Journal of Heredity最新文献

The Chinese herring (Ilisha elongata) is an economically important clupeiform fish, mostly found along the coast of China and Japan in the western Pacific Ocean. Overfishing and climate change have caused a substantial decline in its annual catch, which may have impacted its population size and structure. Here, we present a chromosome-level genome assembly of the Chinese herring, generated using a combination of Nanopore sequencing, Illumina sequencing, and high-throughput chromatin conformation capture technologies. The total length of this assembly is 802.47 Mbp, anchored to 24 chromosomes, with contig N50 and scaffold N50 values of 13.22 and 33.10 Mbp, respectively. Benchmarking Universal Single-Copy Orthologues analysis indicated high completeness of this assembly, with 94.9% of universal single-copy orthologs. Analysis of resequencing samples from various coastal regions of China and Japan revealed four distinct genetic populations of Chinese herring along the East Asian coast. The Dandong population (Yellow Sea) diverged earliest, exhibiting unique genetic structures and selective sweep signals, whereas the other three populations expanded from a tropical South China Sea ancestral population to the East China Sea and to Japanese waters. Among 23,366 protein-coding genes, several families related to the metabolism of very-long-chain unsaturated fatty acids are particularly contracted compared with the American shad. Additionally, several genes associated with fatty acid synthesis formation have undergone accelerated positive selection. These findings may explain the differential fatty acid ratios in marine versus riverine migratory clupeiforms. This high-quality genome assembly of the Chinese herring may provide valuable resources for comparative study of coastal fishes and benefit the development of a sustainable management strategy for fisheries of the Chinese herring.

Ionizing radiation is a potent environmental mutagen, producing damaged bases and single and double-stranded DNA breaks. Acute high-dose radiation exposure is therefore toxic, causing cellular and organismal mortality, while lower doses can give rise to high mutation rates and cancer. Radiation sensitivity furthermore varies dramatically between organisms and cell types, with certain organisms exhibiting extreme tolerance to ionizing radiation. It is puzzling however, how such radiotolerance evolved in nature, as toxic radiation doses are not observed outside of medical and nuclear settings. In this review, we explore the mechanisms and evolution of extraordinary radiotolerance in metazoans. We contrast two extensively studied genetic models, mammals and Caenorhabditis elegans, as well as two lineages known to tolerate extreme radiation when compared to closely related species: naked mole rats and tardigrades. We describe similar strategies employed by these disparate lineages to protect DNA, repair DNA, and attenuate cellular responses following radiation exposure. We further discuss how these mechanisms may have evolved in response to other extreme conditions tolerated by each species in their natural environment, giving rise to radiotolerance as a correlated response.

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.

Rockfishes (genus Sebastes) are one of the most diverse clades amongst teleosts (ray-finned fishes). The genus includes more than 110 species which are distributed broadly across the North Pacific Ocean, North and South Atlantic Ocean, and Southeastern Pacific Ocean. Rockfishes exhibit particularly high diversity along the western coast of the United States, where their abundance plays a critical role in local marine ecosystems and fisheries. Sebastes paucispinis ("bocaccio") is a rockfish species most commonly found off the coast of California. In 2005, Bocaccio were federally declared overfished following massive depletion by commercial and recreational fisheries from the 1980s to early 2000s. Implementation of significant restrictions has bolstered recovery of critical rockfish populations along the California and Oregon coasts, but the impact of anthropogenic stressors on bocaccio, and other Sebastes species, has yet to be fully evaluated. Here, we present the first de novo reference-quality genome assembly of Sebastes paucispinis, as part of the California Conservation Genomics Project.

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.

A central challenge in biology is to understand how complex behaviors evolve. Reproductive behaviors are frequently subject to strong selection and complex behavioral traits often evolve as an integrated package. However, it is unclear whether suites of traits evolve through a few pleiotropic genetic changes, each affecting many behaviors, or by accumulating several changes that, when combined, give rise to an entire package of correlated traits. Typically, three-spined stickleback exhibit paternal care, a behavior that characterizes the entire Gasterosteidae family. However, an unusual "white" three-spined stickleback ecotype exhibits a suite of traits associated with the evolutionary loss of paternal care. In the white ecotype, males disperse embryos from their nests rather than care for them, build loose nests, exhibit high rates of courtship, and are relatively small in body size. These differences are apparent in stickleback reared in a common garden environment, suggesting the differences have a heritable basis. In an F2 intercross (n=76-133), we show that these traits are genetically uncorrelated and map to different genomic regions, suggesting that components of the white reproductive strategy segregate independently and evolved through the addition of multiple genetic changes. Moreover, distinct sets of genes may be involved in regulating the same motor pattern across contexts. These results contribute to the growing body of evidence that behavioral diversity observed in nature may evolve by accumulating and combining alleles, each with modular effects, and show that this principle applies to a suite of behavioral traits that form an integrated strategy.

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.