G3: Genes|Genomes|Genetics最新文献

{"title":"Detection and Annotation of Unique Regions in Mammalian Genomes.","authors":"Beatriz Vieira Mourato, Bernhard Haubold","doi":"10.1093/g3journal/jkae257","DOIUrl":"https://doi.org/10.1093/g3journal/jkae257","url":null,"abstract":"<p><p>Long unique genomic regions have been reported to be highly enriched for developmental genes in mice and humans. In this paper we identify unique genomic regions using an efficient method based on fast string matching. We quantify the resource consumption and accuracy of this method before applying it to the genomes of 18 mammals. We annotate their unique regions of at least 10 kb and find that they are strongly enriched for developmental genes across the board. We then investigated the subset of unique regions that lack annotations, which we call \"anonymous\". The longest anonymous unique region in the tasmanian devil spanned 83 kb and contained the gene encoding inositol polyphosphate-5-phosphatase A, which is an essential part of intracellular signaling. This discovery of an essential gene in a unique region implies that unique regions might be given priority when annotating mammalian genomes. Our documented pipeline for annotating unique regions in any mammalian genome is available from the repository github.com/evolbioinf/auger; additional data for this study is available from the dataverse at doi.org/10.17617/3.4IKQAG.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582681","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}

{"title":"Correction to: Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki.","authors":"","doi":"10.1093/g3journal/jkae214","DOIUrl":"10.1093/g3journal/jkae214","url":null,"abstract":"","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283227","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}

{"title":"Somy evolution in the honey bee infecting trypanosomatid parasite, Lotmaria passim.","authors":"Lindsey M Markowitz, Anthony Nearman, Zexuan Zhao, Dawn Boncristiani, Anzhelika Butenko, Luis Miguel de Pablos, Arturo Marin, Guang Xu, Carlos A Machado, Ryan S Schwarz, Evan C Palmer-Young, Jay D Evans","doi":"10.1093/g3journal/jkae258","DOIUrl":"https://doi.org/10.1093/g3journal/jkae258","url":null,"abstract":"<p><p>Lotmaria passim is a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome-which was completed before its differentiation from the closely related Crithidia mellificae-has remained the reference for this species despite lacking improvements from newer methodologies. Here we report the updated sequencing, assembly, and annotation of the BRL type strain (ATCC PRA-422) of Lotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provides evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582683","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}

{"title":"The Gongora gibba genome assembly provides new insights into the evolution of floral scent in male euglossine bee-pollinated orchids.","authors":"Maria Fernanda Guizar Amador, Kathy Darragh, Jasen W Liu, Cheryl Dean, Diego Bogarín, Oscar A Pérez-Escobar, Zuleika Serracín, Franco Pupulin, Santiago R Ramírez","doi":"10.1093/g3journal/jkae211","DOIUrl":"10.1093/g3journal/jkae211","url":null,"abstract":"<p><p>Orchidaceae is one of the most prominent flowering plant families, with many species exhibiting highly specialized reproductive and ecological adaptations. An estimated 10% of orchid species in the American tropics are pollinated by scent-collecting male euglossine bees; however, to date, there are no published genomes of species within this pollination syndrome. In this study, we present the first draft genome of an epiphytic orchid from the genus Gongora, a representative of the male euglossine bee-pollinated subtribe Stanhopeinae. The 1.83-Gb de novo genome with a scaffold N50 of 1.7 Mb was assembled using short- and long-read sequencing and chromosome capture (Hi-C) information. Over 17,000 genes were annotated, and 82.95% of the genome was identified as repetitive content. Furthermore, we identified and manually annotated 26 terpene synthase genes linked to floral scent biosynthesis and performed a phylogenetic analysis with other published orchid terpene synthase genes. The Gongora gibba genome assembly will serve as the foundation for future research to understand the genetic basis of floral scent biosynthesis and diversification in orchids.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The epistatic relationship of Drosophila melanogaster CtIP and Rif1 in homology-directed repair of DNA double-strand breaks.","authors":"Makenzie S Thomas, Gautham S Pillai, Margaret A Butler, Joel Fernandez, Jeannine R LaRocque","doi":"10.1093/g3journal/jkae210","DOIUrl":"10.1093/g3journal/jkae210","url":null,"abstract":"<p><p>Double-strand breaks (DSBs) are genotoxic DNA lesions that pose significant threats to genomic stability, necessitating precise and efficient repair mechanisms to prevent cell death or mutations. DSBs are repaired through nonhomologous end-joining (NHEJ) or homology-directed repair (HDR), which includes homologous recombination (HR) and single-strand annealing (SSA). CtIP and Rif1 are conserved proteins implicated in DSB repair pathway choice, possibly through redundant roles in promoting DNA end-resection required for HDR. Although the roles of these proteins have been well-established in other organisms, the role of Rif1 and its potential redundancies with CtIP in Drosophila melanogaster remain elusive. To examine the roles of DmCtIP and DmRif1 in DSB repair, this study employed the direct repeat of white (DR-white) assay, tracking across indels by decomposition (TIDE) analysis, and P{wIw_2 kb 3'} assay to track repair outcomes in HR, NHEJ, and SSA, respectively. These experiments were performed in DmCtIPΔ/Δ single mutants, DmRif1Δ/Δ single mutants, and DmRif1Δ/Δ; DmCtIPΔ/Δ double mutants. This work demonstrates significant defects in both HR and SSA repair in DmCtIPΔ/Δ and DmRif1Δ/Δ single mutants. However, experiments in DmRif1Δ/Δ; DmCtIPΔ/Δ double mutants reveal that DmCtIP is epistatic to DmRif1 in promoting HDR. Overall, this study concludes that DmRif1 and DmCtIP do not perform their activities in a redundant pathway, but rather DmCtIP is the main driver in promoting HR and SSA, most likely through its role in end resection.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462210","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}

