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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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

Comparative analysis of the diversity of trinucleotide repeats in bacterial genomes. 细菌基因组中三核苷酸重复序列多样性的比较分析。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-09 DOI: 10.1139/gen-2023-0097

Bobby Paul, S. Siddaramappa

{"title":"Comparative analysis of the diversity of trinucleotide repeats in bacterial genomes.","authors":"Bobby Paul, S. Siddaramappa","doi":"10.1139/gen-2023-0097","DOIUrl":"https://doi.org/10.1139/gen-2023-0097","url":null,"abstract":"The human gut is the most favorable niche for microbial populations, and few studies have explored the possibilities of horizontal gene transfer between host and pathogen. Trinucleotide repeat (TNR) expansion in humans can cause more than 40 neurodegenerative diseases. Furthermore, TNRs are a type of microsatellite that resides on coding regions can contribute to the synthesis of homopolymeric amino acids. Hence, the present study aims to estimate the occurrence and diversity of TNRs in bacterial genomes available in the NCBI Genome database. Genome-wide analyses revealed that several bacterial genomes contain different types of uninterrupted TNRs. It was found that TNRs are abundant in the genomes of Alcaligenes faecalis, Mycoplasma gallisepticum, Mycoplasma genitalium, Sorangium cellulosum, and Thermus thermophilus. Interestingly, the genome of Bacillus thuringiensis strain YBT-1518 contained 169 uninterrupted ATT repeats. The genome of Leclercia adecarboxylata had 46 uninterrupted CAG repeats, which potentially translate into polyglutamine. In some instances, the TNRs were present in genes that potentially encode essential functions. Similar occurrences in human genes is known to cause genetic disorders. Further analysis of the occurrence of TNRs in bacterial genomes is likely to provide a better understanding of mismatch repair, genetic disorders, host-pathogen interaction, and homopolymeric amino acids.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140722567","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 organization of different repetitive sequences in four wasp species of the genus Trypoxylon Latreille (Hymenoptera: Crabronidae) and insights into the composition of wasp telomeres. Trypoxylon Latreille 属（膜翅目：螃蟹科）四种黄蜂不同重复序列的染色体组织以及对黄蜂端粒组成的见解。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-09 DOI: 10.1139/gen-2023-0132

G. Teixeira, N. Travenzoli, M. G. Tavares

{"title":"Chromosomal organization of different repetitive sequences in four wasp species of the genus Trypoxylon Latreille (Hymenoptera: Crabronidae) and insights into the composition of wasp telomeres.","authors":"G. Teixeira, N. Travenzoli, M. G. Tavares","doi":"10.1139/gen-2023-0132","DOIUrl":"https://doi.org/10.1139/gen-2023-0132","url":null,"abstract":"This study characterizes the chromosomal organization of DNA repetitive sequences and the karyotypic evolution in four representatives of the solitary wasp genus Trypoxylon using conventional and molecular cytogenetic techniques. Our findings present the first cytogenetic data for T. rogenhoferi (2n=30) and T. albonigrum (2n=32) while the karyotypes of T. nitidum (2n=30) and T. lactitarse (2n=30) were similar to those described previously. Fluorochrome staining and microsatellite distribution data revealed differences in the constitutive heterochromatin composition among species. Trypoxylon nitidum and T. albonigrum exhibited a single rRNA gene site, potentially representing an ancestral pattern for aculeate Hymenoptera, while T. rogenhoferi and T. lactitarse showed two pericentromeric rRNA gene sites, suggesting amplification events in their ancestral clade. The (TCAGG)n motif hybridized in the terminal regions of the chromosomes in all four Trypoxylon species, which may suggest that this sequence is part of their telomeres. Notably, the presence of this repetitive sequence in the centromeric regions of certain chromosome pairs in two species supports the hypothesis of chromosomal fusions or inversions in the ancestral karyotype of Trypoxylon. The study expands the chromosomal mapping data of repetitive sequences in wasps and offers insights into the dynamic evolutionary landscape of karyotypes in these insects.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140722210","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

Chloroplast genome of Ecbolium viride: Plastome evolution and Phylogenomics of Justiceae (Acanthaceae, Acanthoideae). Ecbolium viride 的叶绿体基因组：爵床科（Acanthaceae，Acanthoideae）的质体进化和系统发生组学。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-09 DOI: 10.1139/gen-2024-0020

