Journal of Heredity最新文献

A central goal of evolutionary biology is to understand the mechanisms conferring adaptation. Gene expression is sensitive to environmental variability; thus, investigating gene expression differentiation among populations may reveal signatures of selection from predictable environmental conditions. Environmental pressures that covary with elevation gain (e.g., temperature) result in stark environmental differences along short distances. The phenological and life history traits of plants inhabiting elevational gradients might track these variables, providing an opportunity for testing hypotheses. Boechera stricta occupies a steep elevation gradient in the Rocky Mountains. Here, we grew F3 seeds from at least two genotypes each from five populations of B. stricta in a greenhouse. Analysis of leaf RNAseq data permitted tests of these hypotheses: 1) populations exhibit significant among population genetic variation in gene expression; 2) differentiation in gene expression (QST) exceeds neutral expectations (FST); and 3) the putative functions of differentially expressed genes are predicable based on a priori knowledge of environmental pressures that vary with elevation. Differentiation in gene expression (average QST = 0.53) significantly exceeded neutral differentiation (average FST = 0.17), implicating selection as a potential cause of genetically divergent patterns of gene expression. The putative functions of differentially expressed genes covarying with elevation were enriched for biological processes related to conditions that vary with elevation (circadian rhythm, response to light, chloroplast organization, and vegetative to reproductive meristem transitions). This study reveals considerable differentiation in gene expression, which may provide a mechanism for rapid adaptation to local environmental conditions in this and other species.

Mule deer (Odocoileus hemionus) is an ecologically and economically important cervid species that is widely distributed across western North America. Their broad range and use of diverse habitats, including those linked to historical glacial refugia, have made them an ideal model for studying the effects of climatic fluctuations and environmental heterogeneity on lineage diversification. The effects of this complex evolutionary history on the genome are further complicated by evidence of hybridization with other members of the genus, leading to extreme cases of mito-nuclear discordance. More recently, the influence of specific gene variants on disease dynamics, particularly the progression and morbidity of chronic wasting disease, has become an important topic of genomic research for this taxon. Here, we present and evaluate a new chromosome-level genome assembly of a representative mule deer from across the species' diverse range as part of the California Conservation Genomics Project (CCGP). We assembled a genome de novo utilizing Pacific Biosciences HiFi long-read and Omni-C chromatin-proximity sequencing data. The assembly consisted of 814 scaffolds and 901 contigs representing a contig N50 of 46.68 Mb and scaffold N50 of 63.29 Mb. Lastly, our benchmarking universal single-copy ortholog (BUSCO) completeness score was 96.3%. This genome represents one of the most complete Odocoileus assemblies and will further our understanding of the comparative genomic architecture of cervids.

Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of Nereocystis luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1562 scaffolds with 449.82 Mb, 80x of coverage and 22 952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Kb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and M. pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPases enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

Colusa grass, Neostapfia colusana, is a listed California endangered plant endemic to the vernal pools of California. Vernal pool habitat is highly degraded and threatened by further anthropological development, with only 10% of its historical range remaining. With only 42 confirmed extant populations, it is a major conservation concern to understand patterns of genomic diversity. Here we report the first complete genome assembly of Colusa grass. The assembly includes two haplotypes: haplotype one spans 2.13 Gb with contig N50 of 10.62 Mb, scaffold N50 of 112.31 Mb, and BUSCO completeness of 98.1%. Haplotype two spans 2.04 Gb with contig N50 of 10.05 Mb and scaffold N50 of 138.31 Mb, with a BUSCO completeness of 97.6%. This genome assembly will allow for in-depth analysis of genomic variation and gene flow in populations of this threatened grass and will be a major asset to studies supporting its conservation. This genome was assembled as part of the California Conservation Genomics Project (CCGP), which contributes to a collection of resources and tools to support state-wide conservation efforts.

Pine siskins (Spinus pinus) are irruptive migratory songbirds of biological interest in studies of endocrine regulation, immune function, and behavioral flexibility. Here, we present a chromosome-level reference genome from a female pine siskin, assembled de novo using long-read sequencing and scaffolded with a reference-guided approach. Synteny analyses also showed that our assembly can reliably reveal genomic rearrangements relative to other finches. Using reference-based annotation, we identified thousands of protein-coding genes, including loci relevant to metabolism and immune function that demonstrate the utility of this assembly for downstream studies. We also found evidence of gene duplications and pseudogenization in immune loci, showing the utility of our assembly for immunogenetic studies. Our analysis provides the first genome-wide view of transposable element (TE) activity in Spinus, revealing multiple bursts of long terminal repeat (LTR) retrotransposon expansion, including a recent one that coincides with the estimated diversification of North and South American siskins approximately 2.7 million years ago. We also detected putative lineage-specific LTR sequences, suggesting recent or ongoing TE diversification. This assembly fills a critical gap in passerine genomic resources and provides a resource for comparative, transcriptomic, and population-level studies across species with diverse migratory strategies.

