G3: Genes|Genomes|Genetics最新文献

A haplotype-resolved reference genome for Eucalyptus grandis. 巨桉单倍型解析参考基因组。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-30 DOI: 10.1093/g3journal/jkaf112

Anneri Lötter, Tomas Bruna, Tuan A Duong, Kerrie Barry, Anna Lipzen, Chris Daum, Yuko Yoshinaga, Jane Grimwood, Jerry W Jenkins, Jayson Talag, Justin Borevitz, John T Lovell, Jeremy Schmutz, Jill L Wegrzyn, Alexander A Myburg

{"title":"A haplotype-resolved reference genome for Eucalyptus grandis.","authors":"Anneri Lötter, Tomas Bruna, Tuan A Duong, Kerrie Barry, Anna Lipzen, Chris Daum, Yuko Yoshinaga, Jane Grimwood, Jerry W Jenkins, Jayson Talag, Justin Borevitz, John T Lovell, Jeremy Schmutz, Jill L Wegrzyn, Alexander A Myburg","doi":"10.1093/g3journal/jkaf112","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf112","url":null,"abstract":"E. grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials and biorefinery products. The current v2.0 genome reference for the species (Bartholome et al. 2015; Myburg et al. 2014) served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The two haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70 to 90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8% to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4% and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pan-genome variation in the species.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179831","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 B-type cyclin Clb4 prevents meiosis I sister centromere separation in budding yeast. b型细胞周期蛋白Clb4阻止出芽酵母减数分裂I姐妹着丝粒分离。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-30 DOI: 10.1093/g3journal/jkaf121

Gal Lumbroso, Gisela Cairo, Soni Lacefield, Andrew W Murray

引用次数: 0

Mainly high phenotypic stability of black spruce clones for growth and wood traits in contrasted environments within the current breeding zones and multi-trait selection in Québec's seed and breeding zones. 主要是黑云杉无性系在现有育种区对比环境下的生长和木材性状的高表型稳定性，以及在曲氏种子区和育种区多性状选择的高表型稳定性。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-30 DOI: 10.1093/g3journal/jkaf120

Mireille Desponts, Josianne DeBlois, Guillaume Otis-Prud'homme, Martin Perron

{"title":"Mainly high phenotypic stability of black spruce clones for growth and wood traits in contrasted environments within the current breeding zones and multi-trait selection in Québec's seed and breeding zones.","authors":"Mireille Desponts, Josianne DeBlois, Guillaume Otis-Prud'homme, Martin Perron","doi":"10.1093/g3journal/jkaf120","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf120","url":null,"abstract":"Selected trees from various progeny trials cannot be directly compared. As parents of clonal seed orchards and components of the next breeding cycle, it is crucial to verify their stability in different soil and climatic conditions and to rank them for multiple traits. A subset of the best trees selected for height at 10 or 15 years was cloned to establish two clone trials per population for four breeding populations, covering different bioclimatic domains of Québec. Between 80 and 119 clones per population were compared for height, diameter at breast height, indirect measure of wood density (Pilodyn 6J Forest device) and acoustic velocity (Fiber-gen Hitman ST300). Linear mixed models were used to estimate various genetic parameters, including genotypic values, using the BLUP (Best Linear Unbiased Prediction) method. With the genotypic values at 15 or 16 years for acoustic velocity and height, a selection index was calculated for ranking the clones. Clonal variances are significant for all growth and wood traits. Clonal heritabilities are low for growth traits with one exception (0.11-0.30) and range mainly from moderate to high for wood traits (0.29-0.70). Genotype × environment (G×E) interactions for growth traits are low for two populations (0.87-1) and mainly moderate for the two others (0.53-0.92). For wood traits, G × E interactions are low to almost nil, and are mostly moderate for one population (0.69-1). In general, clones exhibit high stability (two BLUP-based stability indexes) for growth and wood traits in contrasting soil and climatic conditions, except for the growth traits of two populations.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179888","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

Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum. 两种茄属植物对龙葵病菌的敏感性比较——dulcamara和Solanum nigrum植物基因组的组装和注释。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-26 DOI: 10.1093/g3journal/jkaf119

Sara Franco Ortega, Sally James, Lesley Gilbert, Karen Hogg, Harry Stevens, Jason Daff, Ville-Petri Friman, Andrea L Harper

