Pub Date : 2024-09-07DOI: 10.1093/g3journal/jkae206
Daniel Matúš, Willem Berend Post, Victoria Elisabeth Groß, Alexander Bernd Knierim, Christina Katharina Kuhn, Franziska Fiedler, Darian Benno Tietgen, Johanna Lena Schön, Torsten Schöneberg, Simone Prömel
Adhesion G protein-coupled receptors (aGPCR) are unique molecules. They are able to transmit classical signals via G-protein activation as well as mediate functions solely through their extracellular N termini, completely independently of the seven transmembrane helices domain (7TM) and the C terminus. This dual mode of action is highly unusual for GPCRs and allows for a plethora of possible cellular consequences. However, the physiological implications and molecular details of this N terminus-mediated signaling are poorly understood. Here, we show that several distinct 7TM-independent/trans functions of the aGPCR Latrophilin homolog LAT-1 in the nematode Caenorhabditis elegans together regulate reproduction: sperm guidance, ovulation, and germ cell apoptosis. In these contexts, the receptor elicits its functions in a non-cell autonomous manner. The functions might be realized through alternative splicing of the receptor specifically generating N terminus-only variants. Thus, our findings shed light on the versatility of 7TM-independent/N terminus-only/trans functions of aGPCR and discuss possible molecular details.
粘附 G 蛋白偶联受体(aGPCR)是一种独特的分子。它们既能通过 G 蛋白激活传递经典信号,又能完全独立于七膜螺旋结构域(7TM)和 C 末端,仅通过细胞外 N 末端介导功能。这种双重作用模式在 GPCR 中极为罕见,并可能对细胞产生多种影响。然而,人们对这种由 N 端介导的信号转导的生理意义和分子细节知之甚少。在这里,我们发现在线虫秀丽隐杆线虫中,aGPCR Latrophilin 同源物 LAT-1 的几种不同的 7TM 独立/反式功能共同调节着生殖:精子引导、排卵和生殖细胞凋亡。在这些情况下,受体以非细胞自主的方式发挥其功能。这些功能可能是通过受体的替代剪接实现的,这种剪接特异性地产生了仅有 N 末端的变体。因此,我们的研究结果揭示了 aGPCR 的 7TM 独立/仅 N 末端/反式功能的多样性,并讨论了可能的分子细节。
{"title":"The N terminus-only (trans) function of the Adhesion GPCR Latrophilin-1 controls multiple processes in reproduction of C. elegans.","authors":"Daniel Matúš, Willem Berend Post, Victoria Elisabeth Groß, Alexander Bernd Knierim, Christina Katharina Kuhn, Franziska Fiedler, Darian Benno Tietgen, Johanna Lena Schön, Torsten Schöneberg, Simone Prömel","doi":"10.1093/g3journal/jkae206","DOIUrl":"https://doi.org/10.1093/g3journal/jkae206","url":null,"abstract":"<p><p>Adhesion G protein-coupled receptors (aGPCR) are unique molecules. They are able to transmit classical signals via G-protein activation as well as mediate functions solely through their extracellular N termini, completely independently of the seven transmembrane helices domain (7TM) and the C terminus. This dual mode of action is highly unusual for GPCRs and allows for a plethora of possible cellular consequences. However, the physiological implications and molecular details of this N terminus-mediated signaling are poorly understood. Here, we show that several distinct 7TM-independent/trans functions of the aGPCR Latrophilin homolog LAT-1 in the nematode Caenorhabditis elegans together regulate reproduction: sperm guidance, ovulation, and germ cell apoptosis. In these contexts, the receptor elicits its functions in a non-cell autonomous manner. The functions might be realized through alternative splicing of the receptor specifically generating N terminus-only variants. Thus, our findings shed light on the versatility of 7TM-independent/N terminus-only/trans functions of aGPCR and discuss possible molecular details.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145506","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}
About two-thirds of the genes in the Drosophila melanogaster genome are also involved in its eye development, making the Drosophila eye an ideal system for genetic studies. We previously developed Flynotyper, a software that uses image processing operations to identify and quantify the degree of roughness by measuring disorderliness of ommatidial arrangement in the fly eye. This software has enabled researchers to quantify morphological defects of thousands of eye images caused by genetic perturbations. Here, we present Flynotyper 2.0, a software that has an updated computer vision library, improved performance, and a streamlined pipeline for high-throughput analysis of multiple eye images. We also tested several batches of Drosophila eye images to ensure robustness and reproducibility of the updated Flynotyper 2.0 software.
