G3: Genes|Genomes|Genetics最新文献

Drought stress is a strong selective pressure for all plant species. Plants respond to water shortage through various strategies that confer drought tolerance. These strategies may be plastic responses that occur with the onset of stress or may comprise continuously-expressed (constitutive) traits regardless of water availability. Here, we used RNA-Seq to characterize transcriptional responses to dehydration in seedlings of a drought tolerant oak, Quercus douglasii, from a local population in the Sierra Nevada Foothills in California. In the greenhouse, we subjected 24 seedlings from six maternal families to dry-down or well-watered treatments and prepared RNA libraries from tissue collected before and after each treatment (48 libraries). Our goals were to characterize the pattern of up- and down-regulated genes in response to dehydration and to assess the extent to which this drought tolerant species shows differential versus constitutive expression as a drought response strategy. We identified few differentially expressed genes in response to dehydration. Up-regulated genes were related to known drought response functions, while down-regulated genes were enriched for gene ontology terms related to growth and carbohydrate metabolism. We discovered high constitutive expression of many putatively drought-responsive genes that had been found to exhibit gene expression plasticity in a different oak species, which is drought sensitive. This novel finding demonstrates the potential for constitutive expression of genes involved in drought stress to provide an additional mechanism of drought tolerance for some tree species, such as Q. douglasii.

Although the publication of high-quality reference genomes is steadily increasing, many clades remain chronically neglected. Skinks (order: Squamata; family: Scincidae) are one of the most diverse lizard families (1,785 species), yet there are currently just six published chromosome-level skink genomes. Here, we present the first telomere-to-telomere, chromosome-level reference genome for one of the most abundant lizards in the eastern United States, the common five-lined skink (Plestiodon fasciatus). Through the sequencing of RNA, long-read DNA, and Hi-C chromatin interactions, we produced an annotated reference genome (N50 = 227MB, L50 = 3) consisting of 6 macrochromosome pairs and 7 microchromosome pairs with 98% of BUSCO genes represented (lineage: Sauropsida; 7480 BUSCO markers) represented, providing one of the most complete skink genomes to date: rPleFas1.1. Functional annotation predicts 32,520 protein-coding genes (16,100 unique, named genes) with an average gene length of 9,372bp. Repeat annotations estimate that transposable elements comprise 46.7% of the genome, for which we show the amount and content is remarkably conserved across Scincidae.

The highly conserved insulin signalling pathway regulates growth and development time in response to nutrition across metazoans. The fruit fly, Drosophila melanogaster, has seven insulin-like peptides, which bind to a single insulin receptor and are differentially expressed across development time, organs, and with nutritional conditions. However, whether individual insulin-like peptides play specific roles in controlling growth remains unknown. Recent studies have revealed that, in addition to the caloric content of the diet, the ratio of protein to carbohydrates in the diet plays a key role in regulating life history traits. Furthermore, individual insulin-like peptides vary in their expression profiles according to nutrient conditions. Whether these differences in expression have any functional significance to animal life history traits remains unclear. Here we report that reducing the protein content of the larval diet through macronutrient restriction - where the calories lost from protein dilution are offset by increased carbohydrate content - results in a more pronounced developmental delay compared to caloric restriction - where both protein and carbohydrate concentrations are reduced. We further reveal that these two diet types result in notable differences in the expression levels of Drosophila insulin-like peptides 2, 3 and 5, and observe distinct phenotypic responses of individual insulin-like peptide mutants raised on each diet type. Taken together, our findings highlight the distinct roles of individual insulin-like peptides in regulating growth and development time in response to changes in dietary macronutrients, and provide key insights into the molecular mechanisms controlling nutritional plasticity in Drosophila.