S. Yaradua, K. Yessoufou

{"title":"Chloroplast genome of Ecbolium viride: Plastome evolution and Phylogenomics of Justiceae (Acanthaceae, Acanthoideae).","authors":"S. Yaradua, K. Yessoufou","doi":"10.1139/gen-2024-0020","DOIUrl":"https://doi.org/10.1139/gen-2024-0020","url":null,"abstract":"Justicieae is the most taxonomically complex tribe in Acanthaceae. Here, we sequenced the plastome of Ecbolium viride, a medicinally important species. The genome was analyzed with previously reported plastome of Justiceae. The plastome of E. viride has quadripartite structure with a length of 151, 185 bp. The comparative genomic analyses revealed no structural inversion in Justiceae and some regions (rpoC2, ycf2, ycf1 and ndhH rps16-trnQ-UGG, and trnL-CAA-ycf15) exhibiting a significant level of nucleotide divergence. The positive selection analyses revealed that some species in the tribe have undergone adaptive evolution. The visualization of the boundaries between the single copy and inverted repeat regions revealed that Justiceae chloroplast genome experienced some levels of variation which give an insight into the evolution of the species. The longest genome was in the earliest diverged taxa of the tribe P. haikangense and from this genome, a series of contraction and expansion occurred contributing to the evolution of other lineages. The plastome-based phylogeny revealed and confirmed the monophyly of Justiceae, polyphyly of Justicia and supported the tribal classification Graptophyllinae, Tetrameriinae, Isoglossinae. We proposed that Declipterinae should be treated as subtribe and the status of Justiciinae can only be confirmed after the resolution of the polyphyletic Justicia.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140726598","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

"DNA at the whim of the water": Environmental DNA as a course-based undergraduate research experience. "DNA随心所欲"：环境 DNA 作为基于课程的本科生研究体验。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-09 DOI: 10.1139/gen-2023-0102

Kathleen P. Nolan, Daniel Z. Grunspan, Erika Myler, Nava Brimble, Andreas Heyland, Robert H. Hanner

{"title":"\"DNA at the whim of the water\": Environmental DNA as a course-based undergraduate research experience.","authors":"Kathleen P. Nolan, Daniel Z. Grunspan, Erika Myler, Nava Brimble, Andreas Heyland, Robert H. Hanner","doi":"10.1139/gen-2023-0102","DOIUrl":"https://doi.org/10.1139/gen-2023-0102","url":null,"abstract":"Course-based undergraduate research experiences (CUREs) increase student access to high impact research experiences. CUREs engage students in the scientific process by learning how to pose scientific questions, develop hypotheses, and generate data to test them. Environmental DNA (eDNA), is a growing field of research that is gaining accessibility through decreasing laboratory costs, which can make a foundation for multiple, engaging CUREs. This manuscript describes three case studies that used eDNA in an upper year undergraduate course. The first focusses on a systematic literature review of eDNA metadata reporting. The second describes the biomonitoring of brook trout in southern Ontario using eDNA. The third involves eDNA metabarcoding for freshwater fish detection in southern Ontario. Undergraduates were involved in the development and execution of experiments, scientific communication, the peer review process, and fundraising. Through this manuscript, we show the novel application of eDNA CUREs and provide a roadmap for other instructors interested in implementing similar projects. Interviews with seven students from these courses indicate the benefits experienced from taking these courses. We argue that the use of eDNA in CUREs should be expanded in undergraduate biology programs due to the benefit to students and the increasing accessibility of this technology.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140725843","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

Genomic regions associated with coat color in Gir cattle. 与吉尔牛毛色相关的基因组区域。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-05 DOI: 10.1139/gen-2023-0115

Silel Vinicius Simões Andrade Maciel, Ingrid Pereira Pinto Oliveira, B. B. Senes, J. A. V. Vasconcelos Silva, Fabieli Loise Braga Feitosa, J. S. Alves, Raphael Bermal Costa, Gregorio Camargo

{"title":"Genomic regions associated with coat color in Gir cattle.","authors":"Silel Vinicius Simões Andrade Maciel, Ingrid Pereira Pinto Oliveira, B. B. Senes, J. A. V. Vasconcelos Silva, Fabieli Loise Braga Feitosa, J. S. Alves, Raphael Bermal Costa, Gregorio Camargo","doi":"10.1139/gen-2023-0115","DOIUrl":"https://doi.org/10.1139/gen-2023-0115","url":null,"abstract":"Indicine cattle breeds are adapted to the tropical climate and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies in order to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140737508","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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