{"title":"Flynotyper 2.0: An updated tool for rapid quantitative assessment of Drosophila eye phenotypes.","authors":"Johnathan Ray, Deepro Banerjee, Qingyu Wang, Santhosh Girirajan","doi":"10.1093/g3journal/jkae212","DOIUrl":"https://doi.org/10.1093/g3journal/jkae212","url":null,"abstract":"<p><p>About two-thirds of the genes in the Drosophila melanogaster genome are also involved in its eye development, making the Drosophila eye an ideal system for genetic studies. We previously developed Flynotyper, a software that uses image processing operations to identify and quantify the degree of roughness by measuring disorderliness of ommatidial arrangement in the fly eye. This software has enabled researchers to quantify morphological defects of thousands of eye images caused by genetic perturbations. Here, we present Flynotyper 2.0, a software that has an updated computer vision library, improved performance, and a streamlined pipeline for high-throughput analysis of multiple eye images. We also tested several batches of Drosophila eye images to ensure robustness and reproducibility of the updated Flynotyper 2.0 software.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142143049","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}
Pub Date : 2024-09-04DOI: 10.1093/g3journal/jkae093
Jacqueline Heckenhauer, David Plotkin, Jose I Martinez, Jacob Bethin, Steffen U Pauls, Paul B Frandsen, Akito Y Kawahara
While most species of butterflies and moths (Lepidoptera) have entirely terrestrial life histories, ∼0.5% of the described species are known to have an aquatic larval stage. Larvae of aquatic Lepidoptera are similar to caddisflies (Trichoptera) in that they use silk to anchor themselves to underwater substrates or to build protective cases. However, the physical properties and genetic elements of silks in aquatic Lepidoptera remain unstudied, as most research on lepidopteran silk has focused on the commercially important silkworm, Bombyx mori. Here, we provide high-quality PacBio HiFi genome assemblies of 2 distantly-related aquatic Lepidoptera species [Elophila obliteralis (Pyraloidea: Crambidae) and Hyposmocoma kahamanoa (Gelechioidea: Cosmopterigidae)]. As a step toward understanding the evolution of underwater silk in aquatic Lepidoptera, we used the genome assemblies and compared them to published genetic data of aquatic and terrestrial Lepidoptera. Sequences of the primary silk protein, h-fibroin, in aquatic moths have conserved termini and share a basic motif structure with terrestrial Lepidoptera. However, these sequences were similar to aquatic Trichoptera in that the percentage of positively and negatively charged amino acids was much higher than in terrestrial Lepidoptera, indicating a possible adaptation of silks to aquatic environments.
