G3: Genes|Genomes|Genetics最新文献

Hexaploid tall fescue is a widely adapted forage and turf grass with three synonyms in botanical nomenclature. It is one of the most drought-tolerant cool-season forage and turf species and can host Neotyphodium endophytes that can further affect physiological traits. The cultivated variety "Kentucky-31" (K31) was one of the original tall fescue varieties, yet it still has a large presence in the current market. We generated a haplotype-aware assembly of K31 tall fescue along with its chloroplast genome, with structural and functional gene annotation. Each haplotype assembly was approximately 7.1Gb. The three sub-genomes within each haplotype assembly were discernible and syntenic, with the Festuca pratensis (P) sub-genome intermediate in size between the two sub-genomes from F. glaucescens (G1 and G2). Interspersed repeat levels were high in the assemblies, with long terminal repeats alone comprising over 50% of the genome space. With an interest in testing for K31 as a variety, 15 seed sources of K31 were obtained from forage and turf industry sources, and their genetic relationship was tested with pairwise PhiST statistics from over 3,400 SNP markers that mapped across the genome. All but four seed sources coalesced into a group that differed from turf-type cultivated variety checks; three were broad-based and did not differ from any other entry; and K31-4 was genetically differentiated from all other K31 sources. These results provide a chromosome-scale and haplotype-aware tall fescue genome assembly for mapping and functional genomic studies.

The two-spotted cricket, Gryllus bimaculatus, is a key hemimetabolous model organism for developmental biology, neuroscience, and regeneration. The existing reference genome is, however, highly fragmented into 47,877 scaffolds, hampering chromosome-scale analyses for these fields. Here, we report a high-quality, chromosome-scale genome assembly for the white-eyed mutant strain of this cricket, generated using a combination of Nanopore and PacBio HiFi long reads, integrated with Hi-C data. The final 1.62-Gbp assembly achieves a scaffold N50 of 107.4 Mbp, a significant improvement in contiguity over the previous 6.3-Mbp N50. We anchored 94.45% of the assembly into 15 pseudomolecules, consistent with the known karyotype (n = 15). The genome completeness (BUSCO v6.0.0 insecta_odb12) reached 98.1%. We also updated the annotation, identifying 14,964 protein-coding genes. This gene set shows markedly improved completeness (BUSCO v6.0.0 insecta_odb12: 95.7%) compared with the previous annotation (81.2%) and successfully recovers all 9 essential neuropeptide genes previously reported as missing from the draft assembly. This chromosome-scale genomic resource provides an essential foundation for comparative and functional genomics in G. bimaculatus.

Caenorhabditis elegans insulin/insulin-like growth factor 1 signaling, IIS, affects diverse physiological processes through the DAF-16/FOXO transcription factor. Despite its ubiquitous presence in somatic cells, DAF-16's effects exhibit prevalent tissue specificity as well as tissue crosstalk. This implies that tissue-specific DAF-16 transcriptional programs contribute to functional diversity of IIS. To further investigate this possibility, we sought muscle-cell-specific DAF-16 transcriptional targets. Using fluorescence-activated cell sorting to enrich for body wall muscle cells from young hermaphroditic adults, we compared the muscle cell mRNA transcriptomes under conditions of high and low IIS activity, with and without DAF-16. We further analyzed DAF-16a's binding sites in muscle and intestine cells by chromatin-immunoprecipitation sequencing. Combined output of these analyses is 12 candidate DAF-16 targets enriched for muscle cells. Transcriptional and translational reporters for three out of the four top candidates-a secreted protein C54F6.5, a calcium-binding protein CEX-1/calexcitin, and a fatty acid metabolic enzyme MLCD-1/MCD-showed DAF-16-dependent activation specifically in body wall muscle cells. Notably, reporters for C54F6.5 and cex-1 exhibit DAF-16-independent, constitutive expression in nonmuscle cells, explaining their low rank or absence from the DAF-16 target lists generated by whole-animal microarray or mRNA-sequencing analyses. These results highlight the need to examine FOXO targets in a cell-type-specific manner.

