IF 3.1 3区生物学

Genome Pub Date : 2024-06-01 Epub Date: 2024-02-12 DOI: 10.1139/gen-2023-0101

Rafael Kretschmer, Marcelo Santos de Souza, Ricardo José Gunski, Analía Del Valle Garnero, Thales Renato Ochotorena de Freitas, Edison Zefa, Gustavo Akira Toma, Marcelo de Bello Cioffi, Edivaldo Herculano Corrêa de Oliveira, Rebecca E O'Connor, Darren K Griffin

{"title":"Understanding the chromosomal evolution in cuckoos (Aves, Cuculiformes): a journey through unusual rearrangements.","authors":"Rafael Kretschmer, Marcelo Santos de Souza, Ricardo José Gunski, Analía Del Valle Garnero, Thales Renato Ochotorena de Freitas, Edison Zefa, Gustavo Akira Toma, Marcelo de Bello Cioffi, Edivaldo Herculano Corrêa de Oliveira, Rebecca E O'Connor, Darren K Griffin","doi":"10.1139/gen-2023-0101","DOIUrl":"10.1139/gen-2023-0101","url":null,"abstract":"The Cuculiformes are a family of over 150 species that live in a range of habitats, such as forests, savannas, and deserts. Here, bacterial artificial chromosome (BAC) probes (75 from chicken and 14 from zebra finch macrochromosomes 1-10 +ZW and for microchromosomes 11-28 (except 16)) were used to investigate chromosome homologies between chicken and the squirrel cuckoo (Piaya cayana). In addition, repetitive DNA probes were applied to characterize the chromosome organization and to explore the role of these sequences in the karyotype evolution of P. cayana. We also applied BAC probes for chicken chromosome 17 and Z to the guira cuckoo (Guira guira) to test whether this species has an unusual Robertsonian translocation between a microchromosome and the Z chromosome, recently described in the smooth-billed ani (Crotophaga ani). Our results revealed extensive chromosome reorganization with inter- and intrachromosomal rearrangements in P. cayana, including a conspicuous chromosome size and heterochromatin polymorphism on chromosome pair 20. Furthermore, we confirmed that the Z-autosome Robertsonian translocation found in C. ani is also found in G. guira, not P. cayana. These findings suggest that this translocation occurred prior to the divergence between C. ani and G. guira, but after the divergence with P. cayana.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"168-177"},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139722300","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

Meta-analyses of the global multilocus genotypes of the human pathogen Campylobacter jejuni. 人类病原体空肠弯曲杆菌全球多焦点基因型的元分析。

IF 2.3 3区生物学

Genome Pub Date : 2024-06-01 Epub Date: 2024-03-01 DOI: 10.1139/gen-2023-0041

Monir Poorrashidi, Megan Hitchcock, Jianping Xu

{"title":"Meta-analyses of the global multilocus genotypes of the human pathogen Campylobacter jejuni.","authors":"Monir Poorrashidi, Megan Hitchcock, Jianping Xu","doi":"10.1139/gen-2023-0041","DOIUrl":"10.1139/gen-2023-0041","url":null,"abstract":"Campylobacter infections are a leading cause of bacterial diarrheal illness worldwide, with increasing reports of outbreaks in both developing and developed countries. Most studies investigating strain genotypes and epidemiology of Campylobacter jejuni examined on a local scale. Using the archived multilocus sequence typing data at seven loci, and associated strain metadata from the PubMLST database, here we investigated the spatial and temporal genetic structure of the global population of C. jejuni. Our analyses revealed evidence for clonal dispersals of multiple sequence types (STs) among countries and continents. However, despite the observed clonal dispersal and that most genetic variations were found within individual geographic subpopulations, both the non-clone-corrected and clone-corrected samples showed evidence of significant genetic differentiation among national and continental subpopulations, with non-clone-corrected samples showing greater differentiation than clone-corrected samples. Phylogenetic incompatibility analyses provided evidence for recombination within each continental subpopulation. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across the samples. Temporally, multiple STs were found to persist across four decades and the five globally most common STs showed relatively stable frequencies over the last two decades. We discussed the implications of our results to food security, disease transmission, and public health management.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"189-203"},"PeriodicalIF":2.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012466","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