{"title":"Genomic resources of aquatic Lepidoptera, Elophila obliteralis and Hyposmocoma kahamanoa, reveal similarities with Trichoptera in amino acid composition of major silk genes.","authors":"Jacqueline Heckenhauer, David Plotkin, Jose I Martinez, Jacob Bethin, Steffen U Pauls, Paul B Frandsen, Akito Y Kawahara","doi":"10.1093/g3journal/jkae093","DOIUrl":"10.1093/g3journal/jkae093","url":null,"abstract":"<p><p>While most species of butterflies and moths (Lepidoptera) have entirely terrestrial life histories, ∼0.5% of the described species are known to have an aquatic larval stage. Larvae of aquatic Lepidoptera are similar to caddisflies (Trichoptera) in that they use silk to anchor themselves to underwater substrates or to build protective cases. However, the physical properties and genetic elements of silks in aquatic Lepidoptera remain unstudied, as most research on lepidopteran silk has focused on the commercially important silkworm, Bombyx mori. Here, we provide high-quality PacBio HiFi genome assemblies of 2 distantly-related aquatic Lepidoptera species [Elophila obliteralis (Pyraloidea: Crambidae) and Hyposmocoma kahamanoa (Gelechioidea: Cosmopterigidae)]. As a step toward understanding the evolution of underwater silk in aquatic Lepidoptera, we used the genome assemblies and compared them to published genetic data of aquatic and terrestrial Lepidoptera. Sequences of the primary silk protein, h-fibroin, in aquatic moths have conserved termini and share a basic motif structure with terrestrial Lepidoptera. However, these sequences were similar to aquatic Trichoptera in that the percentage of positively and negatively charged amino acids was much higher than in terrestrial Lepidoptera, indicating a possible adaptation of silks to aquatic environments.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.1093/g3journal/jkae166
Krista G Freeman, Michael J Lauer, Danny Jiang, Jennifer Roscher, Sterling Sandler, Nicholas Mercado, Robert Fryberger, Julia Kovalski, Abigail R Lutz, Lee E Hughes, Andrew P VanDemark, Graham F Hatfull
Mycobacterium phage Adephagia is a cluster K phage that infects Mycobacterium smegmatis and some strains of Mycobacterium pathogens. Adephagia has a siphoviral virion morphology and is temperate. Its genome is 59,646 bp long and codes for one tRNA gene and 94 predicted protein-coding genes; most genes not associated with virion structure and assembly are functionally ill-defined. Here, we determined the Adephagia gene expression patterns in lytic and lysogenic growth and used structural predictions to assign additional gene functions. We characterized 66 nonstructural genes for their toxic phenotypes when expressed in M. smegmatis, and we show that 25 of these (38%) are either toxic or strongly inhibit growth, resulting in either reduced viability or small colony sizes. Some of these genes are predicted to be involved in DNA metabolism or regulation, but others are of unknown function. We also characterize the HicAB-like toxin-antitoxin (TA) system encoded by Adephagia (gp91 and gp90, respectively) and show that the gp90 antitoxin is lysogenically expressed, abrogates gp91 toxicity, and is required for normal lytic and lysogenic growth.
分枝杆菌噬菌体 Adephagia 是一种 K 群噬菌体,可感染烟曲霉分枝杆菌和一些分枝杆菌病原体菌株。Adephagia 具有虹吸病毒病毒形态,性情温和。其基因组长 59,646 bp,编码一个 tRNA 基因和 94 个预测的蛋白质编码基因;大多数与病毒结构和组装无关的基因功能不明确。在这里,我们确定了阿德法吉亚基因在裂解和溶解性生长过程中的表达模式,并利用结构预测确定了其他基因的功能。我们对 66 个非结构基因在 M. smegmatis 中表达时的毒性表型进行了鉴定,结果表明其中 25 个基因(38%)具有毒性或强烈抑制生长,导致存活率降低或菌落体积变小。我们预测其中一些基因参与了 DNA 代谢或调控,但其他基因的功能尚不清楚。我们还描述了阿德菲格编码的类似 HicAB 的毒素-抗毒素系统(分别为 gp91 和 gp90)的特征,结果表明 gp90 抗毒素具有溶解性表达,可减弱 gp91 的毒性,并且是正常溶解和溶解性生长所必需的。
{"title":"Characterization of mycobacteriophage Adephagia cytotoxic proteins.","authors":"Krista G Freeman, Michael J Lauer, Danny Jiang, Jennifer Roscher, Sterling Sandler, Nicholas Mercado, Robert Fryberger, Julia Kovalski, Abigail R Lutz, Lee E Hughes, Andrew P VanDemark, Graham F Hatfull","doi":"10.1093/g3journal/jkae166","DOIUrl":"10.1093/g3journal/jkae166","url":null,"abstract":"<p><p>Mycobacterium phage Adephagia is a cluster K phage that infects Mycobacterium smegmatis and some strains of Mycobacterium pathogens. Adephagia has a siphoviral virion morphology and is temperate. Its genome is 59,646 bp long and codes for one tRNA gene and 94 predicted protein-coding genes; most genes not associated with virion structure and assembly are functionally ill-defined. Here, we determined the Adephagia gene expression patterns in lytic and lysogenic growth and used structural predictions to assign additional gene functions. We characterized 66 nonstructural genes for their toxic phenotypes when expressed in M. smegmatis, and we show that 25 of these (38%) are either toxic or strongly inhibit growth, resulting in either reduced viability or small colony sizes. Some of these genes are predicted to be involved in DNA metabolism or regulation, but others are of unknown function. We also characterize the HicAB-like toxin-antitoxin (TA) system encoded by Adephagia (gp91 and gp90, respectively) and show that the gp90 antitoxin is lysogenically expressed, abrogates gp91 toxicity, and is required for normal lytic and lysogenic growth.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.1093/g3journal/jkae163