True oysters, molluscs in the family Ostreidae, are important species in fisheries and aquaculture. As such, genome-enabled research can improve these industries and the conservation of these species. The tropical rock oyster Magallana bilineata (known as the black scar oyster or Indian backwater oyster) is naturally distributed in the tropical Indo-Pacific Ocean excluding Australia and is intensively cultured in India and the Philippines. It is also an aquaculture species in Sri Lanka with potential for much greater cultivation. We present the first reference genome for M. bilineata sourced from a Sri Lankan individual along with genetic variants that can be used in tool development for questions of molecular ecology and evolution as well as in breeding and commercial applications. Long-read PacBio data from a single M. bilineata were assembled following the Vertebrate Genomes Project workflow on the Galaxy Australia platform. A primary assembly composed of 105 contigs that is 551.94 Mbp in size was produced. The assembly N50 is 13.42 Mb and has a BUSCO completeness score of 98.1%. As collection and transport conditions challenged transcriptomic as well as scaffolding data generation, these approaches were undertaken computationally. Genetic variants in the form of SNPs from 90 individuals representing three naturally occurring populations in Sri Lanka and a fourth introduced population in Fiji was generated through DArTseq and a set of 3,115 SNPs produced after filtering. Combined, we present the first known genome assembly and the first genome-wide SNP data from M. bilineata, both of which have diverse applications for conservation and aquaculture.

As modest increases in temperature become more common due to global climate change, organisms are being subjected to moderate temperature stresses that can disproportionally affect fertility. Species that can buffer fluctuations in temperature through tissue or cellular responses in the germ line will therefore be more likely to survive moderate temperature stresses. Currently, what mechanisms are used in the germ line to facilitate maintenance of fertility under moderate temperature stress remain unknown. To address this, we investigated how germline apoptosis is modulated in Caenorhabditis elegans nematodes in response to moderate temperature stress. We found that wild-type animals increase their germline apoptosis levels from the physiological baseline in response to the moderate temperature stress. This induction of germline apoptosis was dependent on known and novel regulators of germline apoptosis including members of the conserved DREAM (Dp, Retinoblastoma (Rb)-like, E2F, MuvB) complex: LIN-35/pRB, LIN-54, and LIN-37, and proteins that regulate the synapsis checkpoint, BUB-3 and PCH-2. Additionally, repression of CED-9 function, the C. elegans Bcl2 ortholog, was necessary for full induction of apoptosis during moderate temperature stress. Finally, we found that changes in cytoplasmic streaming are correlated with changes to oocyte provisioning in wild-type animals but not mutants. Together, these data suggest an expanded role for LIN-35, the MuvB core of the DREAM complex, CED-9, and the synapsis checkpoint in maintaining fertility by activating apoptosis during moderate temperature stress.

Grasshoppers represent true outliers in genome sizes, both within insects and within animals in general. Their genomes are large and generally variable in sizes and feature a high abundance of repetitive DNA sequences. This has hampered the assembly of grasshopper genomes to the chromosome level. Here we present a chromosome-level reference genome for the club-legged grasshopper (Gomphocerus sibiricus, Acrididae: Gomphocerinae) using PacBio HiFi long-read and Hi-C sequencing technologies. In male haploid cells, the species has a chromosome set of n = 9 with an X0 sex-determination system, characterized by an absence of a Y chromosome. Our assembly spans 9.57 Gb in total, with 8.87 Gb organized into 9 chromosomes-8 autosomes and the X chromosome. The final assembly has a scaffold N50 value of 1.58 Gb, covers 96.7% single copy Insecta orthologs, and contains 42,665 predicted protein-coding genes and 43,385 mRNA transcripts. We compiled a curated, nonredundant, species-specific repeat library and used it to annotate repetitive DNA, covering 81.69% of the genome, mostly DNA transposons, long-interspersed nuclear element and long-terminal repeat retrotransposons. The genome of the club-legged grasshopper shows high degree of synteny with the locusts Schistocerca gregaria and Locusta migratoria, and the analysis strongly indicates 3 autosome-autosome centric fusions in Gomphocerinae. The genome offers a valuable resource for grasshopper genomics and for exploring the genetic basis of a transspecies color polymorphism.

Chemical stimuli, including odorants and tastants, provide information about food availability and allow animals to avoid harmful environments. Over 6 decades of research using primarily 1 laboratory-adapted strain of the nematode Caenorhabditis elegans has yielded a wealth of information about how this animal senses and responds to chemical cues to survive. However, it was not known whether the chemosensory behavioral profile of this strain (named N2) is representative of the species. Using a collection of hundreds of wild C. elegans strains collected from around the globe, we assessed their abilities to respond to 3 aversive stimuli (the bitter tastant quinine, the heavy metal copper, and the detergent SDS) in a laboratory setting and found ∼10- to 20-fold differences in response sensitivities among the strains. Further, response sensitivities to one stimulus were largely uncoupled from responses to the other stimuli and uncorrelated with the geographical locations from which the wild strains were collected. Using genome-wide association studies, we identified unique regions significantly correlated with different responses to each stimulus. Near-isogenic lines were created to confirm the effects of 2 genomic regions on differential avoidance behavior to the bitter tastant quinine. Combined, we report remarkable natural variation in chemosensory behavioral responses among wild C. elegans strains and describe 2 new quantitative trait loci associated with decreased response sensitivity to quinine.

