Chromosome Research最新文献_第10页

Communal living: the role of polyploidy and syncytia in tissue biology. 群落生活:多倍体和合胞体在组织生物学中的作用。

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-12-01 DOI: 10.1007/s10577-021-09664-3

Nora G Peterson, Donald T Fox

引用次数: 18

Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition 厚柱头菟丝子亚属核型不对称反映了其重复DNA组成

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-08-10 DOI: 10.1101/2021.08.09.455742

Amalia Ibiapino, M. Báez, M. García, M. Costea, S. Stefanović, A. Pedrosa‐Harand

{"title":"Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition","authors":"Amalia Ibiapino, M. Báez, M. García, M. Costea, S. Stefanović, A. Pedrosa‐Harand","doi":"10.1101/2021.08.09.455742","DOIUrl":"https://doi.org/10.1101/2021.08.09.455742","url":null,"abstract":"Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 127-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"91 - 107"},"PeriodicalIF":2.6,"publicationDate":"2021-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43389471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae 比较细胞基因组学揭示豆科菜豆基因组改组和着丝粒重新定位

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-08-09 DOI: 10.1101/2021.08.06.455448

Claudio Montenegro, Lívia do Vale Martins, F. de Oliveira Bustamante, A. C. Brasileiro-Vidal, A. Pedrosa‐Harand

{"title":"Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae","authors":"Claudio Montenegro, Lívia do Vale Martins, F. de Oliveira Bustamante, A. C. Brasileiro-Vidal, A. Pedrosa‐Harand","doi":"10.1101/2021.08.06.455448","DOIUrl":"https://doi.org/10.1101/2021.08.06.455448","url":null,"abstract":"The tribe Phaseoleae includes several legume crops with assembled genomes. Comparative genomic studies have evidenced the preservation of large genomic blocks among legumes, although chromosome dynamics during Phaseoleae evolution has not been investigated. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We identified GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata and searched for GBs in different genomes of the Phaseolinae ( P. lunatus ) and Glycininae ( Amphicarpaea edgeworthii ) subtribes and Spatholobus suberectus (sister to Phaseolinae and Glycininae), using Medicago truncatula as the outgroup. We also used oligo-FISH probes of two P. vulgaris chromosomes to paint the orthologous chromosomes of two non-sequenced Phaseolinae species. We inferred the APK as having n = 11 and 19 GBs (A to S), hypothesizing five chromosome fusions that reduced the ancestral legume karyotype to n = 11. We identified the rearrangements among the APK and the subtribes and species, with extensive centromere repositioning in Phaseolus . We also reconstructed the chromosome number reduction in S. suberectus . The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"477-492"},"PeriodicalIF":2.6,"publicationDate":"2021-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44888532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization. 两种黄斑钩端绦虫在无性系生长过程中组蛋白修饰的全基因组图谱显示了不同的基因组组织。

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-06-01 Epub Date: 2021-05-21 DOI: 10.1007/s10577-021-09658-1

Jessica L Soyer, Colin Clairet, Elise J Gay, Nicolas Lapalu, Thierry Rouxel, Eva H Stukenbrock, Isabelle Fudal

{"title":"Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization.","authors":"Jessica L Soyer, Colin Clairet, Elise J Gay, Nicolas Lapalu, Thierry Rouxel, Eva H Stukenbrock, Isabelle Fudal","doi":"10.1007/s10577-021-09658-1","DOIUrl":"10.1007/s10577-021-09658-1","url":null,"abstract":"Leptosphaeria maculans 'brassicae' (Lmb) and Leptosphaeria maculans 'lepidii' (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains.","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"29 2","pages":"219-236"},"PeriodicalIF":2.6,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09658-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39005035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Male sterile 28 encodes an ARGONAUTE family protein essential for male fertility in maize. 雄性不育28编码玉米雄性育性必需的ARGONAUTE家族蛋白。

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-06-01 Epub Date: 2021-03-02 DOI: 10.1007/s10577-021-09653-6

Yunfei Li, Yumin Huang, Lingling Pan, Yue Zhao, Wei Huang, Weiwei Jin

{"title":"Male sterile 28 encodes an ARGONAUTE family protein essential for male fertility in maize.","authors":"Yunfei Li, Yumin Huang, Lingling Pan, Yue Zhao, Wei Huang, Weiwei Jin","doi":"10.1007/s10577-021-09653-6","DOIUrl":"https://doi.org/10.1007/s10577-021-09653-6","url":null,"abstract":"Male sterility is a common biological phenomenon in plants and is a useful trait for hybrid seed production. Normal tapetum development is essential for viable pollen generation. Although many genes involved in tapetum differentiation and degradation have been isolated in maize, elements that regulate tapetum development during pollen mother cell (PMC) meiosis are less studied. Here, we characterized a classical male-sterile mutant male sterile 28 (ms28) in maize. The ms28 mutant had a regular male meiosis process, while its tapetum cells showed premature vacuolation at the early meiotic prophase stage. Using map-based cloning, we cloned the Ms28 gene and confirmed its role in male fertility in maize together with two allelic mutants. Ms28 encodes the ARGONAUTE (AGO) family protein ZmAGO5c, and its transcripts primarily accumulate in premeiosis anthers, with more intense signals in PMCs. Transcriptomic analysis revealed that genes related to anther development, cell division, and reproductive structure development processes were differentially expressed between the ms28 mutant and its fertile siblings. Moreover, small RNA (sRNA) sequencing revealed that the small interfering RNA (siRNA) and microRNA (miRNA) abundances were obviously changed in ms28 meiotic anthers, which indicated that Ms28 may regulate tapetal cell development through small RNA-mediated epigenetic regulatory pathways. Taken together, our results shed more light on the functional mechanisms of the early development of the tapetum for male fertility in maize.","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"29 2","pages":"189-201"},"PeriodicalIF":2.6,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09653-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25420229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