Neandra brunnea, commonly known as the pole borer, is a species of wood-boring (xylophagous) longhorn beetle (family Cerambycidae) found throughout most of eastern North America. We sequenced, assembled and annotated the genome of N. brunnea and compared it to publicly available genomes of other Cerambycidae. The 1.23 Gb N. brunnea genome assembly was distributed across 78 contigs, with an N50 of 38.88 Mb and largest contig of 74.28 Mb. Most of the genome was comprised of repetitive sequences, with 81.39% comprising interspersed repeats. Most (99.7%) of the expected orthologous genes (BUSCOs) were present and fully assembled, with only 2.5 % duplicated. The genome annotation identified 13,003 genes (15,574 transcripts), including 301 putative horizontally transferred loci from a diversity of both prokaryotic and eukaryotic donors. The assembled mitochondrial genome is relatively large at 17 kb and shows an unusual repeating array of d-loop segments. As the first representative of the longhorn beetle subfamily Parandrinae with a sequenced genome, N. brunnea provides an important new point of reference for the comparative study of beetle genomes and a further resource for studies of the evolution and genomic basis of xylophagy.

Oculocutaneous albinism-characterised by absent or decreased melanin in the skin, eyes and hair-often co-occurs with sensory, skin and immunity disorders. The genetic basis of albinism in humans is complex, with many loci implicated in multiple forms of the disorder. Less is known about the underlying genetic causes of albinism and leucism in other species, and cross-species studies of the molecular correlates of hypopigmentation could highlight common and conserved pathways underlying mammalian pigmentation disorders. We characterise the putative causal loci of reduced pigmentation in an Egyptian fruit bat (Rousettus aegyptiacus) that displayed features indicative of albinism. Despite albino or leucistic individuals having been reported in > 100 bat species, the associated genetic backgrounds have not previously been studied. We used a digital gene expression panel to quantify mRNA levels in wing membrane samples of four candidate pigmentation genes in the focal albino fruit bat and control individuals. Significantly reduced SLC45A2 mRNA expression was found in the albino compared to five bats with typical colouration. Additionally, intraspecific sequence analyses of the albino bat SLC45A2 coding sequence identified two missense mutations, E18A and Q298R, the former of which was private to the albino bat. Position 18 of SLC45A2 was otherwise found to be highly conserved across 60 bat species and has not been previously linked to human albinism. By identifying SLC45A2 as the likely contributing locus, our results also indicate further support for the necessity of genetic testing for the reliable categorisation of hypopigmented animals as either albino or leucistic.

Breed management and genomic evaluation rely on understanding population structure and genetic diversity. The primary objective of this study was to evaluate genetic diversity in Rambouillet enrolled in the National Sheep Improvement Program (NSIP) in comparison to other U.S. and international sheep breeds. We considered genotypes of 667 NSIP Rambouillet from a 50K single nucleotide polymorphism (SNP) array and 600K SNP genotypes on 64 each of NSIP Rambouillet, Suffolk, and Katahdin sheep. Pedigree analyses were also conducted on the NSIP Rambouillet. International comparisons incorporated 50K SNP data from 9 international breeds. After genomic quality control measures to reduce bias in analyses, the NSIP Rambouillet had the greatest diversity among the 3 NSIP breeds (expected heterozygosity: 0.404; average individual inbreeding: 9.94%). Conversely, the NSIP Rambouillet had the lowest genetic diversity when compared to the international breeds. Based on principal component analyses, NSIP Rambouillet were divergent from the international populations except for evidence of connectivity between the NSIP and European Rambouillet. Population structure within the NSIP Rambouillet, demonstrated by cluster analysis and a significant loss of heterozygosity (FIS) was driven primarily by one flock. Using complete pedigrees of the NSIP population, effective population size, effective number of founders, and average generation interval was 87 to 218, 95, and 3.4 yr, respectively. This pedigree and genomic assessment of genetic diversity provides the basis for genomic selection and monitoring of the NSIP Rambouillet.

The ornate shrew (Sorex ornatus) is a small predatory mammal with a broad distribution in northern, central, and southern California as well as in Baja California, Mexico. The ornate shrew is a highly productive consumer in wetland environments and is known to hybridize with the closely related vagrant shrew, S. vagrans. Here we present a high-quality de novo genome assembly for S. ornatus generated as a part of the California Conservation Genomics Project. The S. ornatus genome was generated using PacBio HiFi long reads and Omni-C chromatin interaction sequencing. The primary assembly is highly contiguous, with a contig N50 of 15.9 Mb, a scaffold N50 of 115.2 Mb, and a BUSCO completeness score of 95.10%. The ornate shrew genome will serve as a valuable resource for future North American Sorex conservation genomics as well as for research into shrew biology more generally.

Sexual conflict over shared traits-intralocus sexual conflict (IaSC)-may be common and consequential, but experimental tests of its relative magnitude are challenging and limited in number. We use a sex-limited selection experiment, designed to subject haplotypes of Drosophila melanogaster to selection for male fitness without opposing selection acting on female fitness. Importantly, we use three novel base populations to compare results with those from the LHM population, the sole population investigated using this technique. In contrast with previous studies, we find that male fitness of haplotypes subject to male-limited selection (ML populations) are not consistently better than their matched (MC) controls when tested in the 'wildtype' state. Males from ML lines did not outperform controls in competitive fitness assays, mate choice trials, fecundity induction or sperm offense tests. As predicted, genetic variation for male fitness was reduced, with low fitness haplotypes apparently removed by selection, but this was only surveyed in one replicate population pair and included a potential artefact in the protocol. Female fitness was markedly reduced by carriage of ML haplotypes, as predicted by sexual antagonism. Hence, our results are only partially consistent with the IaSC hypothesis, raising questions about the relative contribution of sexual conflict to the standing genetic variation in these populations and the potential role of artefacts in the protocol that may have obscured our ability to detect IaSC.