Gonzalo Casorzo, Luis Felipe Ferrão, Paul Adunola, Estefania Tavares Flores, Camila Azevedo, Rodrigo Amadeu, Patricio R Munoz
Blueberry (Vaccinium spp.) is among the most-consumed soft fruit and has been recognized as an important source of health-promoting compounds. Highly perishable and susceptible to rapid spoilage due to fruit softening and decay during postharvest storage, modern breeding programs are looking to maximize the quality and extend the market life of fresh blueberries. However, it is uncertain how genetically controlled postharvest quality traits are in blueberries. This study aimed to investigate the prediction ability and the genetic basis of the main fruit quality traits affected during blueberry postharvest to create breeding strategies for developing cultivars with an extended shelf life. To achieve this goal, we carried out target genotyping in a breeding population of 588 individuals and evaluated several fruit quality traits after 1 day, 1 week, 3 weeks, and 7 weeks of postharvest storage at 1°C. Using longitudinal genome-based methods, we estimated genetic parameters and predicted unobserved phenotypes. Our results showed large diversity, moderate heritability, and consistent predictive accuracies along the postharvest storage for most of the traits. Regarding the fruit quality, firmness showed the largest variation during postharvest storage, with a surprising number of genotypes maintaining or increasing their firmness, even after 7 weeks of cold storage. Our results suggest that we can effectively improve the blueberry postharvest quality through breeding and use genomic prediction to maximize the genetic gains in the long term. We also emphasize the potential of using longitudinal genomic prediction models to predict the fruit quality at extended postharvest periods by integrating known phenotypic data from harvest.
{"title":"Understanding the genetic basis of blueberry postharvest traits to define better breeding strategies.","authors":"Gonzalo Casorzo, Luis Felipe Ferrão, Paul Adunola, Estefania Tavares Flores, Camila Azevedo, Rodrigo Amadeu, Patricio R Munoz","doi":"10.1093/g3journal/jkae163","DOIUrl":"10.1093/g3journal/jkae163","url":null,"abstract":"<p><p>Blueberry (Vaccinium spp.) is among the most-consumed soft fruit and has been recognized as an important source of health-promoting compounds. Highly perishable and susceptible to rapid spoilage due to fruit softening and decay during postharvest storage, modern breeding programs are looking to maximize the quality and extend the market life of fresh blueberries. However, it is uncertain how genetically controlled postharvest quality traits are in blueberries. This study aimed to investigate the prediction ability and the genetic basis of the main fruit quality traits affected during blueberry postharvest to create breeding strategies for developing cultivars with an extended shelf life. To achieve this goal, we carried out target genotyping in a breeding population of 588 individuals and evaluated several fruit quality traits after 1 day, 1 week, 3 weeks, and 7 weeks of postharvest storage at 1°C. Using longitudinal genome-based methods, we estimated genetic parameters and predicted unobserved phenotypes. Our results showed large diversity, moderate heritability, and consistent predictive accuracies along the postharvest storage for most of the traits. Regarding the fruit quality, firmness showed the largest variation during postharvest storage, with a surprising number of genotypes maintaining or increasing their firmness, even after 7 weeks of cold storage. Our results suggest that we can effectively improve the blueberry postharvest quality through breeding and use genomic prediction to maximize the genetic gains in the long term. We also emphasize the potential of using longitudinal genomic prediction models to predict the fruit quality at extended postharvest periods by integrating known phenotypic data from harvest.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.1093/g3journal/jkae135
Eng-Ti Leslie Low, Kuang-Lim Chan, Noorhariza Mohd Zaki, Elizaveta Taranenko, Jared M Ordway, Corey Wischmeyer, Jaap Buntjer, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Rozana Rosli, Eugeniya Bondar, Nadzirah Amiruddin, Norashikin Sarpan, Ngoot-Chin Ting, Pek-Lan Chan, Meilina Ong-Abdullah, Marhalil Marjuni, Suzana Mustaffa, Norziha Abdullah, Norazah Azizi, Blaire Bacher, Nathan Lakey, Tatiana V Tatarinova, Mohamad Arif Abd Manaf, Ravigadevi Sambanthamurti, Rajinder Singh
Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.
