Chromosome ResearchPub Date : 2022-03-01Epub Date: 2022-01-06DOI: 10.1007/s10577-021-09680-3
Kai Wang, Hon Cheng, Jinlei Han, Ayman Esh, Jiayong Liu, Yuebin Zhang, Baohua Wang
{"title":"A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars.","authors":"Kai Wang, Hon Cheng, Jinlei Han, Ayman Esh, Jiayong Liu, Yuebin Zhang, Baohua Wang","doi":"10.1007/s10577-021-09680-3","DOIUrl":"https://doi.org/10.1007/s10577-021-09680-3","url":null,"abstract":"<p><p>Modern sugarcane cultivars are derived from the hybridization of Saccharum officinarum (2n = 80) and S. spontaneum (2n = 40-128), leading to a variety of complex genomes with highly polyploid and varied chromosome structures. These complex genomes have hindered deciphering the genome structure and marker-assisted selection in sugarcane breeding. Ten cultivars were analyzed by fluorescence in situ hybridization adopting chromosome painting and S. spontaneum-specific probes. The results showed six types of chromosomes in the studied cultivars, including S. spontaneum or S. officinarum chromosomes, interspecific recombinations from homoeologous or nonhomoeologous chromosomes, and translocations of S. spontaneum or S. officinarum chromosomes. The results showed unexpectedly high proportions of interspecific recombinations in these cultivars (11.9-40.9%), which renew our knowledge that less than 13% of chromosomes result from interspecific exchanges. Also, the results showed a high frequency of translocations (an average of 2.15 translocations per chromosome) between S. officinarum chromosomes. The diverse types of chromosomes in cultivars imply that hybrid gametes of S. spontaneum and S. officinarum may form unusual chromosome pairs, including homoeologous or nonhomoeologous chromosomes either between or within S. spontaneum and S. officinarum. Moreover, we consistently observed 11 or 12 copies for the four studied chromosomes, i.e., chromosomes 1, 2, 7, and 8, suggesting steady transmission during the breeding program. By comparison, we found a relatively fewer copies of S. spontaneum chromosome 1 than those of S. spontaneum chromosomes 2, 7, and 8. These results provide deep insights into the structure of cultivars and may facilitate chromosome-assisted selection in sugarcane breeding.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"29-41"},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39901397","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}
J. Agundez, A. Alfirevic, S. Aliño, L. Becquemont, S. Bell, L. Benhaim, W. Berrettini, M. Białecka, E. Bleecker, L. Cavallari, A. Cederbaum, D. Chasman, L. Chen, B. Chowbay, M. Coenen, J. Corvol, W. Sadee, Y. Saito, R. Sargis, A. Schatzberg, S. Scherer, C. Schindler, M. Schirmer, K. Schmiegelow, W. Schroth, B. Tomlinson, J. Trontelj, T. Tsunoda, A. Turkistani, M. Tzvetkov, R. Uher, J. Upham, T. V. Gelder, L. H. J. Huis, R. V. Schaik
{"title":"Thanks to Referees","authors":"J. Agundez, A. Alfirevic, S. Aliño, L. Becquemont, S. Bell, L. Benhaim, W. Berrettini, M. Białecka, E. Bleecker, L. Cavallari, A. Cederbaum, D. Chasman, L. Chen, B. Chowbay, M. Coenen, J. Corvol, W. Sadee, Y. Saito, R. Sargis, A. Schatzberg, S. Scherer, C. Schindler, M. Schirmer, K. Schmiegelow, W. Schroth, B. Tomlinson, J. Trontelj, T. Tsunoda, A. Turkistani, M. Tzvetkov, R. Uher, J. Upham, T. V. Gelder, L. H. J. Huis, R. V. Schaik","doi":"10.1007/s10577-005-1902-8","DOIUrl":"https://doi.org/10.1007/s10577-005-1902-8","url":null,"abstract":"","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"13 1","pages":"839"},"PeriodicalIF":2.6,"publicationDate":"2022-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-005-1902-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41788936","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}
{"title":"Communal living: the role of polyploidy and syncytia in tissue biology.","authors":"Nora G Peterson, Donald T Fox","doi":"10.1007/s10577-021-09664-3","DOIUrl":"https://doi.org/10.1007/s10577-021-09664-3","url":null,"abstract":"<p><p>Multicellular organisms are composed of tissues with diverse cell sizes. Whether a tissue primarily consists of numerous, small cells as opposed to fewer, large cells can impact tissue development and function. The addition of nuclear genome copies within a common cytoplasm is a recurring strategy to manipulate cellular size within a tissue. Cells with more than two genomes can exist transiently, such as in developing germlines or embryos, or can be part of mature somatic tissues. Such nuclear collectives span multiple levels of organization, from mononuclear or binuclear polyploid cells to highly multinucleate structures known as syncytia. Here, we review the diversity of polyploid and syncytial tissues found throughout nature. We summarize current literature concerning tissue construction through syncytia and/or polyploidy and speculate why one or both strategies are advantageous.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"29 3-4","pages":"245-260"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09664-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9291922","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}
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}
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}
Chromosome ResearchPub Date : 2021-06-01Epub Date: 2021-05-21DOI: 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":"<p><p>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.</p>","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}
{"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":"<p><p>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.</p>","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}
Chromosome ResearchPub Date : 2021-06-01Epub Date: 2021-02-24DOI: 10.1007/s10577-021-09647-4
Beth A Sullivan
{"title":"The new year for chromosome research: a change of guard amidst a shifting scientific landscape and global pandemic.","authors":"Beth A Sullivan","doi":"10.1007/s10577-021-09647-4","DOIUrl":"https://doi.org/10.1007/s10577-021-09647-4","url":null,"abstract":"","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"29 2","pages":"127-130"},"PeriodicalIF":2.6,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09647-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25400295","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}
Chromosome ResearchPub Date : 2021-06-01Epub Date: 2021-02-27DOI: 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":"<p><p>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.</p>","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}
S W Botchway, S Farooq, A Sajid, I K Robinson, M Yusuf
{"title":"Correction to: Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure.","authors":"S W Botchway, S Farooq, A Sajid, I K Robinson, M Yusuf","doi":"10.1007/s10577-021-09662-5","DOIUrl":"https://doi.org/10.1007/s10577-021-09662-5","url":null,"abstract":"","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"29 2","pages":"239"},"PeriodicalIF":2.6,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09662-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38904969","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}
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