Journal of Heredity最新文献

The rough limpet, Lottia scabra, a generalist grazer in the upper intertidal zone of the northeastern Pacific, spans the California Transition Zone, where southern warm-water populations gradually replace northern cold-water ones, providing a valuable system for studying genomic adaptation. We present the first high-quality reference genome for L. scabra, making a significant advancement over previously available molecular resources for both L. scabra and the genus Lottia. We used PacBio HiFi long reads and Omni-C chromatin proximity sequences to assemble a genome comprising 70 scaffolds spanning 414.08 Mb, with an N50 of 5.33 Mb and a completeness of 96.4% single-copy ortholog genes. The assembly contains 10 chromosome-scale scaffolds, consistent with previously published karyotypes of sister taxa. This high-quality genome will enhance our understanding of the mechanisms underlying adaptation to environmental differences and species responses to environmental change, with implications for coastal biodiversity conservation.

Mimulus laciniatus (syn. Erythranthe lacinata) is an annual plant endemic to the Sierra Nevada region of California. Mimulus laciniatus is notable for its specialized ecological niche, thriving in granite outcrops of alpine environments characterized by shallow soils that dry out rapidly as the snowpack is exhausted during season-ending droughts. Due to its narrow habitat range and sensitivity to environmental change, this species serves as an important model for studying adaptation and survival in marginal habitats. As part of the California Conservation Genomics Project, here we report the sequencing and assembly of a high-quality nuclear genome and chloroplast genome of M. laciniatus. The primary assembly is 309.96 Mb and consists of 104 scaffolds with a scaffold N50 of 20.99 Mb, a largest contig size of 24.29 Mb and a contig N50 of 11.09 Mb, The alternate haplotype assembly consists of 194 scaffolds spanning 213.84 Mb. BUSCO completeness of the primary assembly is 98.6%. This high quality genome adds a valuable resource to the expanding collection of sequenced genomes of the monkeyflowers (Mimulus sensu lato), which have become a model clade for studying ecological adaptation, speciation, and evolutionary genetics.

Intrapopulation variation in the age at return and reproduction of Chinook Salmon (Oncorhynchus tshawytscha), or age-at-maturity, acts as a buffer against stochastic environmental variation. We investigated the genetic component of this trait by estimating the heritability of age-at-maturity and the genomic basis of both sex and age-at-maturity in stocks representing the 3 major lineages of the Columbia River Basin. We found that heritability of age-at-maturity was generally stronger for fathers with male offspring (mean h2 = 0.37, SD = 0.164) than mothers with female offspring (mean h2 = 0.29, SD = 0.077), fathers with female offspring (mean h2 = 0.29, SD = 0.155), or mothers with male offspring (mean h2 = 0.25, SD = 0.100). We identified several regions of the genome that were consistently associated with sex across all 3 lineages that included expected sex-chromosomes (Chr17 and 18), but also putative copies of sex-linked regions in several autosomal chromosomes. Furthermore, large regions of the same 2 chromosomes (17 and 18) were associated with age-at-maturity in a lineage-specific manner. Patterns of genotype by phenotype with multi-marker haplotypes confirmed the association of SNPs on chromosome 17 with both sizes (fork length) in natural-origin males from the 2 interior lineages, and age-at-maturity (ocean age) in interior ocean-type males, but not in females. Further studies will be necessary to verify other candidate regions and polygenic effects on size and age-at-maturity in this species. Although the rearing environment and growth play a major role in age-at-maturity, these results provided evidence for genetic heritability and candidate genes associated with this trait that will assist in monitoring genetic variation to maintain life history variation in Chinook Salmon.

Azolla is a genus of freshwater ferns that is economically important as a nitrogen-fixing biofertilizer, biofuel, bioremediator, and for potential carbon sequestration, but also contains weedy invasive species. In California, only 2 species are currently recognized but the actual diversity may include up to 6 species, with the discrepancy being due to the difficulty in identifying taxa, hybridization, and the introduction of non-native species. Here, we report a new haplotype-resolved, chromosome-level assembly and annotation of Azolla caroliniana as part of the California Conservation Genomics Project (CCGP), using a combination of PacBio HiFi and Omni-C sequencing technologies. The assembly is 521 Mb in length, with a contig N50 of 1.6 Mb, and is scaffolded into 22 pseudochromosomes. A total of 21,848 protein-coding genes was predicted with a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 89.88%. In combination with the previously published Azola filiculoides genome, this A. caroliniana genome will be a powerful tool for understanding the population genetics and taxonomy of one of the most cryptic, economically important, and poorly circumscribed fern taxa, and for facilitating land plant genomics more broadly.

