Journal of Heredity最新文献

The Savannah cat is a popular cat breed derived from an interspecific hybrid cross between the domestic cat (Felis silvestris catus) and the African serval (Leptailurus serval). Within the family Felidae, Savannahs represent the most divergent interspecific hybrid breed, with ~13 million years separating the parental species. Here, we apply trio-binning of an F1 interspecific hybrid to achieve near-gapless chromosome-level genome assemblies for the domestic cat and serval. Using a hybrid assembly approach combining Pacific Biosciences (PacBio) High-Fidelity (HiFi) and Continuous Long Reads (CLR) reads, we generated domestic cat and serval genome assemblies, each comprising ~2.5 Gb of sequence with contig N50s of 107.4 and 112.3 Mb, respectively. We anchored >99% of the contigs into 19 chromosome-length scaffolds for each species, supported by base-quality (QV) metrics exceeding 61. The serval reference genome assembly represents the first for the species, providing an essential resource for future population and comparative genomic studies. The new domestic cat assembly adds an average of 36-Mb of novel sequence to chromosomes missing in earlier long-read assemblies. These sequence gains include the first resolution of multi-megabase FA-SAT macrosatellite arrays with putative functions in cell cycle regulation. These new assemblies add to the growing list of highly complete chromosome-level felid genomes and improve our understanding of complex genome architecture and satellite evolution within mammals.

The northern elephant seal (Mirounga angustirostris) is the largest pinniped species in the northern hemisphere. The species is classified as being of least conservation concern by the IUCN-a triumph of conservation efforts despite hunting pressure that nearly led to its extinction more than a century ago. The historical range of the northern elephant seal extended from Baja California to Alaska, but overexploitation caused a severe demographic collapse and genetic bottleneck, with only an estimated 10-30 survivors left on Isla Guadalupe, Mexico. As part of the California Conservation Genomics Project (CCGP), we generated a de novo reference genome and annotation for M. angustirostris, combining PacBio HiFi long-read sequencing data with Dovetail Omni-C chromatin conformation data. Our assembly has a primary haplotype genome length of 2 434 279 988 base pairs (2.4 Gb), with the longest contig of 144 Mb, contig N50 of 58 Mb, longest scaffold of 215 Mb, and scaffold N50 of 154 Mb. The secondary assembly haplotype consists of 482 scaffolds, spanning 2.45 Gb, with contig N50 of 61.24 Mb, scaffold N50 of 152.94 Mb, largest contig of 204.14 Mb, and largest scaffold of 216.16 Mb. We used the primary assembly and annotation for a preliminary investigation of repeat element content, historical demography, genome-wide heterozygosity, and loss-of-function variants. We found that M. angustirostris has one of the lowest estimates of genetic diversity of any marine mammal and a complex demographic history that may have reduced genetic diversity several times. This newly constructed genome will facilitate future in-depth explorations of the mechanisms behind resilience and recovery following a severe population bottleneck.

Disease can impact the long-term viability of threatened species. Levels of genetic variation in disease response genes could influence the magnitude of these impacts, but identifying candidate genes in endangered species is difficult. We used a multifaceted approach to identify candidate genes involved in disease response and resistance of an endangered snake, the eastern massasauga rattlesnake (Sistrurus catenatus), possibly related to an emerging infectious disease, Snake Fungal Disease (SFD). We assessed whether genes differentially expressed in an SFD disease challenge experiment showed patterns of non-neutral evolution in outlier tests of nucleotide diversity and Tajima's D. We evaluated these patterns in two populations of S. catenatus with varying effective population sizes, and a closely-related non-endangered species, S. tergeminus. In general, we find reduced diversity in functional sites in S. catenatus relative to the outbred sister species, but not between S. catenatus populations of different sizes. Further, genetic drift in the smaller populations likely limited the number of outlier genes detected. Finally, FST outlier tests identified a small set of protein coding genes that may be linked to local adaptation in disease response. In sum, our approach identified 218 candidate genes that were differentially expressed in response to disease that contain functional variation relevant to disease resistance or defense, pending further validation for SFD specifically. Our results also demonstrate how drift complicates the detection of functional variation in rare species with small population sizes, a process that is essential for assessing adaptive variation and load.