{"title":"Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness.","authors":"Kosmas Hench, David L J Vendrami, Jaume Forcada, Joseph I Hoffman","doi":"10.1093/g3journal/jkae179","DOIUrl":"10.1093/g3journal/jkae179","url":null,"abstract":"<p><p>The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability. However, the current reference genome (\"arcGaz3\") shows considerable room for improvement in terms of both completeness and contiguity. We therefore combined PacBio sequencing, haplotype-aware HiRise assembly, and scaffolding based on Hi-C information to generate a refined assembly of the Antarctic fur seal reference genome (\"arcGaz4_h1\"). The new assembly is 2.53 Gb long, has a scaffold N50 of 55.6 Mb and includes 18 chromosome-sized scaffolds, which correspond to the 18 chromosomes expected in otariids. Genome completeness is greatly improved, with 23,408 annotated genes and a Benchmarking Universal Single-Copy Orthologs score raised from 84.7% to 95.2%. We furthermore included the new genome in a reference-free alignment of the genomes of 11 pinniped species to characterize evolutionary conservation across the Pinnipedia using genome-wide Genomic Evolutionary Rate Profiling. We then implemented Gene Ontology enrichment analyses to identify biological processes associated with those genes showing the highest levels of either conservation or differentiation between the 2 major pinniped families, the Otariidae and Phocidae. We show that processes linked to neuronal development, the circulatory system, and osmoregulation are overrepresented both in conserved as well as in differentiated regions of the genome.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855325","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}

{"title":"Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens Blastomyces dermatitidis and Blastomyces gilchristii.","authors":"Lisa R McTaggart, Thomas W A Braukmann, Julianne V Kus","doi":"10.1093/g3journal/jkae194","DOIUrl":"10.1093/g3journal/jkae194","url":null,"abstract":"<p><p>Blastomyces dermatitidis and Blastomyces gilchristii are cryptic species of fungi that cause blastomycosis, an often severe disease involving pulmonary infection capable of systemic dissemination. While these species appear morphologically identical, differences exist in the genetic makeup, geographical range, and possibly the clinical presentation of infection. Here, we show genetic divergence between the cryptic species through both a Blastomyces species tree constructed from orthologous protein sequences and whole genome single-nucleotide variant phylogenomic analysis. Following linked-read sequencing and de novo genome assembly, we characterized and compared the genomes of 3 B. dermatitidis and 3 B. gilchristii isolates. The B. gilchristii genomes (73.25-75.4 Mb) were ∼8 Mb larger than the B. dermatitidis genomes (64.88-66.61 Mb). Average nucleotide identity was lower between genomes of different species than genomes of the same species, yet functional classification of genes suggested similar proteomes. The most striking difference involved long terminal repeat retrotransposons. Although the same retrotransposon elements were detected in the genomes, the quantity of elements differed between the 2 species. Gypsy retrotransposon content was significantly higher in B. gilchristii (38.04-39.26 Mb) than in B. dermatitidis (30.85-32.40 Mb), accounting for the majority of genome size difference between species. Age estimation and phylogenetic analysis of the reverse transcriptase domains suggested that these retrotransposons are relatively ancient, with genome insertion predating the speciation of B. dermatitidis and B. gilchristii. We postulate that different trajectories of genome contraction led to genetic incompatibility, reproductive isolation, and speciation, highlighting the role of transposable elements in fungal evolution.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008637","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}

