G3: Genes|Genomes|Genetics最新文献

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A chromosome-level genome assembly of the disco clam, Ctenoides ales. 迪斯科蛤(Ctenoides ales)染色体级基因组组装。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae115
Kyle E McElroy, Rick Masonbrink, Sivanandan Chudalayandi, Andrew J Severin, Jeanne M Serb
{"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}
引用次数: 0
Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions. 通过精确绘制交叉位置图揭示鸣禽染色体末端的雄性偏向重组。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae150
Hongkai Zhang, Max Lundberg, Suvi Ponnikas, Dennis Hasselquist, Bengt Hansson
{"title":"Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions.","authors":"Hongkai Zhang, Max Lundberg, Suvi Ponnikas, Dennis Hasselquist, Bengt Hansson","doi":"10.1093/g3journal/jkae150","DOIUrl":"10.1093/g3journal/jkae150","url":null,"abstract":"<p><p>Recombination plays a crucial role in evolution by generating novel haplotypes and disrupting linkage between genes, thereby enhancing the efficiency of selection. Here, we analyze the genomes of 12 great reed warblers (Acrocephalus arundinaceus) in a 3-generation pedigree to identify precise crossover positions along the chromosomes. We located more than 200 crossovers and found that these were highly concentrated toward the telomeric ends of the chromosomes. Apart from this major pattern in the recombination landscape, we found significantly higher frequencies of crossovers in genic compared with intergenic regions, and in exons compared with introns. Moreover, while the number of recombination events was similar between the sexes, the crossovers were located significantly closer to the ends of paternal compared with maternal chromosomes. In conclusion, our study of the great reed warbler revealed substantial variation in crossover frequencies within chromosomes, with a distinct bias toward the sub-telomeric regions, particularly on the paternal side. These findings emphasize the importance of thoroughly screening the entire length of chromosomes to characterize the recombination landscape and uncover potential sex-biases in recombination.</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/PMC11373659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579434","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}
引用次数: 0
On the evolutionary origin of discrete phenotypic plasticity. 关于离散表型可塑性的进化起源。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae144
Takahiro Sakamoto, Hideki Innan
{"title":"On the evolutionary origin of discrete phenotypic plasticity.","authors":"Takahiro Sakamoto, Hideki Innan","doi":"10.1093/g3journal/jkae144","DOIUrl":"10.1093/g3journal/jkae144","url":null,"abstract":"<p><p>Phenotypic plasticity provides an attractive strategy for adapting to various environments, but the evolutionary mechanism of the underlying genetic system is poorly understood. We use a simple gene regulatory network model to explore how a species acquires phenotypic plasticity, particularly focusing on discrete phenotypic plasticity, which has been difficult to explain by quantitative genetic models. Our approach employs a population genetic framework that integrates the developmental process, where each individual undergoes growth to develop its phenotype, which subsequently becomes subject to selection pressures. Our model considers two alternative types of environments, with the gene regulatory network including a sensor gene that turns on and off depending on the type of environment. With this assumption, we demonstrate that the system gradually adapts by acquiring the ability to produce two distinct optimum phenotypes under two types of environments without changing genotype, resulting in phenotypic plasticity. We find that the resulting plasticity is often discrete after a lengthy period of evolution. Our results suggest that gene regulatory networks have a notable capacity to flexibly produce various phenotypes in response to environmental changes. This study also shows that the evolutionary dynamics of phenotype may differ significantly between mechanistic-based developmental models and quantitative genetics models, suggesting the utility of incorporating gene regulatory networks into evolutionary models.</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/PMC11373660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141563167","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}
引用次数: 0
First draft reference genome and annotation of the alternative oil species Physaria fendleri. 替代油物种 Physaria fendleri 的参考基因组初稿和注释。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae114
Christopher R Johnston, Patrick J Horn, Ana Paula Alonso