Recent genomics research has redefined the taxonomy of giraffes (genus Giraffa), identifying four distinct species rather than just one. This new understanding raises concerns about the ancestry of North American giraffe populations in human care (ex situ) and whether they still serve as meaningful conservation assurance populations for wild giraffe taxa. To address this, we performed whole-genome sequencing and analyses of 52 giraffes kept ex situ across North America, comparing them to wild giraffes representing all four recognized species. The analyses-including principal component analysis, admixture estimation, local ancestry inference, and mitochondrial phylogenetics-revealed extensive hybridization in giraffes kept ex situ. Most demonstrated mixed ancestry, primarily between northern and reticulated giraffes, with only a few individuals retaining un-admixed ancestries. Although some wild giraffes are known to be natural hybrids, overall there is strong reproductive isolation among giraffe species in the wild. Thus hybridization across species boundaries and potentially founder misclassification are responsible for the patterns observed ex situ. These findings highlight substantial genetic admixture in captivity, diminishing the conservation value of the current ex situ population. We recommend phasing out hybrid individuals from breeding programs and establishing new conservation-relevant stocks through collaboration with willing African governments and conservation organizations. Success will require coordinated international efforts and updates to global conservation frameworks, building on the formal recognition by the IUCN of distinct giraffe species and subspecies, to support taxon-specific conservation strategies that reflect the genetic distinctiveness of giraffe taxa.

Invasive species are reshaping aquatic ecosystems worldwide at an accelerating pace, with profound ecological and economic impacts. Many crustacean species have demonstrated invasive potential or are already well-established invaders. The green shore crab, Carcinus maenas, native to Europe and North Africa, is one of the most successful global marine invaders and is now present on six continents. Although the role of genomics in invasion science is increasingly recognized, genomic resources for brachyuran crabs remain limited, including the notable absence of a reference genome for C. maenas. Here we report on a de novo whole genome assembly of C. maenas via long-read Oxford Nanopore Technology sequencing. The assembly spans 1.09 Gbp across 21,887 scaffolds (NG50 = 13 Mbp) with a BUSCO completeness of 98.4%, providing a high-quality resource for future genomic analyses. We provide a detailed protocol for obtaining high-quality DNA to successfully sequence brachyuran crabs using a long-read approach. This new resource expands available genomic data for the species-rich infraorder Brachyura, and provides a valuable foundation for understanding the genetic factors underlying the global invasion success of C. maenas, supporting future research in marine invasion genomics.

The Orcuttiinae subtribe of the grass tribe Cynodonteae (Poaceae) represents an ancient and unique group of amphibious grasses adapted to the winter-wet, summer-dry conditions of seasonally flooded vernal pools. The subtribe consists of nine species represented across three genera (Neostapfia, Tuctoria, Orcuttia), most of which are endemic to, and found exclusively in, vernal pools throughout the California Floristic Province (from the Modoc Plateau to Baja California, Mexico) and in the Magdalena Plain in the southern Baja California peninsula. All species are rare and most have state and federal Threatened and/or Endangered protected status in the U.S. - except T. fragilis, which inhabits Baja California Sur, Mexico, and does not have official protected status in Mexico. Here, we report a new chromosome-level reference genome assembly and annotation for Greene's tuctoria (Tuctoria greenei) developed in collaboration with the California Conservation Genomics Project. The assembly includes two haplotypes: haplotype one spans 2.59 Gb with contig N50 of 3.22 Mb, scaffold N50 of 216.09 Mb, largest contig N50 of 19.5 Mb, and BUSCO completeness of 96.8%. Haplotype two spans 258.89 Gb with contig N50 of 3.27 Mb and scaffold N50 of 213.15 Mb, with a BUSCO completeness of 97.4%. This genome assembly confirms earlier chromosome counts of n=24 for T. greenei (Reeder, 1982) and represents a powerful new tool that can be used to test hypotheses of gene flow, adaptation and comparative genomics between recently diverged species, and to assist in regional conservation priorities and restoration efforts.

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.