The geographic expansion of chronic wasting disease (CWD) in North American elk (Cervus canadensis) has not been well-mitigated by traditional best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom Affymetrix Axiom® genetic variant array, we demonstrate that differential susceptibility to CWD is highly heritable (h2 = 0.630 ± 0.061 - 0.678 ± 0.056) among farmed North American elk; with loci other than PRNP involved. Genome-wide association analyses using 173,674 quality filtered variants for a geographically diverse cohort of 904 farmed North American elk (n = 357 CWD positive; n = 547 CWD non-detect) confirmed the prion gene (PRNP codon 132 Met→Leu and promoter variants) as a large-effect risk locus (P-value < 5.135E-08), as evidenced by the estimated proportion of phenotypic variance explained (PVE ≥ 0.032). However, more phenotypic variance was collectively explained by loci other than PRNP. Genomic best linear unbiased prediction (GBLUP; n = 173,674 markers) with k-fold cross validation (k = 3; k = 5) and random sampling (n = 50 iterations) for the same cohort of 904 farmed North American elk produced mean genomic prediction accuracies ≥ 0.791; thereby providing a foundation to explore a genomically-estimated CWD genetic improvement program.

Single nucleotide polymorphism (SNP) arrays are commonly used in livestock genetics to investigate complex traits including genome-wide associations and fine mapping, genomic prediction and genetic diversity analyses. In a European equine diversity study, we analysed the AxiomTM Equine 670K SNP genotype data from 2,768 equids representing 20 horse breeds and one donkey breed. Using a strict detection setting to identify genome-wide runs of homozygosity (ROH), 169 purebred horses displayed fewer ROH segments than F1 crosses. Under medium and relaxed settings, ROH counts increased, while some horses continued to exhibit low ROH levels. Therefore, we additionally assessed genotype performance using a four-fold concordance analysis of replicate pairs on the same AxiomTM batch, between two different AxiomTM batches, between Illumina EquineSNP50 BeadChip® and between Illumina paired-end HiSeq 2000 whole genome sequencing data. Replicates within the same AxiomTM batch showed the highest average genotype concordance (98.81%), followed by Illumina 50K (97.88%) and whole genome sequencing (96.84%). Re-genotyped horses with few ROH segments showed the lowest concordance (93.52%). According to SNPolisherTM classification, 120,838 genome-wide SNPs were not recommended for reproducibility. After calling genotypes of the two different batches together following AxiomTM Best Practice (e.g. removing failing samples before the final genotyping) and excluding non-recommended SNPs, concordance improved in all comparisons. Therefore, we recommend excluding horses exhibiting an unusually high number of heterozygous calls, using only SNPs with validated genotype performance, and accounting for batch effects when analyzing AxiomTM Equine 670K SNP genotype data from different batches.

Yeast ribosomal protein genes RPL18B, RPL28 and RPS22B are autoregulated by inhibition of splicing. This is demonstrated by inserting their introns into a chromosomal copy of GFP and observing repression upon induction of the cognate protein. In RPL18B and RPS22B, a predicted conserved secondary structure within the intron is required for regulation, while in RPL28 it is not.

Genome-wide association studies (GWAS) routinely implicate broad loci that span tens of megabases and contain dozens of genes, making the leap from locus to causal gene challenging, especially in model organism cohorts with reduced mapping resolution. We developed LocusPackRat, an easily extendable R package that assembles standardized 'packets' of evidence to accelerate candidate gene prioritization. Each packet merges study-specific information for each gene in a locus such as differential expression between conditions or presence of cis-eQTLs with functional/disease annotations pulled from InterMine and Open Targets. Packets are identically structured and easily disseminated to support side-by-side comparison and team review. We demonstrate LocusPackRat's efficacy on a recent GWAS study of cardiac hypertrophy and failure in the Collaborative Cross. LocusPackRat streamlines the transition from statistical associations to mechanistic hypotheses by providing a systematic, transparent framework for GWAS data integration, and is readily adaptable to other genetic reference populations or human cohorts.