Elaeis guineensis 和 E. oleifera 是两种油棕榈树。E. guineensis 是最广泛种植的商业品种,从 E. oleifera 引种的理想性状正在进行中。我们报告了改进后的 E. guineensis 基因组组装,其连续性和完整性得到了大幅提高,同时还报告了首个染色体规模的 E. oleifera 基因组组装。每个基因组都是通过整合长线程测序、近距离连接测序、光学图谱和遗传图谱获得的。在这两个物种之间观察到了高度的种间基因组保护。该研究提供了迄今为止最广泛的基因注释,包括 46,697 个 E. guineensis 和 38,658 个 E. oleifera 基因预测。对重复元件家族的分析进一步确定了两个基因组的 DNA 重复结构。比较基因组分析确定了经实验验证的油棕榈树物种间的小结构变异,并解析了染色体融合机制,该机制是导致染色体非整倍性从 18 条进化到 16 条的原因。
{"title":"Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.","authors":"Eng-Ti Leslie Low, Kuang-Lim Chan, Noorhariza Mohd Zaki, Elizaveta Taranenko, Jared M Ordway, Corey Wischmeyer, Jaap Buntjer, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Rozana Rosli, Eugeniya Bondar, Nadzirah Amiruddin, Norashikin Sarpan, Ngoot-Chin Ting, Pek-Lan Chan, Meilina Ong-Abdullah, Marhalil Marjuni, Suzana Mustaffa, Norziha Abdullah, Norazah Azizi, Blaire Bacher, Nathan Lakey, Tatiana V Tatarinova, Mohamad Arif Abd Manaf, Ravigadevi Sambanthamurti, Rajinder Singh","doi":"10.1093/g3journal/jkae135","DOIUrl":"10.1093/g3journal/jkae135","url":null,"abstract":"<p><p>Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.1093/g3journal/jkae168
Sixin Liu, Kyle E Martin, Warren M Snelling, Roseanna Long, Timothy D Leeds, Roger L Vallejo, Gregory D Wiens, Yniv Palti
With the rapid and significant cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS), followed by genotype imputation, is becoming a cost-effective alternative to single-nucleotide polymorphism (SNP)-array genotyping. The objectives of this study were 2-fold: (1) construct a haplotype reference panel for genotype imputation from lcWGS data in rainbow trout (Oncorhynchus mykiss); and (2) evaluate the concordance between imputed genotypes and SNP-array genotypes in 2 breeding populations. Medium-coverage (12×) whole-genome sequences were obtained from a total of 410 fish representing 5 breeding populations with various spawning dates. The short-read sequences were mapped to the rainbow trout reference genome, and genetic variants were identified using GATK. After data filtering, 20,434,612 biallelic SNPs were retained. The reference panel was phased with SHAPEIT5 and was used as a reference to impute genotypes from lcWGS data employing GLIMPSE2. A total of 90 fish from the Troutlodge November breeding population were sequenced with an average coverage of 1.3×, and these fish were also genotyped with the Axiom 57K rainbow trout SNP array. The concordance between array-based genotypes and imputed genotypes was 99.1%. After downsampling the coverage to 0.5×, 0.2×, and 0.1×, the concordance between array-based genotypes and imputed genotypes was 98.7, 97.8, and 96.7%, respectively. In the USDA odd-year breeding population, the concordance between array-based genotypes and imputed genotypes was 97.8% for 109 fish downsampled to 0.5× coverage. Therefore, the reference haplotype panel reported in this study can be used to accurately impute genotypes from lcWGS data in rainbow trout breeding populations.
