G3: Genes|Genomes|Genetics最新文献_第2页

Bellymount-Pulsed Tracking: A Novel Approach for Real-Time In vivo Imaging of Drosophila Abdominal Tissues. 腹模脉冲跟踪：果蝇腹部组织实时活体成像的新方法

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-18 DOI: 10.1093/g3journal/jkae271

Shruthi Balachandra, Amanda A Amodeo

引用次数: 0

The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki. 低温深海南极秃艽--Trematomus borchgrevinki 的基因组。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-16 DOI: 10.1093/g3journal/jkae267

Niraj Rayamajhi, Angel G Rivera-Colón, Bushra Fazal Minhas, C-H Christina Cheng, Julian M Catchen

{"title":"The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.","authors":"Niraj Rayamajhi, Angel G Rivera-Colón, Bushra Fazal Minhas, C-H Christina Cheng, Julian M Catchen","doi":"10.1093/g3journal/jkae267","DOIUrl":"https://doi.org/10.1093/g3journal/jkae267","url":null,"abstract":"The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643488","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

Establishment of a locally adaptive allele in multidimensional continuous space. 在多维连续空间建立局部适应性等位基因

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-15 DOI: 10.1093/g3journal/jkae266

Takahiro Sakamoto

{"title":"Establishment of a locally adaptive allele in multidimensional continuous space.","authors":"Takahiro Sakamoto","doi":"10.1093/g3journal/jkae266","DOIUrl":"https://doi.org/10.1093/g3journal/jkae266","url":null,"abstract":"Local adaptation is widely seen when species adapt to spatially heterogeneous environments. Although many theoretical studies have investigated the dynamics of local adaptation using two-population models, there remains a need to extend the theoretical framework to continuous space settings, reflecting the real habitats of species. In this study, we use a multidimensional continuous space model and mathematically analyze the establishment process of local adaptation, with a specific emphasis on the relative roles of mutation and migration. First, the role of new mutations is evaluated by deriving the establishment probability of a locally adapted mutation using a branching process and a diffusion approximation. Next, the contribution of immigrants from a neighboring region with similar environmental conditions is considered. Theoretical predictions of the local adaptation rate agreed with the results of Wright-Fisher simulations in both mutation-driven and migration-driven cases. Evolutionary dynamics depend on several factors, including the strength of migration and selection, population density, habitat size, and spatial dimensions. These results offer a theoretical framework for assessing whether mutation or migration predominantly drives convergent local adaptation in spatially continuous environments in the presence of patchy regions with similar environmental conditions.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638501","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

High-quality genome assembly and annotation of the crested gecko (Correlophus ciliatus). 冠壁虎（Correlophus ciliatus）的高质量基因组组装和注释。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-15 DOI: 10.1093/g3journal/jkae265

Ruyi Huang, Jinghang Zhang, Liang Lu, Song Huang, Chenhong Li

引用次数: 0

De novo whole-genome assembly and annotation of Coffea arabica var. Geisha, a high-quality coffee variety from the primary origin of coffee. 咖啡原产地的优质咖啡品种 Coffea arabica var. Geisha 的全新全基因组组装和注释。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-15 DOI: 10.1093/g3journal/jkae262

Juan F Medrano, Dario Cantu, Andrea Minio, Christian Dreischer, Theodore Gibbons, Jason Chin, Shiyu Chen, Allen Van Deynze, Amanda M Hulse-Kemp

{"title":"De novo whole-genome assembly and annotation of Coffea arabica var. Geisha, a high-quality coffee variety from the primary origin of coffee.","authors":"Juan F Medrano, Dario Cantu, Andrea Minio, Christian Dreischer, Theodore Gibbons, Jason Chin, Shiyu Chen, Allen Van Deynze, Amanda M Hulse-Kemp","doi":"10.1093/g3journal/jkae262","DOIUrl":"https://doi.org/10.1093/g3journal/jkae262","url":null,"abstract":"Geisha coffee is recognized for its unique aromas and flavors and accordingly, has achieved the highest prices in the specialty coffee markets. We report the development of a chromosome-level, well-annotated, genome assembly of Coffea arabica var. Geisha. Geisha is considered an Ethiopian landrace that represents germplasm from the Ethiopian center of origin of coffee. We used a hybrid de novo assembly approach combining two long-reads single molecule sequencing technologies, Oxford Nanopore and Pacific Biosciences, together with scaffolding with Hi-C libraries. The final assembly is 1.03GB in size with BUSCO assessment of the assembly completeness of 97.7% of single-copy orthologs clusters. RNAseq and IsoSeq data were used as transcriptional experimental evidence for annotation and gene prediction revealing the presence of 47,062 gene loci encompassing 53,273 protein-coding transcripts. Comparison of the assembly to the progenitor subgenomes separated the set of chromosome sequences inherited from C. canephora from those of C. eugenioides. Corresponding orthologs between the two Arabica varieties, Geisha and Red Bourbon, had a 99.67% median identity, higher than what we observe with the progenitor assemblies (median 97.28%). Both Geisha and Red Bourbon contain a recombination event on Chromosome 10 relative to the two progenitors that must have happened before the geographical separation of the two varieties, consistent with a single allopolyploidization event giving rise to C. arabica. Broadening the availability of high-quality genome assemblies of Coffea arabica varieties, paves the way for understanding the evolution and domestication of coffee, as well as the genetic basis and environmental interactions of why a variety like Geisha is capable of producing beans with such exceptional and unique high-quality.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638500","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