Development and application of whole-chromosome painting of chromosomes 7A and 8A of Arachis duranensis based on chromosome-specific single-copy oligonucleotides. 基于染色体特异性单拷贝寡核苷酸的杜兰花7A和8A染色体全染色体涂片的开发与应用

IF 3.1 3区生物学

Genome Pub Date : 2024-06-01 Epub Date: 2024-02-23 DOI: 10.1139/gen-2023-0116

Chenyu Li, Liuyang Fu, Qian Wang, Hua Liu, Guoquan Chen, Feiyan Qi, Maoning Zhang, Yaoguang Jia, Xiaona Li, Bingyan Huang, Wenzhao Dong, Pei Du, Xinyou Zhang

{"title":"Development and application of whole-chromosome painting of chromosomes 7A and 8A of Arachis duranensis based on chromosome-specific single-copy oligonucleotides.","authors":"Chenyu Li, Liuyang Fu, Qian Wang, Hua Liu, Guoquan Chen, Feiyan Qi, Maoning Zhang, Yaoguang Jia, Xiaona Li, Bingyan Huang, Wenzhao Dong, Pei Du, Xinyou Zhang","doi":"10.1139/gen-2023-0116","DOIUrl":"10.1139/gen-2023-0116","url":null,"abstract":"For peanut, the lack of stable cytological markers is a barrier to tracking specific chromosomes, elucidating the genetic relationships between genomes and identifying chromosomal variations. Chromosome mapping using single-copy oligonucleotide (oligo) probe libraries has unique advantages for identifying homologous chromosomes and chromosomal rearrangements. In this study, we developed two whole-chromosome single-copy oligo probe libraries, LS-7A and LS-8A, based on the reference genome sequences of chromosomes 7A and 8A of Arachis duranensis. Fluorescence in situ hybridization (FISH) analysis confirmed that the libraries could specifically paint chromosomes 7 and 8. In addition, sequential FISH and electronic localization of LS-7A and LS-8A in A. duranensis (AA) and A. ipaensis (BB) showed that chromosomes 7A and 8A contained translocations and inversions relative to chromosomes 7B and 8B. Analysis of the chromosomes of wild Arachis species using LS-8A confirmed that this library could accurately and effectively identify A genome species. Finally, LS-7A and LS-8A were used to paint the chromosomes of interspecific hybrids and their progenies, which verified the authenticity of the interspecific hybrids and identified a disomic addition line. This study provides a model for developing specific oligo probes to identify the structural variations of other chromosomes in Arachis and demonstrates the practical utility of LS-7A and LS-8A.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"178-188"},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139939909","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

Diversity and antigenic potentials of Mycoplasmopsis bovis secreted and outer membrane proteins within a core genome of strains isolated from North American bison and cattle. 从北美野牛和牛身上分离出的菌株的核心基因组内牛支原体分泌蛋白和外膜蛋白的多样性和抗原潜能。

IF 3.1 3区生物学

Genome Pub Date : 2024-06-01 Epub Date: 2024-02-08 DOI: 10.1139/gen-2023-0084

Emily L Wynn, A Springer Browne, Michael L Clawson

{"title":"Diversity and antigenic potentials of Mycoplasmopsis bovis secreted and outer membrane proteins within a core genome of strains isolated from North American bison and cattle.","authors":"Emily L Wynn, A Springer Browne, Michael L Clawson","doi":"10.1139/gen-2023-0084","DOIUrl":"10.1139/gen-2023-0084","url":null,"abstract":"Mycoplasmopsis bovis is a worldwide economically important pathogen of cattle that can cause or indirectly contribute to bovine respiratory disease. M. bovis is also a primary etiological agent of respiratory disease in bison with high mortality rates. A major challenge in the development of an efficacious M. bovis vaccine is the design of antigens that contain both MHC-1 and MHC-2 T-cell epitopes, and that account for population level diversity within the species. Publicly available genomes and sequence read archive libraries of 381 M. bovis strains isolated from cattle (n = 202) and bison (n = 179) in North America were used to identify a core genome of 575 genes, including 38 that encode either known or predicted secreted or outer membrane proteins. The antigenic potentials of the proteins were characterized by the presence and strength of their T-cell epitopes, and their protein variant diversity at the population-level. The proteins had surprisingly low diversity and varying predictive levels of T-cell antigenicity. These results provide a reference for the selection or design of antigens for vaccine testing against strains infecting North American cattle and bison.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"204-209"},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139706516","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