{"title":"First draft reference genome and annotation of the alternative oil species Physaria fendleri.","authors":"Christopher R Johnston, Patrick J Horn, Ana Paula Alonso","doi":"10.1093/g3journal/jkae114","DOIUrl":"10.1093/g3journal/jkae114","url":null,"abstract":"<p><p>In the wake of increasing demand for renewable energy sources, plant-based sources including alternative oilseeds have come to the forefront of interest. Hydroxy fatty acids (HFAs), produced in a few oilseed species, are important chemical feed stocks for industrial applications. An integrated approach was taken to assemble the first draft genome of the alternative HFA producer Physaria fendleri (n = 6), an outcrossing species with high heterozygosity. Both de novo transcriptome assemblies and genome assemblies were produced with public and generated sequencing reads. Resulting intermediate assemblies were then scaffolded and patched with multiple data sources, followed by super-scaffolding onto a masked genome of Camelina laxa (n = 6). Despite a current lack of available resources for the physical mapping of genomic scaffolds of P. fendleri, topography of the genome with respect to repeat and gene content was preserved at the scaffold level and not significantly lost via super-scaffolding. Read representation, gene and genome completion statistics, and annotation results illustrated the creation of a functional draft genome and a tool for future research on alternative oil species.</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/PMC11373644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161145","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}
引用次数: 0
Genetic constitution and variability in synthetic populations of intermediate wheatgrass, an outcrossing perennial grain crop. 一种外交多年生谷物作物--中间小麦草合成种群的遗传结构和变异性。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae154
Prabin Bajgain, Jacob M Jungers, James A Anderson
{"title":"Genetic constitution and variability in synthetic populations of intermediate wheatgrass, an outcrossing perennial grain crop.","authors":"Prabin Bajgain, Jacob M Jungers, James A Anderson","doi":"10.1093/g3journal/jkae154","DOIUrl":"10.1093/g3journal/jkae154","url":null,"abstract":"<p><p>Intermediate wheatgrass (IWG) is a perennial grass that produces nutritious grain while offering substantial ecosystem services. Commercial varieties of this crop are mostly synthetic panmictic populations that are developed by intermating a few selected individuals. As development and generation advancement of these synthetic populations is a multiyear process, earlier synthetic generations are tested by the breeders and subsequent generations are released to the growers. A comparison of generations within IWG synthetic cultivars is currently lacking. In this study, we used simulation models and genomic prediction to analyze population differences and trends of genetic variance in 4 synthetic generations of MN-Clearwater, a commercial cultivar released by the University of Minnesota. Little to no differences were observed among the 4 generations for population genetic, genetic kinship, and genome-wide marker relationships measured via linkage disequilibrium. A reduction in genetic variance was observed when 7 parents were used to generate synthetic populations while using 20 led to the best possible outcome in determining population variance. Genomic prediction of plant height, free threshing ability, seed mass, and grain yield among the 4 synthetic generations showed a few significant differences among the generations, yet the differences in values were negligible. Based on these observations, we make 2 major conclusions: (1) the earlier and latter synthetic generations of IWG are mostly similar to each other with minimal differences and (2) using 20 genotypes to create synthetic populations is recommended to sustain ample genetic variance and trait expression among all synthetic generations.</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/PMC11373638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603503","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}
引用次数: 0
Dominant suppressor genes of p53-induced apoptosis in Drosophila melanogaster. 黑腹果蝇中 p53 诱导细胞凋亡的显性抑制基因
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae149
Tamás Szlanka, Tamás Lukacsovich, Éva Bálint, Erika Virágh, Kornélia Szabó, Ildikó Hajdu, Enikő Molnár, Yu-Hsien Lin, Ágnes Zvara, Ildikó Kelemen-Valkony, Orsolya Méhi, István Török, Zoltán Hegedűs, Brigitta Kiss, Beáta Ramasz, Laura M Magdalena, László Puskás, Bernard M Mechler, Adrien Fónagy, Zoltán Asztalos, Gábor Steinbach, Michal Žurovec, Imre Boros, István Kiss