{"title":"Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout.","authors":"Sixin Liu, Kyle E Martin, Warren M Snelling, Roseanna Long, Timothy D Leeds, Roger L Vallejo, Gregory D Wiens, Yniv Palti","doi":"10.1093/g3journal/jkae168","DOIUrl":"10.1093/g3journal/jkae168","url":null,"abstract":"<p><p>With the rapid and significant cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS), followed by genotype imputation, is becoming a cost-effective alternative to single-nucleotide polymorphism (SNP)-array genotyping. The objectives of this study were 2-fold: (1) construct a haplotype reference panel for genotype imputation from lcWGS data in rainbow trout (Oncorhynchus mykiss); and (2) evaluate the concordance between imputed genotypes and SNP-array genotypes in 2 breeding populations. Medium-coverage (12×) whole-genome sequences were obtained from a total of 410 fish representing 5 breeding populations with various spawning dates. The short-read sequences were mapped to the rainbow trout reference genome, and genetic variants were identified using GATK. After data filtering, 20,434,612 biallelic SNPs were retained. The reference panel was phased with SHAPEIT5 and was used as a reference to impute genotypes from lcWGS data employing GLIMPSE2. A total of 90 fish from the Troutlodge November breeding population were sequenced with an average coverage of 1.3×, and these fish were also genotyped with the Axiom 57K rainbow trout SNP array. The concordance between array-based genotypes and imputed genotypes was 99.1%. After downsampling the coverage to 0.5×, 0.2×, and 0.1×, the concordance between array-based genotypes and imputed genotypes was 98.7, 97.8, and 96.7%, respectively. In the USDA odd-year breeding population, the concordance between array-based genotypes and imputed genotypes was 97.8% for 109 fish downsampled to 0.5× coverage. Therefore, the reference haplotype panel reported in this study can be used to accurately impute genotypes from lcWGS data in rainbow trout breeding populations.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.1093/g3journal/jkae157
Sha Sun, Chau-Ti Ting, Chung-I Wu
In organisms with the XY sex-determination system, there is an imbalance in the inheritance and transmission of the X chromosome between males and females. Unlike an autosomal allele, an X-linked recessive allele in a female will have phenotypic effects on its male counterpart. Thus, genes located on the X chromosome are of particular interest to researchers in molecular evolution and genetics. Here we present a model for selection with two alleles of X-linkage to understand fitness components associated with genes on the X chromosome. We apply this model to the fitness analysis of an X-linked gene, OdsH (16D), in the fruit fly Drosophila melanogaster. The function of OdsH is involved in sperm production and the gene is rapidly evolving under positive selection. Using site-directed gene targeting, we generated functional and defective OdsH variants tagged with the eye-color marker gene white. We compare the allele frequency changes of the two OdsH variants, each directly competing against a wild-type OdsH allele in concurrent but separate experimental populations. After 20 generations, the two genetically modified OdsH variants displayed a 40% difference in allele frequencies, with the functional OdsH variant demonstrating an advantage over the defective variant. Using maximum likelihood estimation, we determined the fitness components associated with the OdsH alleles in males and females. Our analysis revealed functional aspects of the fitness determinants associated with OdsH, and that sex-specific fertility and viability consequences both contribute to selection on an X-linked gene.