{"title":"Linear poly-ubiquitin remodels the proteome and influences hundreds of regulators in Drosophila.","authors":"Oluwademilade Nuga, Kristin Richardson, Nikhil C Patel, Xusheng Wang, Vishwajeeth Pagala, Anna Stephan, Junmin Peng, Fabio Demontis, Sokol V Todi","doi":"10.1093/g3journal/jkae209","DOIUrl":"10.1093/g3journal/jkae209","url":null,"abstract":"<p><p>Ubiquitin controls many cellular processes via its posttranslational conjugation onto substrates. Its use is highly variable due to its ability to form poly-ubiquitin chains with various topologies. Among them, linear chains have emerged as important regulators of immune responses and protein degradation. Previous studies in Drosophila melanogaster found that expression of linear poly-ubiquitin that cannot be dismantled into single moieties leads to their ubiquitination and degradation or, alternatively, to their conjugation onto proteins. However, it remains largely unknown which proteins are sensitive to linear poly-ubiquitin. To address this question, here we expanded the toolkit to modulate linear chains and conducted ultra-deep coverage proteomics from flies that express noncleavable, linear chains comprising 2, 4, or 6 moieties. We found that these chains regulate shared and distinct cellular processes in Drosophila by impacting hundreds of proteins, such as the circadian factor Cryptochrome. Our results provide key insight into the proteome subsets and cellular pathways that are influenced by linear poly-ubiquitin chains with distinct lengths and suggest that the ubiquitin system is exceedingly pliable.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344671","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}

{"title":"Prediction of additive genetic variances of descendants for complex families based on Mendelian sampling variances.","authors":"Tobias A M Niehoff, Jan Ten Napel, Mario P L Calus","doi":"10.1093/g3journal/jkae205","DOIUrl":"10.1093/g3journal/jkae205","url":null,"abstract":"<p><p>The ability to predict the outcome of selection and mating decisions enables breeders to make strategically better selection decisions. To improve genetic progress, those individuals need to be selected whose offspring can be expected to show high genetic variance next to high breeding values. Previously published approaches enable to predict the variance of descendants of 2 future generations for up to 4 founding haplotypes, or 2 outbred individuals, based on phased genotypes, allele effects, and recombination frequencies. The purpose of this study was to develop a general approach for the analytical calculation of the genetic variance in any future generation. The core development is an equation for the prediction of the variance of double haploid lines, under the assumption of no selection and negligible drift, stemming from an arbitrary number of founder haplotypes. This double haploid variance can be decomposed into gametic Mendelian sampling variances (MSVs) of ancestors of the double haploid lines allowing usage for non-double haploid genotypes that enables application in animal breeding programs as well as in plant breeding programs. Together with the breeding values of the founders, the gametic MSV may be used in new selection criteria. We present our idea of such a criterion that describes the genetic level of selected individuals in 4 generations. Since breeding programs do select, the assumption made for predicting variances is clearly violated, which decreases the accuracy of predicted gametic MSV caused by changes in allele frequency and linkage disequilibrium. Despite violating the assumption, we found high predictive correlations of our criterion to the true genetic level that was obtained by means of simulation for the \"corn\" and \"cattle\" genome models tested in this study (0.90 and 0.97). In practice, the genotype phases, genetic map, and allele effects all need to be estimated meaning inaccuracies in their estimation will lead to inaccurate variance prediction. Investigation of variance prediction accuracy when input parameters are estimated was not part of this study.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142086039","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}

{"title":"The N terminus-only (trans) function of the adhesion G protein-coupled receptor latrophilin-1 controls multiple processes in reproduction of Caenorhabditis elegans.","authors":"Daniel Matúš, Willem Berend Post, Victoria Elisabeth Groß, Alexander Bernd Knierim, Christina Katharina Kuhn, Franziska Fiedler, Darian Benno Tietgen, Johanna Lena Schön, Torsten Schöneberg, Simone Prömel","doi":"10.1093/g3journal/jkae206","DOIUrl":"10.1093/g3journal/jkae206","url":null,"abstract":"<p><p>Adhesion G protein-coupled receptors are unique molecules. They are able to transmit classical signals via G protein activation as well as mediate functions solely through their extracellular N termini, completely independently of the seven transmembrane helices domain and the C terminus. This dual mode of action is highly unusual for G protein-coupled receptors and allows for a plethora of possible cellular consequences. However, the physiological implications and molecular details of this N terminus-mediated signaling are poorly understood. Here, we show that several distinct seven transmembrane helices domain-independent/trans functions of the adhesion G protein-coupled receptor latrophilin homolog latrophilin-1 in the nematode Caenorhabditis elegans together regulate reproduction: sperm guidance, ovulation, and germ cell apoptosis. In these contexts, the receptor elicits its functions in a noncell autonomous manner. The functions might be realized through alternative splicing of the receptor specifically generating N terminus-only variants. Thus, our findings shed light on the versatility of seven transmembrane helices domain-independent/N terminus-only/trans functions of adhesion G protein-coupled receptor and discuss possible molecular details.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}