Variant functional assessment in Drosophila by overexpression: what can we learn? 通过过表达评估果蝇的变异功能：我们能学到什么？

IF 2.3 3区生物学

Genome Pub Date : 2024-06-01 Epub Date: 2024-02-27 DOI: 10.1139/gen-2023-0135

Yina Her, Danielle M Pascual, Zoe Goldstone-Joubert, Paul C Marcogliese

引用次数: 0

Should I shrink or should I grow: cell size changes in tissue morphogenesis. 我应该缩小还是生长：组织形态发生过程中的细胞大小变化

IF 3.1 3区生物学

Genome Pub Date : 2024-05-01 Epub Date: 2024-01-10 DOI: 10.1139/gen-2023-0091

Gordana Scepanovic, Rodrigo Fernandez-Gonzalez

引用次数: 0

Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus. 黄曲霉菌株的有丝分裂基因组进化：为了更好地理解区分菌属。

IF 3.1 3区生物学

Genome Pub Date : 2024-05-01 Epub Date: 2023-12-20 DOI: 10.1139/gen-2022-0092

Evrim Özkale, Özgül Doğan, Mahir Budak, Ertan Mahir Korkmaz

{"title":"Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus.","authors":"Evrim Özkale, Özgül Doğan, Mahir Budak, Ertan Mahir Korkmaz","doi":"10.1139/gen-2022-0092","DOIUrl":"10.1139/gen-2022-0092","url":null,"abstract":"Trichoderma afroharzianum (Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"139-150"},"PeriodicalIF":3.1,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138829302","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

Conventional cytogenetics and microsatellite chromosomal distribution in social wasp Mischocyttarus cassununga (Ihering, 1903) (Vespidae, Polistinae, Mischocyttarini). 社会黄蜂 Mischocyttarus cassununga (Ihering, 1903) （蝶形目，波利斯蝶科，Mischocyttarini）的常规细胞遗传学和微卫星染色体分布。

IF 3.1 3区生物学

Genome Pub Date : 2024-05-01 Epub Date: 2024-01-23 DOI: 10.1139/gen-2023-0026

Camila Moura Novaes, Gisele Amaro Teixeira, Eydyeliana Month Juris, Denilce Meneses Lopes

{"title":"Conventional cytogenetics and microsatellite chromosomal distribution in social wasp Mischocyttarus cassununga (Ihering, 1903) (Vespidae, Polistinae, Mischocyttarini).","authors":"Camila Moura Novaes, Gisele Amaro Teixeira, Eydyeliana Month Juris, Denilce Meneses Lopes","doi":"10.1139/gen-2023-0026","DOIUrl":"10.1139/gen-2023-0026","url":null,"abstract":"Cytogenetics has allowed the investigation of chromosomal diversity and repetitive genomic content in wasps. In this study, we characterized the karyotype of the social wasp Mischocyttarus cassununga using conventional cytogenetics and chromosomal mapping of repetitive sequences. This study was undertaken to extend our understanding of the genomic organization of repetitive DNA in social wasps and is the first molecular cytogenetic insight into the genus Mischocyttarus. The karyotype of M. cassununga had a chromosome number of 2n = 64 for females and n = 32 for males. Constitutive heterochromatin exhibited three distribution patterns: centromeric and pericentromeric regions along the smaller arms and extending almost the entire chromosome. The major ribosomal DNA sites were located on chromosome pair in females and one chromosome in males. Positive signals for the microsatellite probes (GA)n and (GAG)n were observed in the euchromatic regions of all chromosomes. The microsatellites, (CGG)n, (TAT)n, (TTAGG)n, and (TCAGG)n were not observed in any region of the chromosomes. Our results contrast with those previously obtained for Polybia fastidiosuscula, which showed that the microsatellites (GAG)n, (CGG)n, (TAT)n, (TTAGG)n, and (TCAGG)n are located predominantly in constitutive heterochromatin. This suggests variations in the diversity and chromosomal organization of repetitive sequences in the genomes of social wasps.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"151-157"},"PeriodicalIF":3.1,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139542167","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

