IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0031

Nathaniel T Marshall, Daniel E Symonds, W Cody Fleece

{"title":"Environmental DNA detection of the male mitochondrial genome of freshwater mussels (Unionidae).","authors":"Nathaniel T Marshall, Daniel E Symonds, W Cody Fleece","doi":"10.1139/gen-2024-0031","DOIUrl":"https://doi.org/10.1139/gen-2024-0031","url":null,"abstract":"Environmental DNA (eDNA) has shown promise for the detection of threatened and endangered species and has been implemented for monitoring aquatic spawning events. Freshwater unionid mussels exhibit a rare form of mitochondrial inheritance, in which males possess a unique mitochondrial mitotype that is divergent from the female mitotype. As freshwater mussels are spermcasters, the detection of male mitotype eDNA may provide critical conservation information related to timing of sperm release. This study re-purposed an existing eDNA metabarcoding dataset to detail the unique detection of eDNA pertaining to the male mitotype. Water samples collected alongside an extensive mussel salvage within the Walhonding River, Ohio, detected 16 distinct male mitotypes. However, several constraints limit the proper interpretation of these detections. There is currently a lack of reporting on assay compatibility with the male mitotype within freshwater mussel eDNA literature. Reference genetic databases are critically lacking, with only four of the 16 male eDNA sequences in this study able to be discerned to a species. This study highlights the importance of detailing these detections as the unique inheritance system provides opportunities to document difficult to record spawning behaviors, and eDNA may be employed as a survey tool to evaluate patterns of metapopulation geneflow.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-17"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011200","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

Chromosome identification of Medicago polymorpha by oligonucleotide-based FISH. 多形紫花苜蓿染色体的寡核苷酸FISH鉴定。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0136

Min Cheng, Jia Xu, Ying Li, Yaling Jian, Feng Yu

{"title":"Chromosome identification of Medicago polymorpha by oligonucleotide-based FISH.","authors":"Min Cheng, Jia Xu, Ying Li, Yaling Jian, Feng Yu","doi":"10.1139/gen-2024-0136","DOIUrl":"10.1139/gen-2024-0136","url":null,"abstract":"Medicago polymorpha (2n = 2x = 14) is a valuable forage legume, but the identification of its somatic chromosomes has been challenging due to a lack of distinctive chromosome morphological features. With appropriate probes, oligonucleotide-based FISH is a highly effective method for chromosome identification. However, there are no available probes for M. polymorpha. In this study, we isolated five tandem repeats from the M. polymorpha genome, named Mp51, Mp139, Mp167, Mp179, and Mp497. Mp51 showed two pairs of signals located at the pericentromere. Mp139 exhibited four pairs of signals, located at the pericentromere and short arm of chromosomes. Mp167 and Mp179 showed seven pairs of signals, respectively, concentrated in the pericentromere. Mp497 exhibited three pairs of signals, distributed across the pericentromere and proximal position of the chromosomes. The combined FISH results of Mp51 and Mp139 oligo probes with 5S rDNA and 18S-26S rDNA probes demonstrated distinct signal patterns for each chromosome, enabling the precise identification of all chromosome pairs. Finally, the visual identification of M. polymorpha chromosomes was resolved. This will provide useful cytological information for studying the chromosomal structure and behavior of M. polymorpha.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","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":"143515477","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

The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape. 好战大黄蜂（Bombus bellicosus，膜翅目：蜂科）的核和线粒体基因组，在不断变化的南美景观中受到威胁的传粉者。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0166

Leonardo Tresoldi Gonçalves, Pedro Henrique Pezzi, Flávia Regina Girardi Montagner, Wellington Vasconcelos de Souza, Elaine Françoso, Maríndia Deprá

{"title":"The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape.","authors":"Leonardo Tresoldi Gonçalves, Pedro Henrique Pezzi, Flávia Regina Girardi Montagner, Wellington Vasconcelos de Souza, Elaine Françoso, Maríndia Deprá","doi":"10.1139/gen-2024-0166","DOIUrl":"10.1139/gen-2024-0166","url":null,"abstract":"We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (Bombus pascuorum). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees that suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.","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":"143398740","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

Evolutionary speed of proteins in the genus Staphylococcus: a focus on proteins involved in natural competence. 葡萄球菌属蛋白质的进化速度：对参与自然能力的蛋白质的关注。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0134

Antony T Vincent

引用次数: 0

Single-locus species delimitation of Pronophilina butterflies (Nymphalidae: Satyrini) in the Colombian Andes: congruence between morphology and MOTUs. 哥伦比亚安第斯地区斑蝶（蛱蝶科：蛱蝶）的单位点物种划分：形态与MOTUs的一致性。