{"title":"Dominant suppressor genes of p53-induced apoptosis in Drosophila melanogaster.","authors":"Tamás Szlanka, Tamás Lukacsovich, Éva Bálint, Erika Virágh, Kornélia Szabó, Ildikó Hajdu, Enikő Molnár, Yu-Hsien Lin, Ágnes Zvara, Ildikó Kelemen-Valkony, Orsolya Méhi, István Török, Zoltán Hegedűs, Brigitta Kiss, Beáta Ramasz, Laura M Magdalena, László Puskás, Bernard M Mechler, Adrien Fónagy, Zoltán Asztalos, Gábor Steinbach, Michal Žurovec, Imre Boros, István Kiss","doi":"10.1093/g3journal/jkae149","DOIUrl":"10.1093/g3journal/jkae149","url":null,"abstract":"<p><p>One of the major functions of programmed cell death (apoptosis) is the removal of cells that suffered oncogenic mutations, thereby preventing cancerous transformation. By making use of a Double-Headed-EP (DEP) transposon, a P element derivative made in our laboratory, we made an insertional mutagenesis screen in Drosophila melanogaster to identify genes that, when overexpressed, suppress the p53-activated apoptosis. The DEP element has Gal4-activatable, outward-directed UAS promoters at both ends, which can be deleted separately in vivo. In the DEP insertion mutants, we used the GMR-Gal4 driver to induce transcription from both UAS promoters and tested the suppression effect on the apoptotic rough eye phenotype generated by an activated UAS-p53 transgene. By DEP insertions, 7 genes were identified, which suppressed the p53-induced apoptosis. In 4 mutants, the suppression effect resulted from single genes activated by 1 UAS promoter (Pka-R2, Rga, crol, and Spt5). In the other 3 (Orct2, Polr2M, and stg), deleting either UAS promoter eliminated the suppression effect. In qPCR experiments, we found that the genes in the vicinity of the DEP insertion also showed an elevated expression level. This suggested an additive effect of the nearby genes on suppressing apoptosis. In the eukaryotic genomes, there are coexpressed gene clusters. Three of the DEP insertion mutants are included, and 2 are in close vicinity of separate coexpressed gene clusters. This raises the possibility that the activity of some of the genes in these clusters may help the suppression of the apoptotic cell death.</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/PMC11373661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579431","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}
引用次数: 0
An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. 用于对太平洋牡蛎进行高通量、低成本基因分型的扩增子面板。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae125
Ben J G Sutherland, Neil F Thompson, Liam B Surry, Krishna Reddy Gujjula, Claudio D Carrasco, Srinivas Chadaram, Spencer L Lunda, Christopher J Langdon, Amy M Chan, Curtis A Suttle, Timothy J Green
{"title":"An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster.","authors":"Ben J G Sutherland, Neil F Thompson, Liam B Surry, Krishna Reddy Gujjula, Claudio D Carrasco, Srinivas Chadaram, Spencer L Lunda, Christopher J Langdon, Amy M Chan, Curtis A Suttle, Timothy J Green","doi":"10.1093/g3journal/jkae125","DOIUrl":"10.1093/g3journal/jkae125","url":null,"abstract":"<p><p>Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia, Canada. The use of the panel for parentage applications was evaluated using multiple generations of oysters from a breeding program on Vancouver Island, Canada (n = 181) and families selected for Ostreid herpesvirus-1 resistance from the Molluscan Broodstock Program in Oregon, USA (n = 136). Population characterization was evaluated using wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 189). Technical replicates showed high genotype concordance (97.5%; n = 68 replicates). Parentage analysis found suspected pedigree and sample handling errors, demonstrating the panel's value for quality control in breeding programs. Suspected null alleles were identified and found to be largely population dependent, suggesting population-specific variation impacting target amplification. Null alleles were identified using existing data without the need for pedigree information, and once they were removed, assignment rates increased to 93.0 and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.</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/PMC11373646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310494","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}
引用次数: 0
A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira. 马德拉岛特有果蝇 Drosophila madeirensis 的染色体级基因组组装。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae167
Kenta Tomihara, Ana Llopart, Daisuke Yamamoto
