G3 (Bethesda, Md.)最新文献

{"title":"Genomic and gene expression associations to morphology of a sexual ornament in the chicken.","authors":"Vid Bakovic,&nbsp;Andrey Höglund,&nbsp;Maria Luisa Martin Cerezo,&nbsp;Rie Henriksen,&nbsp;Dominic Wright","doi":"10.1093/g3journal/jkac174","DOIUrl":"https://doi.org/10.1093/g3journal/jkac174","url":null,"abstract":"<p><p>How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (&gt;30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40481698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of the cluster MabR prophages of Mycobacterium abscessus and Mycobacterium chelonae.","authors":"Jacob Cote,&nbsp;Colin Welch,&nbsp;Madeline Kimble,&nbsp;Dakota Archambault,&nbsp;John Curtis Ross,&nbsp;Hector Orellana,&nbsp;Katelyn Amero,&nbsp;Claire Bourett,&nbsp;Andre Daigle,&nbsp;Keith W Hutchison,&nbsp;Sally D Molloy","doi":"10.1093/g3journal/jkac188","DOIUrl":"https://doi.org/10.1093/g3journal/jkac188","url":null,"abstract":"<p><p>Mycobacterium abscessus is an emerging pathogen of concern in cystic fibrosis and immunocompromised patients and is considered one of the most drug-resistant mycobacteria. The majority of clinical Mycobacterium abscessus isolates carry 1 or more prophages that are hypothesized to contribute to virulence and bacterial fitness. The prophage McProf was identified in the genome of the Bergey strain of Mycobacterium chelonae and is distinct from previously described prophages of Mycobacterium abscessus. The McProf genome increases intrinsic antibiotic resistance of Mycobacterium chelonae and drives expression of the intrinsic antibiotic resistance gene, whiB7, when superinfected by a second phage. The prevalence of McProf-like genomes was determined in sequenced mycobacterial genomes. Related prophage genomes were identified in the genomes of 25 clinical isolates of Mycobacterium abscessus and assigned to the novel cluster, MabR. They share less than 10% gene content with previously described prophages; however, they share features typical of prophages, including polymorphic toxin-immunity systems.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40549928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic-interaction screens uncover novel biological roles and regulators of transcription factors in fission yeast.","authors":"Kate Chatfield-Reed,&nbsp;Kurtis Marno Jones,&nbsp;Farah Shah,&nbsp;Gordon Chua","doi":"10.1093/g3journal/jkac194","DOIUrl":"https://doi.org/10.1093/g3journal/jkac194","url":null,"abstract":"<p><p>In Schizosaccharomyces pombe, systematic analyses of single transcription factor deletion or overexpression strains have made substantial advances in determining the biological roles and target genes of transcription factors, yet these characteristics are still relatively unknown for over a quarter of them. Moreover, the comprehensive list of proteins that regulate transcription factors remains incomplete. To further characterize Schizosaccharomyces pombe transcription factors, we performed synthetic sick/lethality and synthetic dosage lethality screens by synthetic genetic array. Examination of 2,672 transcription factor double deletion strains revealed a sick/lethality interaction frequency of 1.72%. Phenotypic analysis of these sick/lethality strains revealed potential cell cycle roles for several poorly characterized transcription factors, including SPBC56F2.05, SPCC320.03, and SPAC3C7.04. In addition, we examined synthetic dosage lethality interactions between 14 transcription factors and a miniarray of 279 deletion strains, observing a synthetic dosage lethality frequency of 4.99%, which consisted of known and novel transcription factor regulators. The miniarray contained deletions of genes that encode primarily posttranslational-modifying enzymes to identify putative upstream regulators of the transcription factor query strains. We discovered that ubiquitin ligase Ubr1 and its E2/E3-interacting protein, Mub1, degrade the glucose-responsive transcriptional repressor Scr1. Loss of ubr1+ or mub1+ increased Scr1 protein expression, which resulted in enhanced repression of flocculation through Scr1. The synthetic dosage lethality screen also captured interactions between Scr1 and 2 of its known repressors, Sds23 and Amk2, each affecting flocculation through Scr1 by influencing its nuclear localization. Our study demonstrates that sick/lethality and synthetic dosage lethality screens can be effective in uncovering novel functions and regulators of Schizosaccharomyces pombe transcription factors.