The new year for chromosome research: a change of guard amidst a shifting scientific landscape and global pandemic. 染色体研究的新一年:在不断变化的科学格局和全球流行病中换岗。

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-06-01 Epub Date: 2021-02-24 DOI: 10.1007/s10577-021-09647-4

Beth A Sullivan

引用次数: 0

Comprehensive mapping of transposable elements reveals distinct patterns of element accumulation on chromosomes of wild beetles. 转座因子的全面定位揭示了野生甲虫染色体上不同的元素积累模式。

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-06-01 Epub Date: 2021-02-27 DOI: 10.1007/s10577-021-09655-4

Igor Costa Amorim, Cibele Gomes Sotero-Caio, Rafaelle Grazielle Coelho Costa, Crislaine Xavier, Rita de Cássia de Moura

{"title":"Comprehensive mapping of transposable elements reveals distinct patterns of element accumulation on chromosomes of wild beetles.","authors":"Igor Costa Amorim, Cibele Gomes Sotero-Caio, Rafaelle Grazielle Coelho Costa, Crislaine Xavier, Rita de Cássia de Moura","doi":"10.1007/s10577-021-09655-4","DOIUrl":"https://doi.org/10.1007/s10577-021-09655-4","url":null,"abstract":"Over the past decades, transposable elements (TEs) have been shown to play important roles shaping genome architecture and as major promoters of genetic diversification and evolution of species. Likewise, TE accumulation is tightly linked to heterochromatinization and centromeric dynamics, which can ultimately contribute to speciation. Despite growing efforts to characterize the repeat landscape of species, few studies have focused on mapping the accumulation profiles of TEs on chromosomes. The few studies on repeat accumulation profiles in populations are biased towards model organisms and inbred lineages. Here, we present a cytomolecular analysis of six mobilome-extracted elements on multiple individuals from a population of a species of wild-captured beetle, Dichotomius schiffleri, aiming to investigate patterns of TE accumulation and uncover possible trends of their chromosomal distribution. Compiling TE distribution data from several individuals allowed us to make generalizations regarding variation of TEs at the gross chromosome level unlikely to have been achieved using a single individual, or even from a whole-genome assembly. We found that (1) transposable elements have differential accumulation profiles on D. schiffleri chromosomes and (2) specific chromosomes have their own TE accumulation landscape. The remarkable variability of their genomic distribution suggests that TEs are likely candidates to contribute to the evolution of heterochromatin architecture and promote high genetic variability in species that otherwise display conserved karyotypes. Therefore, this variation likely contributed to genome evolution and species diversification in Dichotomius.","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"29 2","pages":"203-218"},"PeriodicalIF":2.6,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09655-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25411024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Correction to: Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure. 修正:先进的荧光纳米显微镜对揭示有丝分裂染色体结构的贡献。

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-06-01 DOI: 10.1007/s10577-021-09662-5

S W Botchway, S Farooq, A Sajid, I K Robinson, M Yusuf

引用次数: 0

Correction to: Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH. 更正:用BAC-FISH方法鉴定百香果(Passiflora edulis)染色体。

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-06-01 DOI: 10.1007/s10577-020-09633-2

M A Sader, Y Dias, Z P Costa, C Munhoz, H Penha, H Bergès, M L C Vieira, A Pedrosa-Harand

引用次数: 1

Cyclic DNA remethylation following active demethylation at euchromatic regions in mouse embryonic stem cells. 小鼠胚胎干细胞正色区活性去甲基化后的环状DNA再甲基化。

IF 2.6 4区生物学

Chromosome Research Pub Date : 2021-06-01 Epub Date: 2020-11-17 DOI: 10.1007/s10577-020-09645-y

Musashi Kubiura-Ichimaru, Takamasa Ito, Louis Lefebvre, Masako Tada

{"title":"Cyclic DNA remethylation following active demethylation at euchromatic regions in mouse embryonic stem cells.","authors":"Musashi Kubiura-Ichimaru, Takamasa Ito, Louis Lefebvre, Masako Tada","doi":"10.1007/s10577-020-09645-y","DOIUrl":"https://doi.org/10.1007/s10577-020-09645-y","url":null,"abstract":"DNA methylation is an essential epigenetic mark that regulates normal mammalian embryonic development. DNA methylation profiles are not always static, especially during germline development. In zygotes, DNA is typically highly methylated but, during preimplantation, DNA methylation is erased globally. Then, at the start of post-implantation development in mouse embryos, DNA again becomes dramatically hypermethylated. Chromatin structure regulates the accessibility of DNA-modifying enzymes to target DNA. Beyond that, however, our understanding of the pathway by which chromatin regulation initiates changes in global DNA methylation during mouse embryonic development remains incomplete. To analyse the relationship between global regulation of DNA methylation and chromatin status, we examined 5-methylcytosine (5mC), modified by the DNA methyltransferase DNMT, and the oxidative derivative 5-hydroxymethylation (5hmC), converted from 5mC by TET-family enzymes, by means of immunofluorescence staining of mitotic chromosomes in mouse embryonic stem cells (ESCs). Our comparison of immunostaining patterns for those epigenetic modifications in wild-type, DNMT-deficient, and TET-deficient ESCs allowed us to visualise cell cycle-mediated DNA methylation changes, especially in euchromatic regions. Our findings suggest that DNA methylation patterns in undifferentiated mouse ESCs are stochastically balanced by the opposing effects of two activities: demethylation by TET and subsequent remethylation by DNMT.","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"29 2","pages":"145-157"},"PeriodicalIF":2.6,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-020-09645-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38615236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1