{"title":"A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira.","authors":"Kenta Tomihara, Ana Llopart, Daisuke Yamamoto","doi":"10.1093/g3journal/jkae167","DOIUrl":"10.1093/g3journal/jkae167","url":null,"abstract":"<p><p>Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, Drosophila madeirensis, is endemic to the island of Madeira in the Atlantic Ocean. D. subobscura is known for its strict light-dependence in mating and its unique courtship displays, including nuptial gift-giving. D. subobscura has also attracted the interest of researchers because of its abundant variations in chromosomal polymorphisms correlated to the latitude and season, which have been used as a tool to track global climate warming. Although D. madeirensis can be an important resource for understanding the evolutionary underpinning of these genetic characteristics of D. subobscura, little work has been done on the biology of this species. Here, we used a HiFi long-read sequencing data set to produce a de novo genome assembly for D. madeirensis. This assembly comprises a total of 111 contigs spanning 135.5 Mb and has an N50 of 24.2 Mb and a BUSCO completeness score of 98.6%. Each of the 6 chromosomes of D. madeirensis consisted of a single contig except for some centromeric regions. Breakpoints of the chromosomal inversions between D. subobscura and D. madeirensis were characterized using this genome assembly, updating some of the previously identified locations.</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/PMC11373663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731060","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}
引用次数: 0
PAX3 haploinsufficiency in Maine Coon cats with dominant blue eyes and hearing loss resembling the human Waardenburg syndrome. 缅因库恩猫的 PAX3 单倍体缺乏症会导致显性蓝眼和听力损失,类似于人类的瓦登堡综合征。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae131
Gabriela Rudd Garces, Daniela Farke, Martin J Schmidt, Anna Letko, Katja Schirl, Marie Abitbol, Tosso Leeb, Leslie A Lyons, Gesine Lühken
{"title":"PAX3 haploinsufficiency in Maine Coon cats with dominant blue eyes and hearing loss resembling the human Waardenburg syndrome.","authors":"Gabriela Rudd Garces, Daniela Farke, Martin J Schmidt, Anna Letko, Katja Schirl, Marie Abitbol, Tosso Leeb, Leslie A Lyons, Gesine Lühken","doi":"10.1093/g3journal/jkae131","DOIUrl":"10.1093/g3journal/jkae131","url":null,"abstract":"<p><p>This study investigated the dominant blue eyes (DBE) trait linked to hearing impairment and variable white spotting in Maine Coon cats. Fifty-eight animals descending from 2 different DBE lineages, the Dutch and the Topaz lines, were sampled. They comprised 48 cats from the Dutch bloodline, including 9 green-eyed and 31 blue-eyed cats, with some individuals exhibiting signs of deafness, and 8 stillborn kittens. Samples from the Topaz lineage included 10 blue-eyed animals. A brainstem auditory evoked response test revealed a reduced to absent response to auditory stimuli and absent physiological waveforms in all of the 8 examined DBE animals. We sequenced the genome of 2 affected cats from the Dutch line and searched for variants in 19 candidate genes for the human Waardenburg syndrome and pigmentary disorders. This search yielded 9 private protein-changing candidate variants in the genes PAX3, EDN3, KIT, OCA2, SLC24A5, HERC2, and TYRP1. The genotype-phenotype cosegregation was observed for the PAX3 variant within all animals from the Dutch lineage. The mutant allele was absent from 461 control genomes and 241 additionally genotyped green-eyed Maine Coons. We considered the PAX3 variant as the most plausible candidate-a heterozygous nonsense single base pair substitution in exon 6 of PAX3 (NC_051841.1:g.205,787,310G>A, XM_019838731.3:c.937C>T, XP_019694290.1:p.Gln313*), predicted to result in a premature stop codon. PAX3 variants cause auditory-pigmentary syndrome in humans, horses, and mice. Together with the comparative data from other species, our findings strongly suggest PAX3:c.937C>T (OMIA:001688-9685) as the most likely candidate variant for the DBE, deafness, and minimal white spotting in the Maine Coon Dutch line. Finally, we propose the designation of DBERE (Rociri Elvis Dominant Blue Eyes) allele in the domestic cat.</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/PMC11373664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310495","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}
引用次数: 0
Genomic co-localization of variation affecting agronomic and human gut microbiome traits in a meta-analysis of diverse sorghum. 高粱多样性荟萃分析中影响农艺学和人类肠道微生物组性状的基因组共定位变异。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI: 10.1093/g3journal/jkae145
Nate Korth, Qinnan Yang, Mallory J Van Haute, Michael C Tross, Bo Peng, Nikee Shrestha, Mackenzie Zwiener-Malcom, Ravi V Mural, James C Schnable, Andrew K Benson
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