IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-11-05 DOI: 10.1139/gen-2024-0053

Virginia Natali Miguel, Jacqueline Monaghan

引用次数: 0

A phylogenetic perspective of chromosome evolution in Formicidae. 从系统进化的角度看姬蜂科的染色体进化。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-12-16 DOI: 10.1139/gen-2024-0124

Danon Clemes Cardoso, Maykon Passos Cristiano

{"title":"A phylogenetic perspective of chromosome evolution in Formicidae.","authors":"Danon Clemes Cardoso, Maykon Passos Cristiano","doi":"10.1139/gen-2024-0124","DOIUrl":"10.1139/gen-2024-0124","url":null,"abstract":"Chromosomes, as carriers of genes, are the fundamental units of heredity, with the eukaryotic genome divided into multiple chromosomes. Each species typically has a consistent number of chromosomes within its lineage. Ants, however, display remarkable diversity in chromosome numbers, and previous studies have shown that this variation may correlate with ant diversity. As ants evolved, various karyotypes emerged, primarily through chromosomal fissions, leading to an increase in chromosome number and a decrease in chromosome size. In this study, we investigate chromosome evolution in ants from a phylogenetic perspective using ancestral reconstruction. Our analysis indicates that the most recent common ancestor of ants had an ancestral haploid chromosome number of 11, likely composed of biarmed chromosomes. The bimodal distribution of karyotypes and the trend toward increased chromosome numbers align with previous assumptions. However, both dysploidy and ploidy changes have been indicated as likely mechanisms of chromosome number evolution. Descending dysploidy occurs consistently throughout the phylogeny, while changes in ploidy are believed to occur occasionally within the subfamilies during genus diversification. We propose, based on our results and previous evidence (e.g., genome size in ants), that both fusions and fissions contribute equally to karyotype changes in Formicidae. Additionally, changes in ploidy should not be fully ignored, as they can occur across specific lineages.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142835349","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}

引用次数: 0

Chromosomal diversity in Crematogaster Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest. 亚马逊雨林中 Crematogaster Lund, 1831 (Formicidae: Myrmicinae) 的染色体多样性。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-09-03 DOI: 10.1139/gen-2023-0130

Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Abdala Dergam, Hilton Jeferson Alves Cardoso de Aguiar

{"title":"Chromosomal diversity in Crematogaster Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest.","authors":"Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Abdala Dergam, Hilton Jeferson Alves Cardoso de Aguiar","doi":"10.1139/gen-2023-0130","DOIUrl":"10.1139/gen-2023-0130","url":null,"abstract":"Crematogaster Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical Crematogaster, several taxonomical issues remain unresolved. While cytogenetic approaches can help to delimit species, cytogenetic data are only available for 18 taxa. In this study, classical and molecular cytogenetic analyses were performed on five Crematogaster species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2n = 22 chromosomes were observed in Crematogaster erecta Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. Crematogaster aff. erecta had 2n = 28, while Crematogaster limata Smith, 1858, Crematogaster tenuicula Forel, 1904, and Crematogaster sp. had 2n = 38. The telomeric motif (TTAGG) n was found in all five species, and the (TCAGG) n motif was detected in the telomeres of C. limata. This peculiar motif was also detected in the centromeric regions of C. erecta cytotype I. The microsatellite (GA) n was dispersed in the chromosomes of all species studied, which also had a single intrachromosomal rDNA site. The cytogenetic results revealed notable interspecific and intraspecific variation, which suggests different chromosomal rearrangements involved in the origin of these variations, also highlighting the taxonomic value of cytogenetic data on Crematogaster.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125506","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}

引用次数: 0

Asp/ASPM phospho-regulation throughout the cell cycle. Asp/ASPM在整个细胞周期中的磷酸化调控。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0111

Maria C Burns, Lori Borgal

{"title":"Asp/ASPM phospho-regulation throughout the cell cycle.","authors":"Maria C Burns, Lori Borgal","doi":"10.1139/gen-2024-0111","DOIUrl":"10.1139/gen-2024-0111","url":null,"abstract":"In mammals and Drosophila melanogaster, Asp/ASPM proteins contribute to cell proliferation and spindle formation. Recent evidence also suggests interphase roles for Asp/ASPM proteins, but little is known about the regulation allowing distinct roles in different cell cycle phases. In this review, we consider a cross-species comparison of Asp/ASPM protein sequences in light of cyclin-CDK literature, and suggest Asp/ASPM proteins to be prime candidates for cyclin-CDK regulation. Conserved regulatory features include an N-terminal proline directed serine/threonine (S/T-P) \"supershift\" phosphorylation domain common to proteins with bistable interphase and mitotic roles, as well as putative cyclin-binding sites positioned to allow multisite phosphorylation by cyclin-CDK complexes. Human, mouse, and Drosophila Asp/ASPM protein structural predictions show that multisite phosphorylation of the N-term supershift domain could alter the availability of CH-domains and HEAT-motifs, which can contribute to microtubule binding and protein aggregation likely required for spindle formation. Structural predictions of the smallest reported microcephaly patient truncation also emphasize the importance of the arrangement of these motifs. We position this in silico analysis within recent literature to build new hypotheses for Asp/ASPM regulation in interphase and mitosis, as well as de-regulation in microcephaly and cancer. We also highlight the utility of comparing structural/functional differences between human ASPM and Drosophila Asp to gain further insight.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545115","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}