IF 1.7 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0041

Keyner Moreno-Torres, Carlos Prieto, Tomasz W Pyrcz

{"title":"Single-locus species delimitation of Pronophilina butterflies (Nymphalidae: Satyrini) in the Colombian Andes: congruence between morphology and MOTUs.","authors":"Keyner Moreno-Torres, Carlos Prieto, Tomasz W Pyrcz","doi":"10.1139/gen-2025-0041","DOIUrl":"10.1139/gen-2025-0041","url":null,"abstract":"The subtribe Pronophilina (Nymphalidae: Satyrinae: Satyrini) is one of the most diverse subtribes within the Lepidoptera. In Colombia, these butterflies are distributed throughout the Andes, where they play a key role in montane ecosystems and exhibit high levels of endemism. Despite their complex genital morphology, species within the same genus often exhibit highly similar wing patterns, complicating taxonomic identification. In this study, we analyzed the concordance between DNA barcode-based species delimitation and morphological identifications using 334 cytochrome c oxidase subunit I barcodes from 94 a priori identified morphospecies in Colombia. We applied four molecular species delimitation methods (Automatic Barcode Gap Discovery, Refined Single Linkage, Poisson Tree Processes, and Assemble Species by Automatic Partitioning), delimitating between 98 and 108 molecular operational taxonomic units. Overall, the methods showed high consistency, with high congruence between morphological and molecular delimitations (81%). Additionally, 96.8% of the morphospecies exhibited a barcode gap, indicating clear genetic differentiation. However, we found some inconsistencies, including 6 cases of species merging and 12 cases of species splitting. Our findings underscore the utility of DNA barcoding for species delimitation in Pronophilina, while highlighting the need for integrative approaches to resolve taxonomic uncertainties in this diverse group.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-11"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591123","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

Empowering canine genomics: design and validation of a high-density SNP array for Indian dogs. 授权犬基因组学：印度犬高密度SNP阵列的设计和验证。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0094

Raja Kolandanoor Nachiappan, Reena Arora, Ramesh Kumar Vijh, Upasna Sharma, Meenal Raheja, Manisha Sharma, Mehak Maggon, Sonika Ahlawat

{"title":"Empowering canine genomics: design and validation of a high-density SNP array for Indian dogs.","authors":"Raja Kolandanoor Nachiappan, Reena Arora, Ramesh Kumar Vijh, Upasna Sharma, Meenal Raheja, Manisha Sharma, Mehak Maggon, Sonika Ahlawat","doi":"10.1139/gen-2024-0094","DOIUrl":"10.1139/gen-2024-0094","url":null,"abstract":"India harbors a substantial population of 9.43 million dogs, showcasing diverse phenotypes and utility. Initiatives focusing on awareness, conservation, and informed breeding can greatly enhance the recognition and welfare of the unique Indian canine heritage. This study describes the design and development of a high-density SNP array for genomic characterization of Indian dogs. Paired-end (150 bp) DNA sequences of 48 samples from four diverse dog populations were generated with 10× coverage, following the standard pipeline of Axiom Array technology for chip design. More than 23 million raw SNPs were initially identified, with 629 597 SNP markers ultimately tiled on the Indian canine array (Axiom_Shwaan) after stringent filtering and processing. With an inter-marker distance of 3.8 kb the Axiom_Shwaan greatly increases the canine genome coverage. The array was validated by genotyping 186 samples representing 11 dog breeds/populations from India. The high call rate (99%) of SNPs on the designed chip indicates its suitability for use in Indian dog populations, reflecting sufficient genetic diversity. The principal component and phylogenetic analyses delineated the native dog breeds into discrete groups. This high-density SNP array will empower future applications in population genetics, breed/selection signature identification, development of trait-specific biomarkers, and genome-wide data mining for various canine abilities.","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":"143051636","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

Pre-assembly NGS correction of ONT reads achieves HiFi-level assembly quality. 装配前NGS校正的ONT读数达到hifi级的装配质量。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0132

Evgeniy Mozheiko, Heng Yi, Anzhi Lu, Heitung Kong, Yong Hou, Yan Zhou, Hui Gao

{"title":"Pre-assembly NGS correction of ONT reads achieves HiFi-level assembly quality.","authors":"Evgeniy Mozheiko, Heng Yi, Anzhi Lu, Heitung Kong, Yong Hou, Yan Zhou, Hui Gao","doi":"10.1139/gen-2024-0132","DOIUrl":"10.1139/gen-2024-0132","url":null,"abstract":"Recently developed hybrid assemblies can achieve telomere-to-telomere (T2T) completeness of some chromosomes. However, such approaches involve sequencing a large volume of both Pacific Biosciences high-fidelity (HiFi) and Oxford Nanopore Technologies (ONT) sequencing reads. Along with this, third-generation sequencing techniques are rapidly advancing, increasing the available length and accuracy. To reduce the final cost of genome assembly, here we investigated the possibility of assembly from low-coverage samples and with only ONT corrected by next-generation sequencing (NGS) sequencing reads. We demonstrated that haploid ONT-based assembly approaches corrected by NGS can achieve performance metrics comparable to more expensive hybrid approaches based on HiFi sequencing. We investigated the assembly of different chromosomes and the low-coverage performance of state-of-the-art hybrid assembly tools, including Verkko and Hifiasm, as well as ONT-based assemblers such as Shasta and Flye. We found that even with one-contig T2T assembly Verkko and Hifiasm still have numerous misassemblies within centromere. Therefore, we recommend using a combination of regular R9 or simplex R10 ONT reads and accurate NGS reads for assembly without aiming for T2T completeness. Additionally, we rigorously evaluated the performance of MGI, Illumina, and stLFR NGS technologies across various aspects of hybrid genome assembly, including pre-assembly correction, haplotype phasing, and polishing.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-9"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735787","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