Development of EST-SSR markers in Bergenia ciliata using de novo transcriptome sequencing. 利用全新转录组测序技术开发纤毛虫 EST-SSR 标记。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-01 Epub Date: 2023-12-13 DOI: 10.1139/gen-2023-0059

Harish Chandra Singh, Vandana Tiwari, Avinash Tiwari, Tikam S Rana

{"title":"Development of EST-SSR markers in Bergenia ciliata using de novo transcriptome sequencing.","authors":"Harish Chandra Singh, Vandana Tiwari, Avinash Tiwari, Tikam S Rana","doi":"10.1139/gen-2023-0059","DOIUrl":"10.1139/gen-2023-0059","url":null,"abstract":"Bergenia ciliata (Haw.) Sternb. is an important herb predominantly found in the Indian Himalayan Region. It is widely used in medicines, healthcare systems, cosmetics, fodder, and ornamental purposes. The Illumina sequencing and de novo transcriptome assembly were carried out in B. ciliata to develop and identify simple sequence repeat markers. A total of 18 226 simple sequence repeats (SSRs) were identified wherein di-nucleotides were found to be abundant (47.88%), followed by mono-nucleotide (35.03%) and tri-nucleotide (15.88%) repeats. A total of 11 839 EST-SSR primers were designed, of which 96 primer pairs were commercially synthesized. Finally, 17 primer pairs revealed clear, distinct polymorphic bands, and these primers were validated with 40 diverse B. ciliata accessions. The present study revealed moderate level of genetic diversity (Ho = 0.389, He = 0.542, and PIC = 0.513). Furthermore, the transcriptome data and EST-SSR markers generated during the present investigation could be an important genetic resource for functional genomics, population studies, and conservation genetics of the genus Bergenia.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"119-124"},"PeriodicalIF":3.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138802843","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

Gene regulation supporting sociality shared across lineages and variation in complexity. 支持跨血统社会性的基因调控和复杂性差异。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-01 Epub Date: 2023-12-14 DOI: 10.1139/gen-2023-0054

Benjamin C Pyenson, Sandra M Rehan

{"title":"Gene regulation supporting sociality shared across lineages and variation in complexity.","authors":"Benjamin C Pyenson, Sandra M Rehan","doi":"10.1139/gen-2023-0054","DOIUrl":"10.1139/gen-2023-0054","url":null,"abstract":"Across evolutionary lineages, insects vary in social complexity, from those that exhibit extended parental care to those with elaborate divisions of labor. Here, we synthesize the sociogenomic resources from hundreds of species to describe common gene regulatory mechanisms in insects that regulate social organization across phylogeny and levels of social complexity. Different social phenotypes expressed by insects can be linked to the organization of co-expressing gene networks and features of the epigenetic landscape. Insect sociality also stems from processes like the emergence of parental care and the decoupling of ancestral genetic programs. One underexplored avenue is how variation in a group's social environment affects the gene expression of individuals. Additionally, an experimental reduction of gene expression would demonstrate how the activity of specific genes contributes to insect social phenotypes. While tissue specificity provides greater localization of the gene expression underlying social complexity, emerging transcriptomic analysis of insect brains at the cellular level provides even greater resolution to understand the molecular basis of social insect evolution.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"99-108"},"PeriodicalIF":3.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138802844","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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