引用次数: 0

Runs of homozygosity assessment using reduced representation sequencing highlight the evidence of random mating in emu (Dromaius novaehollandiae). 使用减少代表性测序的纯合子评估突出了鸸鹋（新荷兰Dromaius novaehollandiae）随机交配的证据。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-12-12 DOI: 10.1139/gen-2024-0084

Rangasai Chandra Goli, Karan Mahar, Kiyevi G Chishi, Sonu Choudhary, Pallavi Rathi, Chandana Chinnareddyvari Sree, Pala Haritha, Nidhi Sukhija, K K Kanaka

{"title":"Runs of homozygosity assessment using reduced representation sequencing highlight the evidence of random mating in emu (Dromaius novaehollandiae).","authors":"Rangasai Chandra Goli, Karan Mahar, Kiyevi G Chishi, Sonu Choudhary, Pallavi Rathi, Chandana Chinnareddyvari Sree, Pala Haritha, Nidhi Sukhija, K K Kanaka","doi":"10.1139/gen-2024-0084","DOIUrl":"10.1139/gen-2024-0084","url":null,"abstract":"The domestication of emu (Dromaius novaehollandiae) began in the 1970s, but their productive characteristics have not undergone significant genetic enhancement. This study investigated the inbreeding and genetic diversity of 50 emus from various farms in Japan using Double digest restriction-site associated DNA sequencing (ddRAD-seq) markers. Single nucleotide polymorphism (SNP) calling revealed 171 975 high-quality SNPs while runs of homozygosity (ROH) analysis identified 1843 homozygous segments, with an average of 36.86 ROH per individual and a mean genome length of 27 Mb under ROH. The majority (86%) of ROH were short (0.5-1 Mb), indicating ancient or remote inbreeding. The average genomic inbreeding coefficient (FROH) was 0.0228, suggesting nearly no inbreeding. Overlapping ROH regions were identified, with top consensus regions found on chromosomes 8 and Z. Seven candidate genes related to egg production, feather development, and energy metabolism were annotated in these regions. The findings highlight the prevalence of genetic diversity and low inbreeding levels in the studied emu population. This research highlights the potentiality of random mating in genetic management and conservation of emus. Further studies should focus on enhancing productive traits through selective breeding while preserving genetic diversity to ensure the sustainable growth of the emu farming.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-8"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817788","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}

引用次数: 0

Comparative satellite DNA mapping in species of the genus Prochilodus (Teleostei, Characiformes) and its evolutionary implications. Prochilodus属（Teleostei，Characiformes）物种的卫星DNA比较图谱及其进化意义。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0085

Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, José Henrique Forte Stornioli, Francisco de Menezes Cavalcante Sassi, Renata Luiza Rosa de Moraes, Jorge Abdala Dergam, Fábio Porto-Foresti, Marcelo de Bello Cioffi, Ricardo Utsunomia

{"title":"Comparative satellite DNA mapping in species of the genus Prochilodus (Teleostei, Characiformes) and its evolutionary implications.","authors":"Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, José Henrique Forte Stornioli, Francisco de Menezes Cavalcante Sassi, Renata Luiza Rosa de Moraes, Jorge Abdala Dergam, Fábio Porto-Foresti, Marcelo de Bello Cioffi, Ricardo Utsunomia","doi":"10.1139/gen-2024-0085","DOIUrl":"10.1139/gen-2024-0085","url":null,"abstract":"Satellite DNA (satDNA) sequences are dynamic components of the eukaryotic genome that can play significant roles in species diversification. The Prochilodontidae family, which includes 21 Neotropical fish species, is characterized by a conserved karyotype of 2n = 54 biarmed chromosomes, with variation in some species and populations regarding the presence or absence of B chromosomes. This study aimed to investigate whether the chromosomal distribution of specific satDNA sequences is conserved among three Prochilodus species (Prochilodus lineatus, Prochilodus costatus, and Prochilodus argenteus) regarding organization and number of loci, and to compare their genomes using comparative genomic hybridization (CGH). Our results demonstrated that most satDNA sequences share a similar distribution pattern across the three species, and CGH analysis corroborated that their karyotypes are very similar in terms of repetitive DNA distribution. We also identified a potential CENP-B box sequence within PliSat01, a satDNA located in the pericentromeric region of all analyzed species. In contrast, PliSat04 and PliSat14 displayed differential locations and variations in the number of loci per genome, underscoring the dynamic nature of repetitive sequences even in species with otherwise highly conserved genomes. These findings represent the first evidence of karyotype diversification in Prochilodus, highlighting the evolutionary dynamism of satDNA sequences.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-8"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545116","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}