{"title":"Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum.","authors":"Sara Franco Ortega, Sally James, Lesley Gilbert, Karen Hogg, Harry Stevens, Jason Daff, Ville-Petri Friman, Andrea L Harper","doi":"10.1093/g3journal/jkaf119","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf119","url":null,"abstract":"To understand why close wild plant relatives of crops, such as Solanum dulcamara, are resistant to Ralstonia solanacearum we need genome resources to perform comparative studies and identify key genes and pathways. We de-novo assembled and annotated the genome of a resistant/tolerant S. dulcamara and susceptible Solanum nigrum plant using a hybrid approach including Oxford Nanopore Technologies and Illumina sequencing. Comparative genomic analysis was then performed to find differences between the genome of S. dulcamara and other susceptible Solanaceous species including potato, tomato, aubergine, and S. nigrum and one susceptible and one resistant S. americanum accession. We identified genes associated with auxin-transport only in S. dulcamara and a collection of pattern recognition receptors (PRRs) in orthogroups only found in resistant/tolerant plant species, which we hypothesise may improve recognition of pathogen-associated molecular patterns (PAMPs) associated with R. solanacearum. We also identified an arsenal of nucleotide-binding leucine-rich repeat receptors (NLRs) in the S. nigrum genome that are shared with the other susceptible species and could be acting as susceptibility factors. Finally, we identified differences in methylation frequency across the gene bodies in both species, which may be associated with epigenetic regulation of resistance. Future work should assess the functional role of these PRRs and NLRs during bacterial wilt development to determine if they could offer potential novel targets for breeding to improve bacterial wilt resistance.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144150059","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

Disrupted development of sensory systems and the cerebellum in a zebrafish ebf3a mutant. 斑马鱼ebf3a突变体的感觉系统和小脑发育中断。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-23 DOI: 10.1093/g3journal/jkaf115

Nghi D P Dang, Alexia K Barcus, Claire L Conklin, Thinh Q Truong, Michael D Vivian, Jun Wang, Holly R Thomas, John M Parant, Nan Cher Yeo, Summer B Thyme

{"title":"Disrupted development of sensory systems and the cerebellum in a zebrafish ebf3a mutant.","authors":"Nghi D P Dang, Alexia K Barcus, Claire L Conklin, Thinh Q Truong, Michael D Vivian, Jun Wang, Holly R Thomas, John M Parant, Nan Cher Yeo, Summer B Thyme","doi":"10.1093/g3journal/jkaf115","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf115","url":null,"abstract":"Mutations in the transcription factor EBF3 result in a neurodevelopmental disorder, and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss, however, have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here, we generated and characterized a zebrafish ebf3a loss-of-function mutant. We discovered morphological and neural phenotypes, including an overall smaller brain size, particularly in the hypothalamus, cerebellum, and hindbrain. Brain function was also compromised, with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. RNA-sequencing of developing larvae revealed significant downregulation of genes that mark olfactory sensory neurons, the lateral line, and cerebellar Purkinje neurons. Corroborating the RNA-sequencing, staining revealed fewer lateral line neuromasts and reduced Parvalbumin signal in the cerebellum. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127112","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

Large effect life-history genomic regions are associated with functional morphological traits in Atlantic salmon. 大效应生活史基因组区域与大西洋鲑鱼的功能形态特征有关。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-23 DOI: 10.1093/g3journal/jkaf106

Tutku Aykanat, Paul V Debes, Shadi Jansouz, Lison Gueguen, Andrew H House, Annukka Ruokolainen, Jaakko Erkinaro, Victoria L Pritchard, Craig R Primmer, Geir H Bolstad

{"title":"Large effect life-history genomic regions are associated with functional morphological traits in Atlantic salmon.","authors":"Tutku Aykanat, Paul V Debes, Shadi Jansouz, Lison Gueguen, Andrew H House, Annukka Ruokolainen, Jaakko Erkinaro, Victoria L Pritchard, Craig R Primmer, Geir H Bolstad","doi":"10.1093/g3journal/jkaf106","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf106","url":null,"abstract":"Understanding pleiotropic architectures of phenotypes is instrumental for identifying the functional basis of adaptive genetic variation in the wild. Life-history variation may have a morphological basis that mediates resource acquisition allocation pathways, but identifying the underlying genetic basis of such traits is challenging. Using Atlantic salmon (Salmo salar) juveniles reared in common garden conditions, we test if two life-history associated loci, six6 and vgll3, are also associated with functional morphological traits. These loci had previously shown to exhibit strong signals of adaptation and are highly correlated with sea age at maturity. We show that genetic variation at the vgll3 locus is linked to variation in morphological traits that underlie swimming performance, along a trade-off axis between efficient cruising and maneuvering, while the genetic variation at the six6 locus was linked to variation in body-head proportions suggesting the potential functional importance of these traits for resource acquisition efficiency. However, the direction of changes in morphological traits associated with late- vs. early-maturing alleles was not always consistent with the expected direction of an effect to maturation timing. Our results reveal a complex morphological landscape associated with the genetic variation in these loci, possibly as a result of pleiotropy or linkage across these genomic regions.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132382","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