在具有 XY 性别决定系统的生物中,X 染色体在雌雄之间的遗传和传递是不平衡的。与常染色体等位基因不同,雌性体内的 X 连锁隐性等位基因会对雄性产生表型效应。因此,分子进化和遗传学研究人员对位于 X 染色体上的基因特别感兴趣。在这里,我们提出了一个具有两个 X 连锁等位基因的选择模型,以了解与 X 染色体上的基因相关的适应性成分。我们将这一模型应用于果蝇黑腹果蝇的 X 连锁基因 OdsH (16D) 的适应性分析。OdsH 的功能涉及精子的产生,该基因在正选择下快速进化。我们利用定点基因打靶技术,产生了以眼色标记基因白色为标签的功能性和缺陷性 OdsH 变体。我们比较了两种 OdsH 变体的等位基因频率变化,每种变体都在同时但独立的实验群体中与野生型 OdsH 等位基因直接竞争。经过二十代后,两种经过基因修饰的 OdsH 变体的等位基因频率相差 40%,其中功能性 OdsH 变体比缺陷变体更具优势。通过最大似然估计(MLE),我们确定了与雄性和雌性 OdsH 等位基因相关的适应性成分。我们的分析揭示了与 OdsH 相关的适应性决定因素的功能方面,以及性别特异性生育力和存活率后果都有助于对 X 连锁基因的选择。
{"title":"Selection with two alleles of X-linkage and its application to the fitness component analysis of OdsH in Drosophila.","authors":"Sha Sun, Chau-Ti Ting, Chung-I Wu","doi":"10.1093/g3journal/jkae157","DOIUrl":"10.1093/g3journal/jkae157","url":null,"abstract":"<p><p>In organisms with the XY sex-determination system, there is an imbalance in the inheritance and transmission of the X chromosome between males and females. Unlike an autosomal allele, an X-linked recessive allele in a female will have phenotypic effects on its male counterpart. Thus, genes located on the X chromosome are of particular interest to researchers in molecular evolution and genetics. Here we present a model for selection with two alleles of X-linkage to understand fitness components associated with genes on the X chromosome. We apply this model to the fitness analysis of an X-linked gene, OdsH (16D), in the fruit fly Drosophila melanogaster. The function of OdsH is involved in sperm production and the gene is rapidly evolving under positive selection. Using site-directed gene targeting, we generated functional and defective OdsH variants tagged with the eye-color marker gene white. We compare the allele frequency changes of the two OdsH variants, each directly competing against a wild-type OdsH allele in concurrent but separate experimental populations. After 20 generations, the two genetically modified OdsH variants displayed a 40% difference in allele frequencies, with the functional OdsH variant demonstrating an advantage over the defective variant. Using maximum likelihood estimation, we determined the fitness components associated with the OdsH alleles in males and females. Our analysis revealed functional aspects of the fitness determinants associated with OdsH, and that sex-specific fertility and viability consequences both contribute to selection on an X-linked gene.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603505","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}
Pub Date : 2024-09-04DOI: 10.1093/g3journal/jkae211
Maria Fernanda Guizar Amador, Kathy Darragh, Jasen W Liu, Cheryl Dean, Diego Bogarín, Oscar A Pérez-Escobar, Zuleika Serracín, Franco Pupulin, Santiago R Ramírez
Orchidaceae is one of the most prominent flowering plant families, with many species exhibiting highly specialized reproductive and ecological adaptations. An estimated 10% of orchid species in the American tropics are pollinated by scent-collecting male euglossine bees; however, to date, there are no published genomes of species within this pollination syndrome. Here we present the first draft genome of an epiphytic orchid from the genus Gongora, a representative of the male euglossine bee-pollinated subtribe Stanhopeinae. The 1.83 Gb de novo genome with a scaffold N50 of 1.7Mb was assembled using short- and long-read sequencing and chromosome capture (Hi-C) information. Over 17,000 genes were annotated, and 82.95% of the genome was identified as repetitive content. Furthermore, we identified and manually annotated 26 terpene synthase (TPS) genes linked to floral scent biosynthesis and performed a phylogenetic analysis with other published orchid TPS genes. The Gongora gibba genome assembly will serve as the foundation for future research to understand the genetic basis of floral scent biosynthesis and diversification in orchids. Las orquídeas (Orchidaceae) son una de las familias de plantas con mayor riqueza de especies y exhiben adaptaciones reproductivas altamente especializadas. Se estima que el 10% de las especies de orquídeas en los trópicos americanos son polinizadas por abejas euglosinas; sin embargo, hasta la fecha no existen genomas publicados de especies con este síndrome de polinización. Aquí presentamos el primer genoma de una orquídea epífita del género Gongora, un representante de la subtribu Stanhopeinae, que es polinizada exclusivamente por abejas euglosinas macho. El genoma de 1,83 Gb se ensambló de novo utilizando secuenciación e información de captura de cromosomas (Hi-C), logrando un N50 de 1,7 Mb. Se anotaron más de 17.000 genes y se identificó que el 82,95% del genoma presenta elementos repetitivos. Además, identificamos y anotamos manualmente 26 genes de la familia de genes terpeno sintasa (TPS) y realizamos un análisis filogenético con otros genes TPS de orquídeas publicados. El ensamblaje del genoma de Gongora gibba servirá como base para futuras investigaciones para comprender la base genética de la biosíntesis y la diversificación de los aromas florales en las orquídeas.