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40691544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae) provides insights into the evolution of a detoxification system.","authors":"Zhongjun Gong,&nbsp;Tong Li,&nbsp;Jin Miao,&nbsp;Yun Duan,&nbsp;Yueli Jiang,&nbsp;Huiling Li,&nbsp;Pei Guo,&nbsp;Xueqin Wang,&nbsp;Jing Zhang,&nbsp;Yuqing Wu","doi":"10.1093/g3journal/jkac161","DOIUrl":"https://doi.org/10.1093/g3journal/jkac161","url":null,"abstract":"<p><p>The orange wheat blossom midge Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae), an economically important pest, has caused serious yield losses in most wheat-growing areas worldwide in the past half-century. A high-quality chromosome-level genome for S. mosellana was assembled using PacBio long read, Illumina short read, and Hi-C sequencing technologies. The final genome assembly was 180.69 Mb, with contig and scaffold N50 sizes of 998.71 kb and 44.56 Mb, respectively. Hi-C scaffolding reliably anchored 4 pseudochromosomes, accounting for 99.67% of the assembled genome. In total, 12,269 protein-coding genes were predicted, of which 91% were functionally annotated. Phylogenetic analysis indicated that S. mosellana and its close relative, the swede midge Contarinia nasturtii, diverged about 32.7 MYA. The S. mosellana genome showed high chromosomal synteny with the genome of Drosophila melanogaster and Anopheles gambiae. The key gene families involved in the detoxification of plant secondary chemistry were analyzed. The high-quality S. mosellana genome data will provide an invaluable resource for research in a broad range of areas, including the biology, ecology, genetics, and evolution of midges, as well as insect-plant interactions and coevolution.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40395335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"G1-Cyclin2 (Cln2) promotes chromosome hypercondensation in eco1/ctf7 rad61 null cells during hyperthermic stress in Saccharomyces cerevisiae.","authors":"Sean Buskirk, Robert V Skibbens","doi":"10.1093/g3journal/jkac157","DOIUrl":"10.1093/g3journal/jkac157","url":null,"abstract":"<p><p>Eco1/Ctf7 is a highly conserved acetyltransferase that activates cohesin complexes and is critical for sister chromatid cohesion, chromosome condensation, DNA damage repair, nucleolar integrity, and gene transcription. Mutations in the human homolog of ECO1 (ESCO2/EFO2), or in genes that encode cohesin subunits, result in severe developmental abnormalities and intellectual disabilities referred to as Roberts syndrome and Cornelia de Lange syndrome, respectively. In yeast, deletion of ECO1 results in cell inviability. Codeletion of RAD61 (WAPL in humans), however, produces viable yeast cells. These eco1 rad61 double mutants, however, exhibit a severe temperature-sensitive growth defect, suggesting that Eco1 or cohesins respond to hyperthermic stress through a mechanism that occurs independent of Rad61. Here, we report that deletion of the G1 cyclin CLN2 rescues the temperature-sensitive lethality otherwise exhibited by eco1 rad61 mutant cells, such that the triple mutant cells exhibit robust growth over a broad range of temperatures. While Cln1, Cln2, and Cln3 are functionally redundant G1 cyclins, neither CLN1 nor CLN3 deletions rescue the temperature-sensitive growth defects otherwise exhibited by eco1 rad61 double mutants. We further provide evidence that CLN2 deletion rescues hyperthermic growth defects independent of START and impacts the state of chromosome condensation. These findings reveal novel roles for Cln2 that are unique among the G1 cyclin family and appear critical for cohesin regulation during hyperthermic stress.