Marginal interaction test for detecting interactions between genetic marker sets and environment in genome-wide studies. 边际交互检验，用于检测全基因组研究中遗传标记集与环境之间的交互作用。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-14 DOI: 10.1093/g3journal/jkae263

Linchuan Shen, Amei Amei, Bowen Liu, Gang Xu, Yunqing Liu, Edwin C Oh, Xin Zhou, Zuoheng Wang

{"title":"Marginal interaction test for detecting interactions between genetic marker sets and environment in genome-wide studies.","authors":"Linchuan Shen, Amei Amei, Bowen Liu, Gang Xu, Yunqing Liu, Edwin C Oh, Xin Zhou, Zuoheng Wang","doi":"10.1093/g3journal/jkae263","DOIUrl":"10.1093/g3journal/jkae263","url":null,"abstract":"As human complex diseases are influenced by the interaction between genetics and the environment, identifying gene-environment interactions (G × E) is crucial for understanding disease mechanisms and predicting risk. Developing robust quantitative tools for G × E analysis can enhance the study of complex diseases. However, many existing methods that explore G × E focus on the interplay between an environmental factor and genetic variants, exclusively for common or rare variants. In this study, we developed MAGEIT_RAN and MAGEIT_FIX to identify interactions between an environmental factor and a set of genetic markers, including both rare and common variants, based on the MinQue for Summary statistics. The genetic main effects in MAGEIT_RAN and MAGEIT_FIX are modeled as random and fixed effects, respectively. Simulation studies showed that both tests had type I error under control, with MAGEIT_RAN being the most powerful test. Applying MAGEIT to a genome-wide analysis of gene-alcohol interactions on hypertension and seated systolic blood pressure in the Multi-Ethnic Study of Atherosclerosis revealed genes like EIF2AK2, CCNDBP1 and EPB42 influencing blood pressure through alcohol interaction. Pathway analysis identified one apoptosis and survival pathway involving PKR and two signal transduction pathways associated with hypertension and alcohol intake, demonstrating MAGEIT_RAN's ability to detect biologically relevant gene-environment interactions.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617953","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

Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction. 完善惩罚性脊回归：优化基因组预测中正则化参数的新方法。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-09 DOI: 10.1093/g3journal/jkae246

Abelardo Montesinos-López, Osval A Montesinos-López, Federico Lecumberry, María I Fariello, José C Montesinos-López, José Crossa

{"title":"Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction.","authors":"Abelardo Montesinos-López, Osval A Montesinos-López, Federico Lecumberry, María I Fariello, José C Montesinos-López, José Crossa","doi":"10.1093/g3journal/jkae246","DOIUrl":"https://doi.org/10.1093/g3journal/jkae246","url":null,"abstract":"The popularity of genomic selection as an efficient and cost-effective approach to estimate breeding values continues to increase, due in part to the significant saving in phenotyping. Ridge regression is one of the most popular methods used for genomic prediction; however, its efficiency (in terms of prediction performance) depends on the appropriate tunning of the penalization parameter. In this paper we propose a novel, more efficient method to select the optimal penalization parameter for Ridge regression. We compared the proposed method with the conventional method to select the penalization parameter in 14 real data sets and we found that in 13 of these, the proposed method outperformed the conventional method and across data sets the gains in prediction accuracy in terms of Pearson's correlation was of 56.15%, with not-gains observed in terms of normalized mean square error. Finally, our results show evidence of the potential of the proposed method, and we encourage its adoption to improve the selection of candidate lines in the context of plant breeding.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617954","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

Correction to: Highly contiguous genome assembly of Drosophila prolongata-a model for evolution of sexual dimorphism and male-specific innovations. Correction to：延长果蝇的高度连续基因组组装--性二型和雄性特异性创新进化的模型。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-07 DOI: 10.1093/g3journal/jkae253

引用次数: 0

Correction to: Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki. 更正：评估基于 Illumina、Nanopore 和 PacBio 基因组组装策略的秃头艽鸡（Trematomus borchgrevinki）。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae214

引用次数: 0

Detection and Annotation of Unique Regions in Mammalian Genomes. 哺乳动物基因组中独特区域的检测与注释

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae257

Beatriz Vieira Mourato, Bernhard Haubold

引用次数: 0