A single high-zinc activation enhancer can control two genes oriented head-to-head in Caenorhabditis elegans. 在秀丽隐杆线虫中，一个单一的高锌活化增强子可以控制两个头对头的定向基因。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-23 DOI: 10.1093/g3journal/jkaf089

Hanwenheng Liu, Brian Earley, Adelita Mendoza, Patrick Hunt, Sean Teng, Daniel Luke Schneider, Kerry Kornfeld

{"title":"A single high-zinc activation enhancer can control two genes oriented head-to-head in Caenorhabditis elegans.","authors":"Hanwenheng Liu, Brian Earley, Adelita Mendoza, Patrick Hunt, Sean Teng, Daniel Luke Schneider, Kerry Kornfeld","doi":"10.1093/g3journal/jkaf089","DOIUrl":"10.1093/g3journal/jkaf089","url":null,"abstract":"Enhancers play critical roles in gene expression, but a full understanding of their complex functions has yet to be defined. The cellular response to excess zinc levels in Caenorhabditis elegans requires the HIZR-1 transcription factor, which binds the high-zinc activation (HZA) enhancer in the promoters of multiple target genes. Cadmium hijacks the excess zinc response by binding and activating HIZR-1. By analyzing the genome-wide transcriptional response to excess zinc and cadmium, we identified two positions in the genome where head-to-head oriented genes are both induced by metals. In both examples, a single predicted HZA enhancer is positioned between the two translational start sites. We hypothesized that a single enhancer can control both head-to-head genes, an arrangement that has not been extensively characterized. To test this hypothesis, we used CRISPR genome editing to precisely delete the HZAmT enhancer positioned between mtl-2 and T08G5.1; in this mutant, both head-to-head genes display severely reduced zinc-activated transcription, whereas zinc-activated transcription of more distant genes was not strongly affected. Deleting the HZAcF enhancer positioned between cdr-1 and F35E8.10 caused both head-to-head genes to display reduced cadmium-activated transcription, whereas cadmium-activated transcription of more distant genes was not strongly affected. These studies rigorously document that a single HZA enhancer can control two head-to-head genes, advancing our understanding of the diverse functions of enhancers.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132379","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 resequencing of a global collection of Napier grass (Cenchrus purpureus) to explore global population structure and QTL governing yield and feed quality traits. 全球纳皮尔草（Cenchrus purpureus）全基因组重测序，探索全球种群结构和控制产量和饲料品质性状的QTL。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-23 DOI: 10.1093/g3journal/jkaf113

Abel Teshome, Hailu Lire, Janet Higgins, Temesgen Olango, Ermias Haile Habte, Alemayehu Teressa Negawo, Meki Shehabu Muktar, Yilkal Assefa, Jorge Fernando Pereira, Ana Luisa Sousa Azevedo, Juarez Campolina Machado, Desterio Nyamongo, Jiyu Zhang, Yan Qi, William Anderson, Jose De Vega, Christopher Stephen Jones

{"title":"Whole genome resequencing of a global collection of Napier grass (Cenchrus purpureus) to explore global population structure and QTL governing yield and feed quality traits.","authors":"Abel Teshome, Hailu Lire, Janet Higgins, Temesgen Olango, Ermias Haile Habte, Alemayehu Teressa Negawo, Meki Shehabu Muktar, Yilkal Assefa, Jorge Fernando Pereira, Ana Luisa Sousa Azevedo, Juarez Campolina Machado, Desterio Nyamongo, Jiyu Zhang, Yan Qi, William Anderson, Jose De Vega, Christopher Stephen Jones","doi":"10.1093/g3journal/jkaf113","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf113","url":null,"abstract":"Napier grass (Cenchrus purpureus) is a C4 perennial grass species native to Sub-Saharan Africa (SSA) and widely used for feed cattle in the region. In this study, we sequenced the genomes of 450 Napier grass individuals from 18 countries, identifying over 170 million DNA variants (SNPs and Indels). Approximately 1% of these SNPs were informative and used to assess genetic diversity within the collection. Our resequencing study provided valuable insights into the global genetic diversity of Napier grass. Additionally, a genome-wide association study on two independent populations identified multiple quantitative trait loci (QTL) significantly associated with key agronomic traits, including biomass yield, nitrogen and cellulose content. These findings serve as a crucial resource for preserving and understanding Napier grass genetic diversity in the context of climate change. Moreover, they will support genomics-based breeding programs aimed at developing high-yielding and drought-tolerant varieties for forage and biofuel production.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132383","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

