Genome最新文献_第3页

Empowering canine genomics: design and validation of a high-density SNP array for Indian dogs.

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

Karyotype evolution of suliformes and description of a ♂Z₁Z₁Z₂Z₂/♀Z₁Z₂W multiple sex chromosome system in boobies (Sula spp.).

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

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

Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting.

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0090

Tatiana V Danilova, Alina R Akhunova, Xiwen Cai

{"title":"Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting.","authors":"Tatiana V Danilova, Alina R Akhunova, Xiwen Cai","doi":"10.1139/gen-2024-0090","DOIUrl":"10.1139/gen-2024-0090","url":null,"abstract":"Aegilops speltoides (2n = 2x = 14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of Aegilops from the Sitopsis section and wheat and found that Ae. speltoides is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from Ae. speltoides more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and Ae. speltoides and develop Ae. speltoides chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low-coverage sequence data were analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in Ae. speltoides and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. Ae. speltoides had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting Ae. speltoides chromatin in the wheat background using fluorescent in situ hybridization.","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":"143064944","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

Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (Eleocharis, Cyperaceae). 穗花杉（Eleocharis，茜草科）全中心染色体中 satDNA 分布的不同模式。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-09-16 DOI: 10.1139/gen-2024-0089

Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Luís Laforga Vanzela

{"title":"Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (Eleocharis, Cyperaceae).","authors":"Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Luís Laforga Vanzela","doi":"10.1139/gen-2024-0089","DOIUrl":"10.1139/gen-2024-0089","url":null,"abstract":"Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. High intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in this genus. In our study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against the kinetochore protein KNL1 and the cell-cycle dependent posttranslational modifications histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in the newly sequenced species Eleocharis maculosa, Eleocharis geniculata, Eleocharis parodii, Eleocharis elegans, and Eleocharis montana. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was distributed irregularly along the chromatid length in a line-like manner. EmaSAT14 monomers were present in a few copies in few species across the Eleocharis phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus Eleocharis. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.","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":"142284426","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

Whole genome sequencing and analysis of benzo(a)pyrene-degrading bacteria Bacillus cereus M72-4. 全基因组测序和苯并（a）芘降解细菌蜡样芽孢杆菌 M72-4 的分析。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0114

Aofei Jin, Dilbar Tursun, Lirong Tan, Zhuonan Yang, Zhixian Duo, Yanan Qin, Rui Zhang

{"title":"Whole genome sequencing and analysis of benzo(a)pyrene-degrading bacteria Bacillus cereus M72-4.","authors":"Aofei Jin, Dilbar Tursun, Lirong Tan, Zhuonan Yang, Zhixian Duo, Yanan Qin, Rui Zhang","doi":"10.1139/gen-2024-0114","DOIUrl":"10.1139/gen-2024-0114","url":null,"abstract":"Benzo(a)pyrene produced by food during high-temperature process enters the body through ingestion, which causes food safety issues to the human body. To alleviate the harm of foodborne benzo(a)pyrene to human health, a strain that can degrade benzo(a)pyrene was screened from Kefir, a traditional fermented product in Xinjiang. Bacillus cereus M72-4 is a Gram-positive bacteria sourced from Xinjiang traditional fermented product Kefir; under benzo(a)pyrene stress conditions, there was 69.39% degradation rate of 20 mg/L benzo(a)pyrene by strain M72-4 after incubation for 72 h. The whole genome of M72-4 was sequenced using PacBio sequencing technology in this study. The genome size was 5754 801 bp and a GC content was 35.24%; a total of 5719 coding genes were predicted bioinformatically. Through functional database annotation, it was found that the strain has a total of 219 genes involved in the transportation and metabolism of hydrocarbons, a total of 9 metabolic pathways related to the degradation and metabolism of exogenous substances, and a total of 67 coding genes. According to the Kyoto Encyclopedia of Genes and Genomes database annotation results, a key enzyme related to benzo(a)pyrene degradation, catechol 2,3-dioxygenase, was detected in the genome data of Bacillus cereus M72-4, encoding genes dmpB and xylE, respectively. There are also monooxygenases and dehydrogenases. Therefore, it can be inferred that this strain mainly degrades benzo(a)pyrene through benzoate metabolic.","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":"143051854","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