Karyotype evolution of suliformes and description of a ♂Z₁Z₁Z₂Z₂/♀Z₁Z₂W multiple sex chromosome system in boobies (Sula spp.). 鲣鸟尾形目核型进化及♂Z1Z1Z2Z2/♀Z1Z2W多性染色体系统描述

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0165

Luciano Cesar Pozzobon, Gustavo Akira Toma, Marcelo de Bello Cioffi, Edivaldo Herculano Corrêa de Oliveira, Rafael Kretschmer, Thales Renato Ochotorena de Freitas

{"title":"Karyotype evolution of suliformes and description of a ♂Z1Z1Z2Z2/♀Z1Z2W multiple sex chromosome system in boobies (Sula spp.).","authors":"Luciano Cesar Pozzobon, Gustavo Akira Toma, Marcelo de Bello Cioffi, Edivaldo Herculano Corrêa de Oliveira, Rafael Kretschmer, Thales Renato Ochotorena de Freitas","doi":"10.1139/gen-2024-0165","DOIUrl":"10.1139/gen-2024-0165","url":null,"abstract":"Our comprehension of avian karyotypes still needs to be improved, especially for Suliform birds. To enhance understanding of chromosomal evolution in this order, we conducted conventional and molecular cytogenetic analysis in five species, named Sula dactylatra, Sula leucogaster, Sula sula (Sulidae), Fregata magnificens (Fregatidae), and Nannopterum brasilianum (Phalacrocoracidae). The diploid chromosome number for S. dactylatra and S. leucogaster was established as 2n = 76 in males, and 2n = 75 in females, but S. sula displayed a karyotype of 2n = 76 chromosomes in males. The disparity in diploid chromosome numbers between male and female Sula is due to a multiple sex chromosome system of the Z1Z1Z2Z2/Z1Z2W type. We propose that the emergence of this multiple-sex chromosome system resulted from a Robertsonian translocation involving the W chromosome and the smallest microchromosome. Fregata magnificens exhibited a diploid number 76 (2n = 76), while N. brasilianum displayed a diploid number of 74 (2n = 74) in both sexes. The ribosomal cluster was located in one microchromosome pair in S. dactylatra, S. leucogaster, S. sula, and F. magnificens and in four pairs in N. brasilianum. Our findings provide evidence of a conserved multiple-sex chromosome system within the Sula genus, shedding light on the high karyotype diversity in Suliformes.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-11"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064945","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 T-cell antigenic potentials of Mycoplasma mycoides subsp. mycoides vaccine candidates. 支原体亚种的多样性和t细胞抗原性。真菌候选疫苗。

IF 1.7 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0177

Emily L Wynn, Rohana P Dassanayake, Daniel W Nielsen, Eduardo Casas, Michael L Clawson

{"title":"Diversity and T-cell antigenic potentials of Mycoplasma mycoides subsp. mycoides vaccine candidates.","authors":"Emily L Wynn, Rohana P Dassanayake, Daniel W Nielsen, Eduardo Casas, Michael L Clawson","doi":"10.1139/gen-2024-0177","DOIUrl":"10.1139/gen-2024-0177","url":null,"abstract":"Mycoplasma mycoides subsp. mycoides (Mmm) is the causative agent of contagious bovine pleuropneumonia (CBPP), a severe respiratory disease affecting cattle mostly in sub-Saharan African countries. CBPP can cause significant economic losses, and there is a need for efficacious vaccines to help bring the disease under control. To that end, all publicly available non-redundant whole genome sequences of Mmm strains isolated from cattle (n = 15) were used to identify a 93% core genome of 806 genes, which included 86 of 208 genes encoding outer membrane and extracellular proteins identified from the literature. Many of them and their encoded protein products were found to be highly conserved at the sequence level, including at the sites of predicted epitope binding with bovine major histocompatibility complex (MHC) Class I and II molecules. Despite the high sequence conservation, multiple proteins had large differences in the numbers of MHC Class I and II epitopes and their predicted binding strengths. These results highlight several promising targets supporting the development of new recombinant protein vaccines for CBPP.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-9"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144215679","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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