To date the Fourth Chromosome Resource Project (FCRP) has deposited over 850 stocks for the genetic analysis of its 79 protein coding genes. Here we employ those stocks to reveal unexpected phenotypes for multiple exemplar genes. Expression studies of the transcript and protein provide clues to an adult function for maverick, a gene that despite prior efforts has remained inscrutable. Loss of function studies reveal an adult brain phenotype for the well studied signal transducer legless and the first phenotype for datilographo, a gene with no prior mutations. Marked clones with a new eyeless null allele in the larval brain elicited the first heterochronic phenotype in flies. Mutant clones of myoglianin encompassing the entire adult glial blood brain barrier elicited overgrowth of the underlying optic lobes. Complete clones of one glial layer within the two layer barrier were obtained for multiple genes and provide an opportunity to interrogate barrier crossing mechanisms for neurological therapeutics. In overexpression studies, rough eye phenotypes were generated by two human genes known to cause autosomal dominant neurological diseases. How YY1 and GRM1 haploinsufficiency leads to inherited cognitive impairment and spinocerebellar ataxia visible from birth is currently unknown. Fly eye phenotypes provide a tractable disease model for understanding their mechanism of action. Taken together, the ease with which mutant phenotypes were revealed suggests that a considerable amount of interesting biology remains to be uncovered on the fourth chromosome.

APOBEC cytidine deaminases can convert cytosines to uracils in DNA as well as in RNA. The knowledge of DNA deamination motifs preferred by individual APOBECs revealed APOBEC3A as a major source of hypermutation in cancer. However, the extent and relative contribution of specific APOBECs into RNA editing remains unclear as their preferred RNA-editing motifs have not been defined. Here, using a parallel DNA and RNA sequencing strategy, coupled with motif-centered statistical analyses, we sought to identify mRNA edits and diagnostic editing motifs in yeast and human cells overexpressing individual APOBEC enzymes. This approach revealed a prevailing global enrichment for the uCg trinucleotide motif with even greater preference to the motif's cytosines located in 3' base of a loop within a hairpin-loop secondary structure when APOBEC3A, but not any other tested APOBEC, was overexpressed. Further analysis revealed the APOBEC3A-like diagnostic motif enrichment in editing calls from human cancers and blood cells. The APOBEC3A-like editing motif also prevailed in the RNA genomes of SARS-CoV-2 pandemic isolates, as well as in infectious persistent rubella viruses, and in polioviruses emerging from live-attenuated vaccine strains. Together, our results indicate that APOBEC3A is the predominant global APOBEC RNA editor with a potential to impact cell physiology and viral evolution.

The genus Abies Mill. (Pinaceae) comprises a group of conifers distributed across boreal and temperate regions, including eight species with disjunct distributions across Mexico's highest mountain chains. Abies religiosa (Kunth) Schltdl. & Cham. is a dominant species of the Trans-Mexican Volcanic Belt in central Mexico, forming forests crucial for water retention, carbon sequestration, and soil stabilization. Despite its ecological importance, peri-urban forests dominated by this species around Mexico City are exposed to high levels of tropospheric ozone, which cause premature senescence and forest decline. Here, we report a saturated linkage map for A. religiosa generated by genotyping 182 megagametophytes from two trees for 9,702 single nucleotide polymorphisms. The linkage map is composed of 12 linkage groups (LGs) containing between 518 and 1,207 markers and spanning 1,567.88 cM (114-208 cM per LG). Annotation of reads containing SNPs allowed us to locate 5,881 coding genes on the map, of which 1,952 had known functions in conifers. Differential expression analyses of these genes in symptomatic and asymptomatic trees growing in a peri-urban forest heavily affected by ozone pollution revealed eight genes that were differentially expressed when ozone levels increased. Co-expression analyses further showed that neighboring genes tended to co-express more often in symptomatic than in asymptomatic trees, especially in clusters within LGs 5, 8, and 10. Gene pairs within co-expression clusters coded for similar proteins, suggesting functional co-localization. Our integrated approach reveals previously uncharacterized metabolic and defense pathways associated with ozone tolerance in conifers and lays the groundwork for developing molecular-based management programs accounting for ozone resistance in peri-urban forests.