G3: Genes|Genomes|Genetics最新文献_第2页

A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation. 花期可塑性反应规范揭示了玉米适应的生理足迹。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-20 DOI: 10.1093/g3journal/jkaf095

Justine Drouault, Carine Palaffre, Emilie J Millet, Jonas Rodriguez, Pierre Martre, Kristian Johnson, Boris Parent, Claude Welcker, Randall J Wisser

{"title":"A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation.","authors":"Justine Drouault, Carine Palaffre, Emilie J Millet, Jonas Rodriguez, Pierre Martre, Kristian Johnson, Boris Parent, Claude Welcker, Randall J Wisser","doi":"10.1093/g3journal/jkaf095","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf095","url":null,"abstract":"Understanding how plant phenotypes are shaped by their environments is crucial for addressing questions about crop adaptation to new environments. This study focused on analyzing the genetic variability underlying genotype-environment interactions and adaptation for flowering time in maize. We present a physiological reaction norm for flowering time plasticity (PRN-FTP), modeled from multi-environment trial networks and decomposed into its physiological components. We show how genotype-specific differences in developmental responses to temperature fluctuations condition differences in photoperiod perceived among genotypes. This occurs not only across but also within common environments, as the perception of photoperiod is altered by variation in rates of development and durations for becoming sensitized to photoperiod. Using a new metric for envirotyping sensed photoperiods for maize, it was found that, at high latitudes, different genotypes in the same environment can experience up to hours-long differences in photoperiod. This emphasizes the importance of considering genotype-specific differences in the experienced environment when investigating plasticity. Modeling the PRN-FTP for globally representative breeding material showed that tropical and temperate germplasm occupy distinct territories of the trait space for PRN-FTP parameters. Placed in the historical context of maize, our findings suggest that the geographical spread and breeding of maize was mediated by a specific modality of ecophysiological adaptation of flowering time. Our study has implications for understanding crop adaptation and for future crop improvement efforts.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110259","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

Optimization of recurrent rapid cycle breeding in maize for sustained long-term genetic improvement via stochastic simulations. 基于随机模拟的玉米快速循环育种优化研究。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-20 DOI: 10.1093/g3journal/jkaf100

Torsten Pook, Mila Leonie Tost, Henner Simianer

{"title":"Optimization of recurrent rapid cycle breeding in maize for sustained long-term genetic improvement via stochastic simulations.","authors":"Torsten Pook, Mila Leonie Tost, Henner Simianer","doi":"10.1093/g3journal/jkaf100","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf100","url":null,"abstract":"In recent years, the turnover of germplasm in plant breeding has substantially increased as the use of genomic information allows for earlier selection and the integration of controlled growing environments reduces the time to reach a particular growing stage. However, high generation turnover and intensive selection of lines before own yield trials are performed come at the risk of a drastic reduction of genetic diversity and lower prediction accuracies. To this end, we investigate strategies to cope with these challenges in a maize rapid cycle breeding scheme using stochastic simulations employing the software MoBPS. We find that genetic gains soon reach a plateau when only the original breeding material is phenotyped. Updating the training data set via additional phenotyping of crosses or doubled haploid lines ensures long-term progress with a gain of 6.80 / 6.95 genetic standard deviations for the performance as a cross / DH after 30 cycles of breeding compared to 3.40 / 4.28 without additional phenotyping. Introducing genetic material from outside the breeding pool to introduce novel genetic diversity led to a further increase to 9.34 / 7.89 genetic standard deviations. In particular, for the management of genetic diversity, further modifications of breeding program design are analyzed to optimize the number of selected lines per cycle and to account for the relatedness of F2 plants in the selection using the software AlphaMate. Balancing short-term genetic gains with long-term diversity preservation is crucial for sustainable breeding. MoBPS provides a tool for quantifying these effects and provides solutions specific to the respective breeding program.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110341","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 assembly of Bougainvillia cf. muscus (Cnidaria: Hydrozoa). 九重根线虫（刺胞纲：水螅纲）基因组组装。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-19 DOI: 10.1093/g3journal/jkaf110