引用次数: 0

Uncovering the complexity of structural variants in four individuals with autism spectrum disorder. 揭示四名自闭症谱系障碍患者结构变异的复杂性。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-12-12 DOI: 10.1139/gen-2024-0121

Sarah Dada, Katherine Dixon, Vahid Akbari, Cameron J Grisdale, Kristina Calli, Sally Martell, Caralyn Reisle, Amanda Lillico-Ouachour, M E Suzanne Lewis, Steven J M Jones

{"title":"Uncovering the complexity of structural variants in four individuals with autism spectrum disorder.","authors":"Sarah Dada, Katherine Dixon, Vahid Akbari, Cameron J Grisdale, Kristina Calli, Sally Martell, Caralyn Reisle, Amanda Lillico-Ouachour, M E Suzanne Lewis, Steven J M Jones","doi":"10.1139/gen-2024-0121","DOIUrl":"10.1139/gen-2024-0121","url":null,"abstract":"Autism spectrum disorder (ASD) is an increasingly recognized childhood developmental disorder. Despite extensive study, causal variants and molecular diagnosis remain elusive. There is both heterogeneity of the phenotype, as well as the genetic landscape associated with phenotype, which includes both inherited and de novo mutations. Currently, diagnosis is complex and behaviourally based, oftentimes occurring years after the ideal 1-2 years of age. Structural variants (SVs) are large and sometimes complex genomic variants that are likely underrepresented contributors to ASD due to the limitations of short-read DNA sequencing, such as alignment in repetitive regions and regions with GC bias. Here, we performed long-read sequencing (LRS) on four individuals with autism spectrum disorder to delineate SV complexity and determine precise breakpoints for SVs, which was not possible with short-read whole-genome sequencing (SRS). We use LRS to interrogate the methylation pattern associated with the SVs and phase the SV haplotypes to further clarify their contribution to disorder. LRS allows insight into the genome and methylome that allow us to uncover variant complexity and contribution that was previously unseen with SRS. Ultimately, this furthers precision diagnosis and contributes to individualized treatment for affected individuals and their families within the clinic.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-8"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817789","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}

引用次数: 0

Note of appreciation. 表示感谢。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0172

引用次数: 0

Epigenetic factors related to recalcitrance in plant biotechnology. 植物生物技术中与顽抗有关的表观遗传因素。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0098

Mohsen Hesami, Marco Pepe, Ben Spitzer-Rimon, Milad Eskandari, Andrew Maxwell Phineas Jones

引用次数: 0

Plant immune resilience to a changing climate: molecular insights and biotechnological roadmaps. 植物对气候变化的免疫复原力：分子见解和生物技术路线图。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-11-05 DOI: 10.1139/gen-2024-0088

Christian Danve M Castroverde, Chi Kuan, Jong Hum Kim

{"title":"Plant immune resilience to a changing climate: molecular insights and biotechnological roadmaps.","authors":"Christian Danve M Castroverde, Chi Kuan, Jong Hum Kim","doi":"10.1139/gen-2024-0088","DOIUrl":"10.1139/gen-2024-0088","url":null,"abstract":"Successful resistance to disease-causing pathogens is underpinned by properly regulated immune signalling and defence responses in plants. The plant immune system is controlled at multiple levels of gene and protein regulation-from chromatin-associated epigenetic processes to protein post-translational modifications. Optimal fine-tuning of plant immune signalling and responses is important to prevent plant disease development, which is being exacerbated by a globally changing climate. In this review, we focus on how changing climatic factors mechanistically intercept plant immunity at different levels of regulation (chromatin, transcriptional, post-transcriptional, translational, and post-translational). We specifically highlight recent studies that have provided molecular insights into critically important climate-sensitive nodes and mechanisms of the plant immune system. We then propose several potential future directions to build climate-resilient plant disease resistance using cutting-edge biotechnology. Overall, this conceptual understanding and promising biotechnological advances provide a foundational platform towards novel approaches to engineer plant immune resilience.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581766","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}

引用次数: 0

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