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40255358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome of the bee Holcopasites calliopsidis-a species showing the common apid trait of brood parasitism.","authors":"Trevor J L Sless,&nbsp;Jeremy B Searle,&nbsp;Bryan N Danforth","doi":"10.1093/g3journal/jkac160","DOIUrl":"https://doi.org/10.1093/g3journal/jkac160","url":null,"abstract":"<p><p>Brood parasites represent a substantial but often poorly studied fraction of the wider diversity of bees. Brood parasitic bees complete their life cycles by infiltrating the nests of solitary host bees thereby enabling their offspring to exploit the food provisions intended for the host's offspring. Here, we present the draft assembly of the bee Holcopasites calliopsidis, the first brood parasitic species to be the subject of detailed genomic analysis. Consistent with previous findings on the genomic signatures of parasitism more broadly, we find that H. calliopsidis has the smallest genome currently known among bees (179 Mb). This small genome does not appear to be the result of purging of repetitive DNA, with some indications of novel repetitive elements which may show signs of recent expansion. Nor does H. calliopsidis demonstrate any apparent net loss of genic content in comparison with nonparasitic species, though many individual gene families do show significant contractions. Although the basis of the small genome size of this species remains unclear, the identification of over 12,000 putative genes-with functional annotation for nearly 10,000 of these-is an important step in investigating the genomic basis of brood parasitism and provides a valuable dataset to be compared against new genomes that remain to be sequenced.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40406698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The arginine methyltransferase Carm1 is necessary for heart development.","authors":"Sophie Jamet, Seungshin Ha, Tzu-Hua Ho, Scott Houghtaling, Andrew Timms, Kai Yu, Alison Paquette, Ali Murat Maga, Nicholas D E Greene, David R Beier","doi":"10.1093/g3journal/jkac155","DOIUrl":"10.1093/g3journal/jkac155","url":null,"abstract":"<p><p>To discover genes implicated in human congenital disorders, we performed ENU mutagenesis in the mouse and screened for mutations affecting embryonic development. In this work, we report defects of heart development in mice homozygous for a mutation of coactivator-associated arginine methyltransferase 1 (Carm1). While Carm1 has been extensively studied, it has never been previously associated with a role in heart development. Phenotype analysis combining histology and microcomputed tomography imaging shows a range of cardiac defects. Most notably, many affected midgestation embryos appear to have cardiac rupture and hemorrhaging in the thorax. Mice that survive to late gestation show a variety of cardiac defects, including ventricular septal defects, double outlet right ventricle, and persistent truncus arteriosus. Transcriptome analyses of the mutant embryos by mRNA-seq reveal the perturbation of several genes involved in cardiac morphogenesis and muscle development and function. In addition, we observe the mislocalization of cardiac neural crest cells at E12.5 in the outflow tract. The cardiac phenotype of Carm1 mutant embryos is similar to that of Pax3 null mutants, and PAX3 is a putative target of CARM1. However, our analysis does not support the hypothesis that developmental defects in Carm1 mutant embryos are primarily due to a functional defect of PAX3.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40255363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A chromosome-level genome assembly of Neotoxoptera formosana (Takahashi, 1921) (Hemiptera: Aphididae).","authors":"Shuai Ye,&nbsp;Chen Zeng,&nbsp;Jian-Feng Liu,&nbsp;Chen Wu,&nbsp;Yan-Fei Song,&nbsp;Yao-Guo Qin,&nbsp;Mao-Fa Yang","doi":"10.1093/g3journal/jkac164","DOIUrl":"https://doi.org/10.1093/g3journal/jkac164","url":null,"abstract":"<p><p>Neotoxoptera formosana (Takahashi), the onion aphid, is an oligophagous pest that mainly feeds on plants from the Allium genus. It sucks nutrients from the plants and indirectly acts as a vector for plant viruses. This aphid causes severe economic losses to Allium tuberosum agriculture in China. To better understand the host plant specificity of N. formosana on Allium plants and provide essential information for the control of this pest, we generated the entire genome using Pacific Biosciences long-read sequencing and Hi-C data. Six chromosomes were assembled to give a final