Aide Macias-Muñoz, Rebecca Varney, Eva Katcher, Maia Everhart, Todd H Oakley

{"title":"Genome assembly of Bougainvillia cf. muscus (Cnidaria: Hydrozoa).","authors":"Aide Macias-Muñoz, Rebecca Varney, Eva Katcher, Maia Everhart, Todd H Oakley","doi":"10.1093/g3journal/jkaf110","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf110","url":null,"abstract":"As one of just a handful of non-Bilaterian animal phyla, Cnidaria are key to understanding genome evolution across Metazoa. Despite their importance and diversity, the genomes of most species in the phylum are unsequenced, due in large part to difficulties cultivating them in a laboratory. Here, we present a genome sequence of Bougainvillia cf. muscus, a hydrozoan with four marginal bulbs each containing seven simple eyes (ocelli). This species appeared in our tanks from contamination. While we lacked sufficient samples for transcriptomic or functional studies, we were able to expand our knowledge of how the genome of this species compares to the few, better studied members of hydrozoans by investigating synteny to other cnidarians, repetitive element content, and phylogenetics and synteny of vision-related genes in this eyed species compared to eyeless relatives. The genome sequence consists of 350 contigs with an N50 of 10 Mb, a total genome length of 375.328 Mb, a BUSCO score of 90.1%, and predicted protein coding genes totaling 46,431. We found a high degree of macrosynteny conservation with Hydra vulgaris, Hydractinia symbiolongicarpus, and Turritopsis rubra. Repetitive elements make up 62% of this Bougainvillia genome. For vision-related genes, we identified 20 cnidarian opsins (cnidops) in Bougainvillia and found instances of gene duplication and loss in families associated with bilaterian eye development, phototransduction, and visual cycling. This high-quality, contiguous genome in an eyed Hydrozoan will be a valuable resource for additional comparative genomic studies.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101650","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

Site-to-site mutational dissection of fission yeast cohesin reveals its dynamics. 裂变酵母内聚蛋白的点对点突变解剖揭示了其动力学。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-19 DOI: 10.1093/g3journal/jkaf111

Qi Wei, Li Wang, Yichen Zhang, Saidaiguli Abulimiti, Jie Wang, Xingya Xu

{"title":"Site-to-site mutational dissection of fission yeast cohesin reveals its dynamics.","authors":"Qi Wei, Li Wang, Yichen Zhang, Saidaiguli Abulimiti, Jie Wang, Xingya Xu","doi":"10.1093/g3journal/jkaf111","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf111","url":null,"abstract":"Cohesin is a heteropentameric protein complex that holds sister chromatids together from S phase to anaphase. Its two structural maintenance of chromosomes (SMC) subunits form a heterodimer, consisting of an ATPase head domain and a hinge domain connected by long coiled coils. Kleisin subunit associates with the head. Here, using Schizosaccharomyces pombe, we genetically dissected cohesin dynamics based on the relationship between the mutations causing temperature-sensitive and their suppressor mutations. First, we identified suppressor mutations that could rescue the lethality caused by cohesin ATPase mutations. Mutations in the DNA binding domain of cohesin loader Mis4, or in cell-cycle genes encoding MBF transcription factor complex or Wee1 kinase, rescued both Psm1 and Psm3 ATPase mutants. Then, we performed targeted mutagenesis in both ATPase domains for single-amino-acid substitutions, that can rescue the lethality of a kleisin ts mutant at restrictive temperature. Comparison of mutations obtained in Psm1 and Psm3 ATPase domains revealed that analogous mutations in the two ATPase domains were frequently observed. Last, suppressors of a coiled-coil mutation were mapped in coiled coils, indicating that proper folding of coiled coils is critical for cohesin functions. Suppressors of a hinge interface mutation frequently located at the other hinge interface, indicating that the two cohesin hinge interfaces work collaboratively in hinge-hinge interactions. Overall, genetic dissection of the relationship between cohesin lethal mutations and their suppressor mutations reflects cohesin dynamics in vivo.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101651","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

Phenological variation associates with the stability of fruit quality traits in cultivated tetraploid blueberry. 栽培四倍体蓝莓果实品质性状的稳定性与物候变异有关。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-15 DOI: 10.1093/g3journal/jkaf108

Ebrahiem Babiker, Kyoka Nagasaka, Soichiro Nishiyama, Hisayo Yamane, Ryohei Nakano, Ryutaro Tao

