Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology最新文献

{"title":"Non-Mendelian transmission of accessory chromosomes in fungi.","authors":"Jovan Komluski,&nbsp;Eva H Stukenbrock,&nbsp;Michael Habig","doi":"10.1007/s10577-022-09691-8","DOIUrl":"https://doi.org/10.1007/s10577-022-09691-8","url":null,"abstract":"<p><p>Non-Mendelian transmission has been reported for various genetic elements, ranging from small transposons to entire chromosomes. One prime example of such a transmission pattern are B chromosomes in plants and animals. Accessory chromosomes in fungi are similar to B chromosomes in showing presence/absence polymorphism and being non-essential. How these chromosomes are transmitted during meiosis is however poorly understood-despite their often high impact on the fitness of the host. For several fungal organisms, a non-Mendelian transmission or a mechanistically unique meiotic drive of accessory chromosomes have been reported. In this review, we provide an overview of the possible mechanisms that can cause the non-Mendelian transmission or meiotic drives of fungal accessory chromosomes. We compare processes responsible for the non-Mendelian transmission of accessory chromosomes for different fungal eukaryotes and discuss the structural traits of fungal accessory chromosomes affecting their meiotic transmission. We conclude that research on fungal accessory chromosomes, due to their small size, ease of sequencing, and epigenetic profiling, can complement the study of B chromosomes in deciphering factors that influence and regulate the non-Mendelian transmission of entire chromosomes.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"241-253"},"PeriodicalIF":2.6,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9508043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40624551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Centromere drive: model systems and experimental progress.","authors":"Damian Dudka,&nbsp;Michael A Lampson","doi":"10.1007/s10577-022-09696-3","DOIUrl":"https://doi.org/10.1007/s10577-022-09696-3","url":null,"abstract":"<p><p>Centromeres connect chromosomes and spindle microtubules to ensure faithful chromosome segregation. Paradoxically, despite this conserved function, centromeric DNA evolves rapidly and centromeric proteins show signatures of positive selection. The centromere drive hypothesis proposes that centromeric DNA can act like a selfish genetic element and drive non-Mendelian segregation during asymmetric female meiosis. Resulting fitness costs lead to genetic conflict with the rest of the genome and impose a selective pressure for centromeric proteins to adapt by suppressing the costs. Here, we describe experimental model systems for centromere drive in yellow monkeyflowers and mice, summarize key findings demonstrating centromere drive, and explain molecular mechanisms. We further discuss efforts to test if centromeric proteins are involved in suppressing drive-associated fitness costs, highlight a model for centromere drive and suppression in mice, and put forth outstanding questions for future research.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"187-203"},"PeriodicalIF":2.6,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9567806/pdf/nihms-1842320.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40193335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences.","authors":"Anahí Mara Yañez-Santos,&nbsp;Rosalía Cristina Paz,&nbsp;Paula Beatriz Paz-Sepúlveda,&nbsp;Juan Domingo Urdampilleta","doi":"10.1007/s10577-021-09663-4","DOIUrl":"https://doi.org/10.1007/s10577-021-09663-4","url":null,"abstract":"<p><p>Capsicum annuum is a species that has undergone an expansion of the size of its genome caused mainly by the amplification of repetitive DNA sequences, including mobile genetic elements. Based on information obtained from sequencing the genome of pepper, the estimated fraction of retroelements is approximately 81%, and previous results revealed an important contribution of lineages derived from Gypsy superfamily. However, the dynamics of the retroelements in the C. annuum genome is poorly understood. In this way, the present work seeks to investigate the phylogenetic diversity and genomic abundance of the families of autonomous (complete and intact) LTR retroelements from C. annuum and inspect their distribution along its chromosomes. In total, we identified 1151 structurally full-length retroelements (340 Copia; 811 Gypsy) grouped in 124 phylogenetic families in the base of their retrotranscriptase. All the evolutive lineages of LTR retroelements identified in plants were present in pepper; however, three of them comprise 83% of the entire LTR retroelements population, the lineages Athila, Del/Tekay, and Ale/Retrofit. From them, only three families represent 70.8% of the total number of the identified retroelements. A massive family-specific wave of amplification of two of them occurred in the last 0.5 Mya (GypsyCa_16; CopiaCa_01), whereas the third is more ancient and occurred 3.0 Mya (GypsyCa_13). Fluorescent in situ hybridization performed with family and lineage-specific probes revealed contrasting patterns of chromosomal affinity. Our results provide a database of the populations LTR retroelements specific to C. annuum genome. The most abundant families were analyzed according to chromosome insertional preferences, suppling useful tools to the design of retroelement-based markers specific to the species.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"261-284"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09663-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39060939","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}