size of 372.470 Mb, with an N50 scaffold of 66.911 Mb. The final draft genome assembly, from 192 Gb of raw data, was approximately 371.791 Mb in size, with an N50 contig of 24.99 Kb and an N50 scaffold of 2.637 Mb. The average GC content was 30.96%. We identified 73 Mb (31.22%) of repetitive sequences, 14,175 protein-coding genes, and 719 noncoding RNAs. The phylogenetic analysis showed that N. formosana and Pentalonia nigronervosa are sister groups. We found significantly expanded gene families that were involved in the THAP domain, the DDE superfamily endonuclease, zinc finger, immunity (ankyrin repeats), digestive enzyme (serine carboxypeptidase) and chemosensory receptor. This genome assembly could provide a solid foundation for future studies on the host specificity of N. formosana and pesticide-resistant aphid management.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40463105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Publishing student-led discoveries in genetics.","authors":"Danielle Heller,&nbsp;Viknesh Sivanathan","doi":"10.1093/g3journal/jkac141","DOIUrl":"https://doi.org/10.1093/g3journal/jkac141","url":null,"abstract":"In a Mutant Screen Report in this issue, we (Heller et al. ) report the findings of a genome-wide screen to identify novel mycobacteriophage gene products capable of inhibiting mycobacterial growth. Overexpression of the 94 genes encoded by phage Waterfoul in the host bacterium Mycobacterium smegmatis revealed 32 gene products capable of hindering mycobacterial growth to varying degrees; half of these gene products harbor no recognizable domains or homol-ogy to gene products of known function, offering many novel growth inhibitors for future characterization. This is the first report from the HHMI Science Education Alliance-Gene-function Exploration by a Network of Emerging Scientists (SEA-GENES) project, a new project that engages undergraduate scientists and their faculty instructors in an exploration of bacteriophage genetics within the context of undergraduate science courses. of","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40139087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription factor retention through multiple polyploidization steps in wheat.","authors":"Catherine E B Evans,&nbsp;Ramesh Arunkumar,&nbsp;Philippa Borrill","doi":"10.1093/g3journal/jkac147","DOIUrl":"https://doi.org/10.1093/g3journal/jkac147","url":null,"abstract":"<p><p>Whole-genome duplication is widespread in plant evolutionary history and is followed by nonrandom gene loss to return to a diploid state. Across multiple angiosperm species, the retained genes tend to be dosage-sensitive regulatory genes such as transcription factors, yet data for younger polyploid species is sparse. Here, we analyzed the retention, expression, and genetic variation in transcription factors in the recent allohexaploid bread wheat (Triticum aestivum L.). By comparing diploid, tetraploid, and hexaploid wheat, we found that, following each of two hybridization and whole-genome duplication events, the proportion of transcription factors in the genome increased. Transcription factors were preferentially retained over other genes as homoeologous groups in tetraploid and hexaploid wheat. Across cultivars, transcription factor homoeologs contained fewer deleterious missense mutations than nontranscription factors, suggesting that transcription factors are maintained as three functional homoeologs in hexaploid wheat populations. Transcription factor homoeologs were more strongly coexpressed than nontranscription factors, indicating conservation of function between homoeologs. We found that the B3, MADS-M-type, and NAC transcription factor families were less likely to have three homoeologs present than other families, which was associated with low expression levels and high levels of tandem duplication. Together, our results show that transcription factors are preferentially retained in polyploid wheat genomes although there is variation between families. Knocking out one transcription factor homoeolog to alter gene dosage, using TILLING or CRISPR, could generate new phenotypes for wheat breeding.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40396245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}