{"title":"Phenological variation associates with the stability of fruit quality traits in cultivated tetraploid blueberry.","authors":"Ebrahiem Babiker, Kyoka Nagasaka, Soichiro Nishiyama, Hisayo Yamane, Ryohei Nakano, Ryutaro Tao","doi":"10.1093/g3journal/jkaf108","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf108","url":null,"abstract":"Fruit quality represent the major constraints to consumer acceptance of new blueberry cultivars. However, breeding for fruit quality is challenging due to its complex inheritance and genotype × environment interaction. Despite previous efforts to detect quantitative trait loci (QTL) associated with fruit quality traits, most of the identified QTL explain only a fraction of the total variability or lack stability across multiple environments. In this study, we investigated multiple fruit quality traits and phenology-related traits of 187 diverse southern highbush blueberry germplasm over two to four years. Significant phenotypic variation across observation years was detected for most traits. Genome-wide association study (GWAS) failed to identify stable peaks supported by multiple observation years, indicating complex control of fruit-related traits. To elucidate factors contributing to phenotypic variation, the relationship between observed phenotypic values and the stability measure of these values was examined. Significant correlations were found between the variation of phenology-related traits and the stability of fruit-related traits; it was found that early blooming and ripening accessions tended to exhibit variable firmness over the years. Additionally, size variability was influenced by the fruit size itself: accessions producing smaller fruit tended to show more variation in size over the years. Furthermore, GWAS conducted on the stability indices identified novel marker-trait associations that were not detected using normalized phenotypic values only, and their effects on fruit-related traits were similarly dependent on environment (observation year). Collectively, these findings deepen our understanding of variability in fruit-related traits and provide insights into their genetic control, thereby advancing breeding for superior cultivars with stable phenotypic performance.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077102","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

Gene expression and pollen performance indicate altered postmating selection between Solanum species with different mating systems. 基因表达和花粉表现表明，不同交配制度的茄属植物在交配后的选择发生了改变。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-15 DOI: 10.1093/g3journal/jkaf107

Timothy J Biewer-Heisler, Matthew J S Gibson, Emily Sornay, Leonie C Moyle

{"title":"Gene expression and pollen performance indicate altered postmating selection between Solanum species with different mating systems.","authors":"Timothy J Biewer-Heisler, Matthew J S Gibson, Emily Sornay, Leonie C Moyle","doi":"10.1093/g3journal/jkaf107","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf107","url":null,"abstract":"Postmating prezygotic (PMPZ) traits play an important role in mating success, especially in species where gametes from multiple males compete. Despite this, the effect of mating system transitions, and attendant shifts in the intensity of sexual selection, on specific PMPZ traits and loci is still poorly understood. Here we assessed differences in pollen PMPZ traits and tissue-specific gene expression (in leaf, pollen, and style) between two closely related plant species with different mating systems-Solanum lycopersicum (selfing) & Solanum pennellii (outcrossing). We focused on species differences in loci with known roles in pollen tube growth rate, including pectin methylesterases (PMEs) and their inhibitors (PMEIs), and in-vitro & in-vivo pollen tube growth rates. Among the gene expression differences observed between species, we found that the expression domain of pollen-biased genes was much narrower in the selfing species S. lycopersicum compared to the outcrossing species S. pennellii, including for most reproductive PMEs and PMEIs. In addition, S. pennellii had faster pollen tube growth rates in-vivo, while S. lycopersicum had faster in-vitro pollen tube growth rates. We propose that the lower expression of pollen tube development genes in S. lycopersicum style tissue, and reduced in-vivo pollen performance, is a result of reduced allocation to stylar mechanisms that modulate pollen tube growth, potentially consistent with relaxed selection on cryptic female choice in the selfing species.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077099","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

Chromosome-length genome assembly of the critically endangered Mountain bongo (Tragelaphus eurycerus isaaci): A resource for conservation and comparative genomics. 极度濒危山邦戈（Tragelaphus eurycerus isaaci）的染色体长度基因组组装：保护和比较基因组学的资源。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-15 DOI: 10.1093/g3journal/jkaf109

Karen M Holm, Klaus-Peter Koepfli, Budhan S Pukazhenthi, Aakrosh Ratan, Karl J Fryxell, Melanie Pham, David Weisz, Olga Dudchenko, Erez Lieberman Aiden, Haw Chuan Lim

