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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 (<i>Bombus bellicosus</i>, 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":"<p><p>We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (<i>Bombus bellicosus</i>). 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 (<i>Bombus pascuorum</i>). 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.</p>","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
{"title":"Evolutionary speed of proteins in the genus <i>Staphylococcus</i>: a focus on proteins involved in natural competence.","authors":"Antony T Vincent","doi":"10.1139/gen-2024-0134","DOIUrl":"10.1139/gen-2024-0134","url":null,"abstract":"<p><p>Bacteria in the genus <i>Staphylococcus</i> include human and animal pathogens. Although the genomic diversity of these bacteria is increasingly well characterized, the rate of protein evolution in staphylococci remains poorly understood. In this study, the genomic sequences of one representative from each of the 63 <i>Staphylococcus</i> species were downloaded from the RefSeq database. Homologous protein sequences were identified, and their evolutionary rates were inferred using a phylogenetic approach. The results demonstrated that some proteins evolve significantly faster than others, with several being involved in DNA-mediated transformation. Further analyses of the genomic sequences revealed that the evolutionary rate of proteins is correlated with codon adaptation of their genes, and that certain protein regions are more prone to accumulating mutations. This study highlights the more rapid evolution of specific proteins in staphylococci, likely reflecting the host diversity of these bacteria and their high adaptive capacity.</p>","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":"143624310","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":"<p><p>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 (<i>Axiom_Shwaan</i>) after stringent filtering and processing. With an inter-marker distance of 3.8 kb the <i>Axiom_Shwaan</i> 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.</p>","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 (<i>Dromaius novaehollandiae</i>).","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":"<p><p>The domestication of emu (<i>Dromaius novaehollandiae)</i> 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 (<i>F</i><sub>ROH</sub>) 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.</p>","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":"<p><p>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.</p>","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 ♂Z<sub>1</sub>Z<sub>1</sub>Z<sub>2</sub>Z<sub>2</sub>/♀Z<sub>1</sub>Z<sub>2</sub>W multiple sex chromosome system in boobies (<i>Sula</i> 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":"<p><p>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 <i>Sula dactylatra</i>, <i>Sula</i> <i>leucogaster</i>, <i>Sula sula</i> (Sulidae), <i>Fregata magnificens</i> (Fregatidae), and <i>Nannopterum brasilianum</i> (Phalacrocoracidae). The diploid chromosome number for <i>S. dactylatra</i> and <i>S. leucogaster</i> was established as 2<i>n</i> = 76 in males, and 2<i>n</i> = 75 in females, but <i>S</i>. <i>sula</i> displayed a karyotype of 2<i>n</i> = 76 chromosomes in males. The disparity in diploid chromosome numbers between male and female <i>Sula</i> is due to a multiple sex chromosome system of the Z<sub>1</sub>Z<sub>1</sub>Z<sub>2</sub>Z<sub>2</sub>/Z<sub>1</sub>Z<sub>2</sub>W 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. <i>Fregata magnificens</i> exhibited a diploid number 76 (2<i>n</i> = 76), while <i>N. brasilianum</i> displayed a diploid number of 74 (2<i>n</i> = 74) in both sexes. The ribosomal cluster was located in one microchromosome pair in <i>S. dactylatra</i>, <i>S. leucogaster</i>, <i>S. sula</i>, and <i>F. magnificens</i> and in four pairs in <i>N. brasilianum</i>. Our findings provide evidence of a conserved multiple-sex chromosome system within the <i>Sula</i> genus, shedding light on the high karyotype diversity in Suliformes.</p>","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 analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting. 峨眉与小麦重复元件的比较分析及S基因组特异性FISH图谱的建立。
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 <i>Aegilops speltoides</i> 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":"<p><p><i>Aegilops speltoides</i> (2<i>n</i> = 2<i>x</i> = 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 <i>Aegilops</i> from the <i>Sitopsis</i> section and wheat and found that <i>Ae. speltoides</i> 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 <i>Ae. speltoides</i> more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and <i>Ae. speltoides</i> and develop <i>Ae. speltoides</i> 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 <i>Ae. speltoides</i> and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. <i>Ae. speltoides</i> 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 <i>Ae. speltoides</i> chromatin in the wheat background using fluorescent in situ hybridization.</p>","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
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 <i>Prochilodus</i> (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":"<p><p>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 2<i>n</i> = 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 <i>Prochilodus</i> species (<i>Prochilodus lineatus, Prochilodus costatus</i>, and <i>Prochilodus argenteus</i>) regarding organization and number of <i>loci</i>, 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 <i>loci</i> 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 <i>Prochilodus</i>, highlighting the evolutionary dynamism of satDNA sequences.</p>","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":"<p><p>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.</p>","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
Detection of polymorphisms in the prion-like protein Doppel (PRND) gene in Jeju black cattle. 济州黑牛朊样蛋白Doppel (PRND)基因多态性检测。
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0145
Thi-Thuy-Duong Nguyen, Da-In Choi, Kyoungtag Do, Nameun Kim, Byung-Hoon Jeong
{"title":"Detection of polymorphisms in the prion-like protein Doppel (<i>PRND</i>) gene in Jeju black cattle.","authors":"Thi-Thuy-Duong Nguyen, Da-In Choi, Kyoungtag Do, Nameun Kim, Byung-Hoon Jeong","doi":"10.1139/gen-2024-0145","DOIUrl":"10.1139/gen-2024-0145","url":null,"abstract":"<p><p>Prion protein (PrP) plays a central role in bovine spongiform encephalopathy (BSE). Given the structural and biological similarity to PrP, recent research has focused on Doppel (Dpl) protein, which is encoded by the prion-like protein Doppel (<i>PRND</i>) gene. In this study, we characterized the <i>PRND</i> genetic polymorphism in 100 Jeju black cattle, a native Korean breed. We predicted the potential effect of nonsynonymous single nucleotide polymorphisms (SNPs) on the Dpl protein function using three in silico tools: SIFT, PANTHER, and PolyPhen-2. Finally, we performed a comparative analysis of the genotype distribution of c.395A>G (Q132R) between German BSE-infected cattle and Korean healthy cattle to assess the BSE susceptibility of Korean cattle. We found eight SNPs, including three novel SNPs c.-7C>T, c.172G>A (A58T), and c.537+83C>T. Only c.172G>A was predicted by SIFT to exert a deleterious effect. According to the comparative analysis, Holstein and Jeju black cattle exhibited a higher potential risk for BSE. To the best of our knowledge, this is the first report on the genetic characteristics of the <i>PRND</i> gene in Jeju black cattle.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-7"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143963178","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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