{"title":"The Gongora gibba genome assembly provides new insights into the evolution of floral scent in male euglossine bee-pollinated orchids.","authors":"Maria Fernanda Guizar Amador, Kathy Darragh, Jasen W Liu, Cheryl Dean, Diego Bogarín, Oscar A Pérez-Escobar, Zuleika Serracín, Franco Pupulin, Santiago R Ramírez","doi":"10.1093/g3journal/jkae211","DOIUrl":"https://doi.org/10.1093/g3journal/jkae211","url":null,"abstract":"<p><p>Orchidaceae is one of the most prominent flowering plant families, with many species exhibiting highly specialized reproductive and ecological adaptations. An estimated 10% of orchid species in the American tropics are pollinated by scent-collecting male euglossine bees; however, to date, there are no published genomes of species within this pollination syndrome. Here we present the first draft genome of an epiphytic orchid from the genus Gongora, a representative of the male euglossine bee-pollinated subtribe Stanhopeinae. The 1.83 Gb de novo genome with a scaffold N50 of 1.7Mb was assembled using short- and long-read sequencing and chromosome capture (Hi-C) information. Over 17,000 genes were annotated, and 82.95% of the genome was identified as repetitive content. Furthermore, we identified and manually annotated 26 terpene synthase (TPS) genes linked to floral scent biosynthesis and performed a phylogenetic analysis with other published orchid TPS genes. The Gongora gibba genome assembly will serve as the foundation for future research to understand the genetic basis of floral scent biosynthesis and diversification in orchids. Las orquídeas (Orchidaceae) son una de las familias de plantas con mayor riqueza de especies y exhiben adaptaciones reproductivas altamente especializadas. Se estima que el 10% de las especies de orquídeas en los trópicos americanos son polinizadas por abejas euglosinas; sin embargo, hasta la fecha no existen genomas publicados de especies con este síndrome de polinización. Aquí presentamos el primer genoma de una orquídea epífita del género Gongora, un representante de la subtribu Stanhopeinae, que es polinizada exclusivamente por abejas euglosinas macho. El genoma de 1,83 Gb se ensambló de novo utilizando secuenciación e información de captura de cromosomas (Hi-C), logrando un N50 de 1,7 Mb. Se anotaron más de 17.000 genes y se identificó que el 82,95% del genoma presenta elementos repetitivos. Además, identificamos y anotamos manualmente 26 genes de la familia de genes terpeno sintasa (TPS) y realizamos un análisis filogenético con otros genes TPS de orquídeas publicados. El ensamblaje del genoma de Gongora gibba servirá como base para futuras investigaciones para comprender la base genética de la biosíntesis y la diversificación de los aromas florales en las orquídeas.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132337","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}
Pub Date : 2024-09-04DOI: 10.1093/g3journal/jkae115
Kyle E McElroy, Rick Masonbrink, Sivanandan Chudalayandi, Andrew J Severin, Jeanne M Serb
The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.
{"title":"A chromosome-level genome assembly of the disco clam, Ctenoides ales.","authors":"Kyle E McElroy, Rick Masonbrink, Sivanandan Chudalayandi, Andrew J Severin, Jeanne M Serb","doi":"10.1093/g3journal/jkae115","DOIUrl":"10.1093/g3journal/jkae115","url":null,"abstract":"<p><p>The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}