First transcriptome analysis of the winter tick (Dermacentor albipictus) reveals sex-specific expression patterns and potential targets for genetic control. 首次对冬季蜱（白纹革蜱）的转录组分析揭示了性别特异性表达模式和遗传控制的潜在靶点。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-23 DOI: 10.1093/g3journal/jkaf116

Rhodri T M Edwards, Igor Antoshechkin, Eddie Hill, Michael W Perry, Pia U Olafson, Perot Saelao, Kimberly H Lohmeyer, Omar S Akbari

{"title":"First transcriptome analysis of the winter tick (Dermacentor albipictus) reveals sex-specific expression patterns and potential targets for genetic control.","authors":"Rhodri T M Edwards, Igor Antoshechkin, Eddie Hill, Michael W Perry, Pia U Olafson, Perot Saelao, Kimberly H Lohmeyer, Omar S Akbari","doi":"10.1093/g3journal/jkaf116","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf116","url":null,"abstract":"The winter tick, Dermacentor albipictus, is a significant North American ectoparasite, posing health risks to ruminants and occasionally humans. Despite its ecological importance, limited genomic resources exist for this species. This study provides the first comprehensive transcriptomic analysis of the recently published winter tick genome, focusing on tissues isolated from early-stage embryos, sexed adults, dissected ovaries, and dissected male reproductive systems. We identified the most abundant gene ontologies and analyzed differential gene expression. Differential gene expression revealed significant sex-biased expression patterns, and functional annotations identified candidate genes involved in sex determination. Notably, we identified the first documented case of sex-specific splicing of a doublesex-like gene in chelicerates, a mechanism previously thought to be absent in this clade. These transcriptome data serve as a critical resource for understanding the biology of D. albipictus and will facilitate the development of novel genetic technologies aimed at population suppression and reduction of tick-borne illnesses.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132380","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

Genome Sequence of a Marine Threespine Stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet. 库克湾兔泥中一种海洋三刺棘鱼的基因组序列。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-23 DOI: 10.1093/g3journal/jkaf114

Eric H Au, Seth Weaver, Anushka Katikaneni, Julia I Wucherpfennig, Yanting Luo, Riley J Mangan, Matthew A Wund, Michael A Bell, Craig B Lowe

{"title":"Genome Sequence of a Marine Threespine Stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet.","authors":"Eric H Au, Seth Weaver, Anushka Katikaneni, Julia I Wucherpfennig, Yanting Luo, Riley J Mangan, Matthew A Wund, Michael A Bell, Craig B Lowe","doi":"10.1093/g3journal/jkaf114","DOIUrl":"10.1093/g3journal/jkaf114","url":null,"abstract":"The Threespine Stickleback, Gasterosteus aculeatus, is an emerging model system for understanding the genomic basis of vertebrate adaptation. A strength of the system is that marine populations have repeatedly colonized freshwater environments, serving as natural biological replicates. While repeated adaptation to freshwater has occurred throughout the northern hemisphere, Cook Inlet in south-central Alaska has been an area of focus. There is a high-quality freshwater reference assembly from a population in the region, Bear Paw Lake. Using a freshwater reference assembly is a potential limitation because genomic segments are repeatedly lost during adaptation to freshwater. Thus, some of the key regions associated with marine-freshwater divergence are absent from freshwater genomes, and therefore absent from the reference assemblies. Here we present a highly-continuous assembly from the marine population that breeds in (anadromous) Rabbit Slough in Cook Inlet. All contigs are from long-read sequencing and have been ordered and oriented with Hi-C. They are anchored to chromosomes and form a 454 Mbp assembly with an N50 of 1.3 Mbp, an L50 of 95, and a BUSCO score greater than 97%. We expect this high-quality marine assembly to more accurately reflect the ancestral genome of the marine stickleback that founded populations in freshwater habitats in the area and will more closely match most other populations from around the world. This marine assembly, which includes repeatedly deleted segments and offers a closer reference sequence for most populations, will enable more comprehensive and accurate computational and functional genomic investigations of Threespine Stickleback evolution.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132381","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