{"title":"Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species.","authors":"Noorhariza Mohd Zaki,&nbsp;Trude Schwarzacher,&nbsp;Rajinder Singh,&nbsp;Maria Madon,&nbsp;Corey Wischmeyer,&nbsp;Nordiana Hanim Mohd Nor,&nbsp;Muhammad Azwan Zulkifli,&nbsp;J S Pat Heslop-Harrison","doi":"10.1007/s10577-021-09675-0","DOIUrl":"https://doi.org/10.1007/s10577-021-09675-0","url":null,"abstract":"<p><p>Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"373-390"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39524277","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}

{"title":"De novo centromere formation on chromosome fragments with an inactive centromere in maize (Zea mays).","authors":"Ryan N Douglas,&nbsp;Hua Yang,&nbsp;Bing Zhang,&nbsp;Chen Chen,&nbsp;Fangpu Han,&nbsp;Jianlin Cheng,&nbsp;James A Birchler","doi":"10.1007/s10577-021-09670-5","DOIUrl":"https://doi.org/10.1007/s10577-021-09670-5","url":null,"abstract":"<p><p>The B chromosome of maize undergoes nondisjunction at the second pollen mitosis as part of its accumulation mechanism. Previous work identified 9-Bic-1 (9-B inactivated centromere-1), which comprises an epigenetically silenced B chromosome centromere that was translocated to the short arm of chromosome 9(9S). This chromosome is stable in isolation, but when normal B chromosomes are added to the genotype, it will attempt to undergo nondisjunction during the second pollen mitosis and usually fractures the chromosome in 9S. These broken chromosomes allow a test of whether the inactive centromere is reactivated or whether a de novo centromere is formed elsewhere on the chromosome to allow recovery of fragments. Breakpoint determination on the B chromosome and chromosome 9 showed that mini chromosome B1104 has the same breakpoint as 9-Bic-1 in the B centromere region and includes a portion of 9S. CENH3 binding was found on the B centromere region and on 9S, suggesting both centromere reactivation and de novo centromere formation. Another mini chromosome, B496, showed evidence of rearrangement, but it also only showed evidence for a de novo centromere. Other mini chromosome fragments recovered were directly derived from the B chromosome with breakpoints concentrated near the centromeric knob region, which suggests that the B chromosome is broken at a low frequency due to the failure of the sister chromatids to separate at the second pollen mitosis. Our results indicate that both reactivation and de novo centromere formation could occur on fragments derived from the progenitor possessing an inactive centromere.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"313-325"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09670-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39322521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scientist Spotlight: Kerry Bloom.","authors":"","doi":"10.1007/s10577-021-09672-3","DOIUrl":"https://doi.org/10.1007/s10577-021-09672-3","url":null,"abstract":"","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"241-244"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39522259","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}

{"title":"Computer simulation of merotelic kinetochore-microtubule attachments: corona size is more important than other cell parameters.","authors":"Maxim A Krivov,&nbsp;Fazoil I Ataullakhanov,&nbsp;Pavel S Ivanov","doi":"10.1007/s10577-021-09669-y","DOIUrl":"https://doi.org/10.1007/s10577-021-09669-y","url":null,"abstract":"<p><p>The even chromosome segregation between daughter cells during mitosis is crucial for genome integrity and is mostly regulated by proper attachments of spindle microtubules to kinetochores. Abnormalities in this process can lead to chromosome mis-segregation and potentially result in severe developmental disorders such as aneuploidy and cancer. Merotelic attachments when tubulin microtubules captured by the kinetochore of one chromatid originate from both spindle poles are considered as one of the key molecular processes that cause such abnormalities. In this paper, we use computer modeling and the Monte Carlo approach to reveal the reasons for retaining merotelic attachments at the end of metaphase. To this end, we varied, in small increments, the basic cell parameters within ensembles of 100, 500, and 1000 virtual cells. The analysis of configurations that ensure the preservation of the largest fraction of merotelic attachments enabled us to conclude that only a change in the size of the kinetochore corona can significantly increase the number of merotelic attachments and the angle between the centromere axis and the spindle axis. The effect of the other changes in model parameters, if any, was steadily suppressed by the end of metaphase. In addition, our computer model was validated by successfully reproducing the results of third-party theoretical studies as well as some experimental observations. We also found that the orientation of chromosomes and the number of merotelic attachments do not have an explicit correlation with each other and within some limits can change independently.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"327-349"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09669-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39341610","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}

