationDate":"2017-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-017-0030-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34958214","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":"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":"154 ","pages":"7"},"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":"154 ","pages":"6"},"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":"154 ","pages":"5"},"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":"154 1","pages":""},"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":" ","pages":""},"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":"Efficient and Site-specific Antibody Labeling by Strain-promoted Azide-alkyne Cycloaddition.","authors":"Sanggil Kim, Wooseok Ko, Hyunji Park, Hyun Soo Lee","doi":"10.3791/54922","DOIUrl":"10.3791/54922","url":null,"abstract":"<p><p>There are currently many chemical tools available to introduce chemical probes into proteins to study their structure and function. A useful method is protein conjugation by genetically introducing an unnatural amino acid containing a bioorthogonal functional group. This report describes a detailed protocol for site-specific antibody conjugation. The protocol includes experimental details for the genetic incorporation of an azide-containing amino acid, and the conjugation reaction by strain-promoted azide-alkyne cycloaddition (SPAAC). This strain-promoted reaction proceeds by simple mixing of the reacting molecules at physiological pH and temperature, and does not require additional reagents such as copper(I) ions and copper-chelating ligands. Therefore, this method would be useful for general protein conjugation and development of antibody drug conjugates (ADCs).</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":"80 2 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2016-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5226445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85460232","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":"153 1","pages":""},"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}