Requirements for the Caenorhabditis elegans Notch ligand APX-1 have been described, but the molecular lesions in mutant alleles remain unknown. Here we report the sequence changes in 3 previously isolated nonconditional alleles and 2 newly isolated alleles, apx-1(or545ts) and a null allele apx-1(or2015). All alleles resulted in highly penetrant embryonic lethality, but only null mutations greatly reduced brood sizes. This reproductive phenotype was likely due to abnormal ovulation rupturing oocytes and, together with vulva defects, resulting in debris accumulation that prevented embryo passage. In addition to identifying molecular lesions in apx-1 alleles and clarifying distinct requirements for C. elegans Notch ligands, our results reveal extensive genotype-by-environment interactions, including haplo-insufficiency of essential loci at a stressfully high growth temperature, and highlight the origins of complex phenotypes as a consequence of multiple seemingly unrelated defects.

The Chinese grape accession Vitis piasezkii DVIT2027 carries 2 loci associated with powdery mildew (PM) resistance, Ren6 and Ren7, which differ in timing and strength of response to Erysiphe necator. Both loci are consistent with recognition by intracellular immune receptors. To identify the underlying nucleotide-binding leucine-rich repeat (NLR) genes, we assembled chromosome-scale diploid genomes of DVIT2027 and the susceptible V. vinifera F2-35, parents of a segregating F1 population. We integrated these assemblies with deep resequencing data from 8 F1 siblines carrying different Ren6/Ren7 combinations and generated trio-binned, parent-phased genomes for 6 progeny. This resolved both PM-resistant (PMR) and PM-susceptible (PMS) haplotypes at Ren6 and Ren7. Comparative analyses revealed extensive structural variation and complete haplotype specificity among NLRs, with several candidate genes lacking allelic counterparts in PMS haplotypes. Expression profiling across PMR siblines identified 4 and 2 CC-NBS-LRR genes potentially associated with Ren6 and Ren7, respectively. Sequence graph reconstruction of these loci across multiple V. piasezkii accessions revealed broad intraspecific diversity and DVIT2027-specific nodes, including within candidate NLR genes. These results provide a high-resolution view of Ren6 and Ren7 and support the identification of resistance gene candidates for functional validation and grapevine breeding.

Local adaptation research often focuses on discrete populations without extensive gene flow that are under differential selective pressures. By contrast, grizzly bears Ursus arctos in British Columbia (BC) are wide-ranging omnivores that span an environmental and resource ecotone from the coastal, salmon-enriched rainforest to dry interior plateau. This ecotone has been associated with local adaptation in other species and the different regions to morphological variation in grizzly bears. To understand genome-wide population genetic patterns across the ecotone and to identify loci or genomic regions associated with these different environments, here we use whole-genome resequencing to characterize 3.9 M SNPs in 31 grizzly bears spanning from central to northern latitudes in coastal and interior regions (to the west and east of the coastal mountain range [CMR], respectively). Clustering grizzly samples by genotypes identified 3 groups that generally correspond to the source geographic regions, with the greatest variation occurring from north to south. The data were best explained by a single ancestry cluster, but K = 3 recovered the 3 geographic groupings and were used to identify putative nonmigrant individuals. The presence of individuals with mixed ancestry (using K = 3) provides evidence for travel across the CMR, but significant differentiation between clusters (mean FST = 0.015 to 0.036) suggests some genetic separation between the regions, supporting an isolation-by-distance or clinal variation model. Putative close-kin were identified and removed, then multiple supervised outlier SNP detection methods were applied to identify regions of the genome consistently segregating between coastal and interior regions. Several associated genomic regions and candidate genes were identified, including a consistently identified outlier region near the gene creatine kinase, m-type. This work provides the first genome-wide analysis of grizzly bears in the studied region. These findings will be useful for connectivity planning and research on the adaptability of coastal and interior grizzlies to future climate change scenarios.