{"title":"Chromosome-length genome assembly of the critically endangered Mountain bongo (Tragelaphus eurycerus isaaci): A resource for conservation and comparative genomics.","authors":"Karen M Holm, Klaus-Peter Koepfli, Budhan S Pukazhenthi, Aakrosh Ratan, Karl J Fryxell, Melanie Pham, David Weisz, Olga Dudchenko, Erez Lieberman Aiden, Haw Chuan Lim","doi":"10.1093/g3journal/jkaf109","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf109","url":null,"abstract":"The Mountain bongo (Tragelaphus eurycerus isaaci), a critically endangered tragelaphine antelope native to the montane forests of Kenya, faces significant threats from habitat loss and hunting. Although the Mountain bongo is a flagship species in Kenya, the majority are found in small, isolated populations of less than 100 animals total, making it a species of high conservation concern. In this report, we present a chromosome-length draft genome assembly for the Mountain bongo, generated using a combination of linked-read and proximity ligation (Hi-C) sequencing techniques. The assembly resulted in a 2.96 Gb sized genome with a contig N50 of 79.5 kb and a scaffold N50 of 192 Mb. Assembly completeness was 95.1% based on 12,234 Benchmarking Universal Single-Copy Orthologs (BUSCO) and annotation revealed 29,820 protein coding genes, of which 27,761 were functionally annotated, and a repetitive content of 47.31%. Synteny analysis against the domestic cattle (Bos taurus) genome assembly revealed numerous chromosomal rearrangements between the two species. Our analysis also revealed insights into the evolutionary and demographic history of the Mountain bongo, offering valuable information for conservation management. We also assembled and annotated the mitochondrial genome which showed <1% differences from the Lowland bongo subspecies, T. e. eurycerus. By integrating genomic data with traditional conservation methods, this reference lays the foundation to evaluate and preserve genetic diversity of both in-situ and ex-situ populations of the Mountain bongo amidst growing environmental pressures.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077096","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

Nuclear and organelle genome assemblies of five Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups. 属不同植物类群的5个甜瓜材料Ananas、Canton、PI 414723、Vedrantais和Zhimali的细胞核和细胞器基因组组装

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-13 DOI: 10.1093/g3journal/jkaf098

Javier Belinchon-Moreno, Aurelie Berard, Aurelie Canaguier, Isabelle Le-Clainche, Vincent Rittener-Ruff, Jacques Lagnel, Damien Hinsinger, Nathalie Boissot, Patricia Faivre-Rampant

{"title":"Nuclear and organelle genome assemblies of five Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups.","authors":"Javier Belinchon-Moreno, Aurelie Berard, Aurelie Canaguier, Isabelle Le-Clainche, Vincent Rittener-Ruff, Jacques Lagnel, Damien Hinsinger, Nathalie Boissot, Patricia Faivre-Rampant","doi":"10.1093/g3journal/jkaf098","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf098","url":null,"abstract":"The construction of accurate whole genome sequences is pivotal for characterizing the genetic diversity of plant species, identifying genes controlling important traits, or understanding their evolutionary dynamics. Here, we generated the nuclear, mitochondrial and chloroplast high-quality assemblies of five melon (Cucumis melo L.) accessions representing five botanical groups, using the Oxford Nanopore sequencing technology. The accessions here studied included varied origins, fruit shapes, sizes, and resistance traits, providing a holistic view of melon genomic diversity. The final chromosome-level genome assemblies ranged in size from 359 to 365 Mb, with approximately 25× coverage for four of them multiplexed in half of a PromethION flowcell, and 48× coverage for the fifth, sequenced individually in another half of a PromethION flowcell. Contigs N50 ranged from seven to 15 Mb for all the assemblies, and very long contigs reaching sizes of 20-25 Mb, almost compatible with complete chromosomes, were assembled in all the accessions. Quality assessment through BUSCO and Merqury indicated the high completeness and accuracy of the assemblies, with BUSCO values exceeding 96% for all accessions, and Merqury QV values ranging between 41 and 47. We focused on the complex NLR resistance gene regions to validate the accuracy of the assemblies in highly complex and repetitive regions. Through Nanopore adaptive sampling, we generated accurate targeted assemblies of these regions with a significantly higher coverage, enabling the comparison to our whole genome assemblies. Overall, these chromosome-level assembled genomes constitute a valuable resource for research focused on melon diversity, disease resistance, evolution, and breeding applications.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143977188","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 Drosophila nucleoporin ELYS is required for parental chromosome arrangement at fertilization. 果蝇核孔蛋白ELYS是受精时亲本染色体排列所必需的。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-13 DOI: 10.1093/g3journal/jkaf104

