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

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 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

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

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

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 (PRND) 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":"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 (PRND) gene. In this study, we characterized the PRND 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 PRND gene in Jeju black cattle.","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

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

Analysis of apoptosis levels and MMP7 gene expression in ovaries of postpartum female rabbits after long-term use of LHRH-A3. 长期使用LHRH-A3对产后雌兔卵巢细胞凋亡水平及MMP7基因表达的影响

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0146

Sen Wang, Fan Wang, Lei Wang, Zhiyuan Bao, Jiawei Cai, Bohao Zhao, Xinsheng Wu, Yang Chen

{"title":"Analysis of apoptosis levels and MMP7 gene expression in ovaries of postpartum female rabbits after long-term use of LHRH-A3.","authors":"Sen Wang, Fan Wang, Lei Wang, Zhiyuan Bao, Jiawei Cai, Bohao Zhao, Xinsheng Wu, Yang Chen","doi":"10.1139/gen-2024-0146","DOIUrl":"https://doi.org/10.1139/gen-2024-0146","url":null,"abstract":"Luteinizing hormone-releasing hormone A3 (LHRH-A3), a reproductive hormone analog, is widely used to stimulate ovulation in female rabbits. However, the long-term impact of sustained LHRH-A3 administration on the reproductive system, particularly ovarian health, remains unclear. In this study, we compared apoptosis levels in ovaries and molecular regulation between LHRH-A3-treated (A3 group) and untreated female rabbits (N group) after their 5th litter. Western blotting showed a significantly lower Bcl-2/Bax ratio in the A3 group compared with the N group (P < 0.01), indicating higher ovarian apoptosis. Ovarian tissues from four rabbits per group were divided into the A3 group and the N group, and RNA-seq technology was then utilized to conduct transcriptome analysis on these two groups. This analysis revealed 220 differentially expressed genes (DEGs), including BMP6, BMP15, CYP1A1, and other reproductive-related genes. KEGG analysis of these DEGs showed their involvement in processes such as the cell cycle, PI3K-Akt signaling pathway, and ovarian steroidogenesis. Subsequently, we selected the key gene Matrix metallopeptidase 7 (MMP7) for functional analysis using CCK8 and Annexin V-FITC/PI techniques. MMP7 was found to promote the proliferation of granulosa cells (GCs) and inhibit apoptosis (P < 0.01). In conclusion, LHRH-A3 treatment can modulate ovarian molecular regulation, with the key gene MMP7 involved in the proliferation and apoptosis of GCs.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","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":"143988490","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

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

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

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