Genome dynamics最新文献_第2页

The genus burkholderia: analysis of 56 genomic sequences. 伯克霍尔德菌属:56个基因组序列分析。

Genome dynamics Pub Date : 2009-01-01 Epub Date: 2009-08-19 DOI: 10.1159/000235768

D W Ussery, K Kiil, K Lagesen, T Sicheritz-Pontén, J Bohlin, T M Wassenaar

{"title":"The genus burkholderia: analysis of 56 genomic sequences.","authors":"D W Ussery, K Kiil, K Lagesen, T Sicheritz-Pontén, J Bohlin, T M Wassenaar","doi":"10.1159/000235768","DOIUrl":"https://doi.org/10.1159/000235768","url":null,"abstract":"The genus Burkholderia consists of a number of very diverse species, both in terms of lifestyle (which varies from category B pathogens to apathogenic soil bacteria and plant colonizers) and their genetic contents. We have used 56 publicly available genomes to explore the genomic diversity within this genus, including genome sequences that are not completely finished, but are available from the NCBI database. Defining the pan- and core genomes of species results in insights in the conserved and variable fraction of genomes, and can verify (or question) historic, taxonomic groupings. We find only several hundred genes that are conserved across all Burkholderia genomes, whilst there are more than 40,000 gene families in the Burkholderia pan-genome. A BLAST matrix visualizes the fraction of conserved genes in pairwise comparisons. A BLAST atlas shows which genes are actually conserved in a number of genomes, located and visualized with reference to a chosen genome. Genomic islands are common in many Burkholderia genomes, and most of these can be readily visualized by DNA structural properties of the chromosome. Trees that are based on relatedness of gene family content yield different results depending on what genes are analyzed. Some of the differences can be explained by errors in incomplete genome sequences, but, as our data illustrate, the outcome of phylogenetic trees depends on the type of genes that are analyzed.","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"6 ","pages":"140-157"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000235768","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28353559","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: 57

Homologue pairing, recombination and segregation in Caenorhabditis elegans. 秀丽隐杆线虫的同源配对、重组与分离。

Genome dynamics Pub Date : 2009-01-01 DOI: 10.1159/000166618

M Zetka

{"title":"Homologue pairing, recombination and segregation in Caenorhabditis elegans.","authors":"M Zetka","doi":"10.1159/000166618","DOIUrl":"https://doi.org/10.1159/000166618","url":null,"abstract":"Meiosis in the free-living, hermaphroditic nematode Caenorhabditis elegans is marked by the same highly conserved features observed in other sexually reproducing systems. Accurate chromosome segregation at the meiotic divisions depends on earlier landmark events of meiotic prophase, including the pairing of homologous chromosomes, synapsis between them, and the formation of crossovers. Dissection of these processes has revealed a unique simplification of meiotic mechanisms that impact the interpretation of meiotic chromosome behaviour in more complex systems. Chromosome sites required for chromosome pairing are consolidated to one end of each chromosome, the many sites of recombination initiation are resolved into a single crossover for each chromosome pair, and the diffuse (holocentric) kinetic activity that extends along the length of the mitotic chromosomes is reduced to a single end of each meiotic chromosome. Consequently, studies from the nematode have illuminated and challenged long-standing concepts of homologue pairing mechanisms, crossover interference, and kinetochore structure. Because chromosome pairing, synapsis, and recombination can proceed independently of one another, C. elegans has provided a simplified system for studying these processes and the mechanisms mediating their coordination during meiosis. This review covers the major features of C. elegans meiosis with emphasis on its contributions to understanding essential meiotic processes.","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"5 ","pages":"43-55"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000166618","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27815803","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: 43

The Mammalian synaptonemal complex: a scaffold and beyond. 哺乳动物突触复合体:支架及其他。

Genome dynamics Pub Date : 2009-01-01 DOI: 10.1159/000166620

F Yang, P J Wang

引用次数: 86

The dance floor of meiosis: evolutionary conservation of nuclear envelope attachment and dynamics of meiotic telomeres. 减数分裂的舞池:核膜附着的进化保护和减数分裂端粒的动力学。

Genome dynamics Pub Date : 2009-01-01 DOI: 10.1159/000166621

M Alsheimer

{"title":"The dance floor of meiosis: evolutionary conservation of nuclear envelope attachment and dynamics of meiotic telomeres.","authors":"M Alsheimer","doi":"10.1159/000166621","DOIUrl":"https://doi.org/10.1159/000166621","url":null,"abstract":"Segregation of the homologous chromosomes is the most important feature of meiosis as it ensures the faithful haploidization of the genome. It essentially depends on an accurate prearrangement of chromosomes that culminates in a precise and unambiguous pairing of the homologs, which in turn is a prere - quisite for their correct segregation. Pairing with the right partner is accompanied by, moreover it implicitly requires characteristic chromosomal movements that, remarkably, appear to be driven by the chromosomal ends. In prophase I, telomeres firmly attach to the nuclear envelope and move to congregate in a small cluster, thus trailing homologs into close vicinity, a condition that was suggested to promote homolog recognition and alignment. The evolutionarily highly conserved phenomenon of the telomere driven meiotic chromosome rearrangement is yet known for a long time, but the molecular mechanisms responsible for telomere attachment and their directed movements have remained largely unknown. However, in the recent years significant progress has been made in this issue, which has provided some novel clues about the molecular requirements and function of the characteristic meiotic telomere dynamics.","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"5 ","pages":"81-93"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000166621","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27815806","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: 29

Maternal origin of the human aneuploidies. Are homolog synapsis and recombination to blame? Notes (learned) from the underbelly. 人类非整倍体的母系起源。同源突触和重组是罪魁祸首吗?从下腹学来的音符。

Genome dynamics Pub Date : 2009-01-01 DOI: 10.1159/000166638

R Garcia-Cruz, I Roig, M Garcia Caldés

引用次数: 19

Pathogenomics of mycobacteria. 分枝杆菌的病理基因组学。

Genome dynamics Pub Date : 2009-01-01 Epub Date: 2009-08-19 DOI: 10.1159/000235772

M C Gutierrez, P Supply, R Brosch

引用次数: 18

Variation in patterns of human meiotic recombination. 人类减数分裂重组模式的变异。

Genome dynamics Pub Date : 2009-01-01 DOI: 10.1159/000166623

P P Khil, R D Camerini-Otero