Kazuyuki Hirai, Hiroki Sakamoto, Yoko Keira, Mika Ozaki, Kanta Yamazoe, Hiroyuki O Ishikawa, Yoshihiro H Inoue, Kyoichi Sawamura

{"title":"The Drosophila nucleoporin ELYS is required for parental chromosome arrangement at fertilization.","authors":"Kazuyuki Hirai, Hiroki Sakamoto, Yoko Keira, Mika Ozaki, Kanta Yamazoe, Hiroyuki O Ishikawa, Yoshihiro H Inoue, Kyoichi Sawamura","doi":"10.1093/g3journal/jkaf104","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf104","url":null,"abstract":"One key aspect of fertilization is the unification of the maternal and paternal genomes driven by the first mitotic spindle. However, little is known about the mechanisms that underlie the formation of a bipolar spindle that interacts with the two discrete chromosome sets in juxtaposition. We here show that, in Drosophila, the maternally provided ELYS-an evolutionarily conserved subunit of the nuclear pore complex-localizes to female and male pronuclei and then redistributes to the interior of the spindle and the resulting zygotic nuclei. Both Elys loss-of-function mutations and ELYS overexpression in the female germline were associated with maternal-effect lethality. Our cytological studies of fertilized eggs revealed that ELYS is primarily involved in the apposition of female and male pronuclei, potentially impacting the parental genome configuration of the first mitotic spindle. We propose that pronuclear apposition is essential for centrosome localization at the emergent pronuclear junction to promote bipolar spindle formation for the first mitosis. In addition, we discuss the possible involvement of ELYS in interspecific hybrid incompatibility.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143997162","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

Draft genome of the endemic alpine ground beetle Carabus (Platycarabus) depressus (Coleoptera: Carabidae) from long-read sequencing of a frozen archived specimen. 从冷冻存档标本的长读测序中绘制特有高山地面甲虫Carabus (Platycarabus) depressus（鞘翅目：Carabidae）的基因组。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-05-08 DOI: 10.1093/g3journal/jkaf027

Jérémy Gauthier, Cody Raul Cardenas, Matilde Nari, Conrad P D T Gillett, Emmanuel F A Toussaint

{"title":"Draft genome of the endemic alpine ground beetle Carabus (Platycarabus) depressus (Coleoptera: Carabidae) from long-read sequencing of a frozen archived specimen.","authors":"Jérémy Gauthier, Cody Raul Cardenas, Matilde Nari, Conrad P D T Gillett, Emmanuel F A Toussaint","doi":"10.1093/g3journal/jkaf027","DOIUrl":"10.1093/g3journal/jkaf027","url":null,"abstract":"The rapid advancement of genomic technologies has enabled the production of highly contiguous reference genomes for nonmodel organisms. However, these methods often require exceptionally fresh material containing unfragmented high-molecular-weight nucleic acids. Researchers who preserve field-collected specimens in ethanol at ambient temperatures, prior to transferring them to long-term frozen archives, face challenges in applying advanced genomic approaches due to DNA and RNA fragmentation under suboptimal preservation conditions. To explore the potential of such preserved specimens as sources of reference genomes, we utilized Nanopore MinION technology to generate genomic data from a frozen archived specimen of the endemic alpine ground beetle Carabus (Platycarabus) depressus. Using a rapid in-house protocol for high-molecular-weight DNA extraction, followed by sequencing on a single flow cell, we produced 8.75 million raw reads with an N50 of 2.8 kb. The resulting assembly achieved remarkable completeness, recovering up to 98% of Benchmarking Universal Single-Copy Orthologs genes, despite a moderate N50 of 945 kb. This genome is only the second available for the taxonomically diverse genus Carabus, demonstrating the feasibility of using short-to-long-read sequencing on frozen archived specimens commonly housed in natural history collections. These findings open new avenues for advancing nonmodel organism genomics and its downstream applications.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491293","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