{"title":"Correction to: Seq'ing identity and function in a repeat-derived noncoding RNA world.","authors":"Rachel J O'Neill","doi":"10.1007/s10577-021-09665-2","DOIUrl":"https://doi.org/10.1007/s10577-021-09665-2","url":null,"abstract":"","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"417"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09665-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39022591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Against the mainstream: exceptional evolutionary stability of ZW sex chromosomes across the fish families Triportheidae and Gasteropelecidae (Teleostei: Characiformes).","authors":"Cassia Fernanda Yano,&nbsp;Alexandr Sember,&nbsp;Rafael Kretschmer,&nbsp;Luiz Antônio Carlos Bertollo,&nbsp;Tariq Ezaz,&nbsp;Terumi Hatanaka,&nbsp;Thomas Liehr,&nbsp;Petr Ráb,&nbsp;Ahmed Al-Rikabi,&nbsp;Patrik Ferreira Viana,&nbsp;Eliana Feldberg,&nbsp;Ezequiel Aguiar de Oliveira,&nbsp;Gustavo Akira Toma,&nbsp;Marcelo de Bello Cioffi","doi":"10.1007/s10577-021-09674-1","DOIUrl":"https://doi.org/10.1007/s10577-021-09674-1","url":null,"abstract":"<p><p>Teleost fishes exhibit a breath-taking diversity of sex determination and differentiation mechanisms. They encompass at least nine sex chromosome systems with often low degree of differentiation, high rate of inter- and intra-specific variability, and frequent turnovers. Nevertheless, several mainly female heterogametic systems at an advanced stage of genetic differentiation and high evolutionary stability have been also found across teleosts, especially among Neotropical characiforms. In this study, we aim to characterize the ZZ/ZW sex chromosome system in representatives of the Triportheidae family (Triportheus auritus, Agoniates halecinus, and the basal-most species Lignobrycon myersi) and its sister clade Gasteropelecidae (Carnegiella strigata, Gasteropelecus levis, and Thoracocharax stellatus). We applied both conventional and molecular cytogenetic approaches including chromosomal mapping of 5S and 18S ribosomal DNA clusters, cross-species chromosome painting (Zoo-FISH) with sex chromosome-derived probes and comparative genomic hybridization (CGH). We identified the ZW sex chromosome system for the first time in A. halecinus and G. levis and also in C. strigata formerly reported to lack sex chromosomes. We also brought evidence for possible mechanisms underlying the sex chromosome differentiation, including inversions, repetitive DNA accumulation, and exchange of genetic material. Our Zoo-FISH experiments further strongly indicated that the ZW sex chromosomes of Triportheidae and Gasteropelecidae are homeologous, suggesting their origin before the split of these lineages (approx. 40-70 million years ago). Such extent of sex chromosome stability is almost exceptional in teleosts, and hence, these lineages afford a special opportunity to scrutinize unique evolutionary forces and pressures shaping sex chromosome evolution in fishes and vertebrates in general.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"391-416"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39554541","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}

{"title":"Correction to: X-ray ptychography imaging of human chromosomes after low-dose irradiation.","authors":"Archana Bhartiya,&nbsp;Darren Batey,&nbsp;Silvia Cipiccia,&nbsp;Xiaowen Shi,&nbsp;Christoph Rau,&nbsp;Stanley Botchway,&nbsp;Mohammed Yusuf,&nbsp;Ian K Robinson","doi":"10.1007/s10577-021-09668-z","DOIUrl":"https://doi.org/10.1007/s10577-021-09668-z","url":null,"abstract":"","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"419-420"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8710439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39291698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}