The Gophersnake, Pituophis catenifer, is a habitat generalist that ranges throughout the western half of the United States and southward into México. Five of the six subspecies, P. catenifer affinis (Sonoran Gophersnake), P. catenifer annectens (San Diego Gophersnake), P. catenifer catenifer (Pacific Gophersnake), P. catenifer deserticola (Great Basin Gophersanke), and P. catenifer pumilus (Santa Cruz Island Gophersnake), occur in California and span virtually all the state's diverse terrestrial habitats. These subspecies are ecologically and morphologically distinct from one another, although existing genetic data indicate there is genetic admixture across some of their contact zones. Given that these subspecies occur in such different environments they will not all respond to climate change and anthropogenic stressors equally. Here, we report a new, chromosome-level assembly of P. catenifer as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 426 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.5 Mb, a scaffold N50 of 161 Mb, and BUSCO completeness score of 95.3%. This genome will be a foundational resource for future studies on the conservation, adaptation, biogeography, and systematics of P. catenifer.

Haplotype-resolved (phased) genome assemblies are emerging as important assets for genomic studies of species with high heterozygosity, but remain lacking for key animal lineages. Here, we use PacBio HiFi and Omni-C technologies to assemble the first phased, annotated, chromosome-level genome for any annelid: the reef-building tubeworm Galeolaria caespitosa (Serpulidae). The assembly is 803.5 Mbp long (scaffold N50 = 76.5 Mbp) for haplotype 1 and 789.3 Mbp long (scaffold N50 = 75.4 Mbp) for haplotype 2, which are arranged into 11 pairs of chromosomes showing no sign of sex chromosomes. This compares with cytological analyses reporting 12 to 13 pairs in G. caespitosa's closest relatives, including species that are protandrous hermaphrodites. We combined long-read and short-read transcriptome sequencing to annotate both haplotypes, resulting in 30,495 predicted proteins for haplotype 1, 27,423 proteins for haplotype two, and 79.5% of proteins with at least one functional annotation. We also assembled a mitochondrial genome 23 kbp long, annotating all genes typically found in mitochondrial DNA apart from those coding the 16S ribosomal subunit (rrnL) and the protein atp8-a short, fast-evolving mitochondrial gene missing in other metazoans. Comparing G. caespitosa's genome to those of three other annelids reveals limited collinearity despite 36.0% of shared orthologous gene clusters (4,238 of 11,763 clusters counted in G. caespitosa), suggesting extensive chromosomal rearrangements among lineages. New high-quality annelid genomes may help resolve the genetic and evolutionary basis of this diversity.

Squamate reptiles are a highly diverse and intriguing group of tetrapods, offering valuable insights into the evolution of amniotes. The Australian water dragon (Intellagama lesueurii) is a member of the Agamidae and sister to the core mesic Australian endemic radiation (Amphibolurinae). The species is renowned for its urban adaptability and complex social systems. We report a 1.8 Gb chromosome-length genome assembly together with the annotation of 23,675 protein-coding genes. Comparative analysis with other squamate genomes highlights gene family expansions associated with immune function, energetic homeostasis, and wound healing. This reference genome will serve as a valuable resource for studies of evolution and environmental resilience in lizards.

The Pismo clam, Tivela stultorum, is an ecologically and economically important species inhabiting sandy beaches and subtidal zones in central and southern California, USA, and northern Baja California, Mexico. This long-lived venerid clam species is of great management, cultural and conservation interest in California where it was harvested for centuries by indigenous people and then nearly extirpated by intense commercial and recreational overfishing in the mid-1900s. A recreational fishery continues today in California; however, T. stultorum faces pressure from poaching, overharvest, and the loss of sandy beaches from rising sea levels and beach erosion. Understanding the susceptibility and resilience of Pismo clams to these pressures is essential for their conservation. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to assemble a highly contiguous genome of 763 Mb. The genome had a contig N50 of 13 Mb and a scaffold N50 of 38 Mb with a BUSCO completeness score of 95%. Most of the genome sequences (96%) were contained in 19 scaffolds at least 10MB long, consistent with prior evidence that venerid clam genomes are composed of 19 autosomes. This reference genome will enable a more complete understanding of the ecology and evolutionary dynamics of T. stultorum via population genomic analyses, which will help assess risks from climate, fishing, environmental change, and susceptibilities due to life history. Our goal is to better support the continued recovery, informed management and conservation, and future persistence of T. stultorum, a long-lived and highly valued clam species.

The faster-X/Z effect hypothesis states that genes linked to X/Z chromosomes should accumulate mutations faster than autosomal genes. Although faster evolution of X/Z-linked genes has been reported in several plant and animal lineages, conflicting results have been reported in others. We examined the faster-Z effect in chameleons of the genus Furcifer, a lineage with differentiated ZZ/ZW chromosomes for at least 20 million yr. We sequenced the genomes of four species of Furcifer chameleons in the Illumina platform and compared the substitution rates of synonymous and non-synonymous mutations and their ratios among autosomal, Z-specific, and pseudoautosomal protein-coding genes. The inclusion of two chameleon outgroups lacking the differentiated ZZ/ZW sex chromosomes allowed us to control for gene-specific evolutionary rates that might confound the testing of the faster-X/Z effect. Significant differences in evolutionary rates were found between autosomal, Z-specific, and pseudoautosomal genes of Furcifer chameleons. However, the inclusion of the outgroups with different sex chromosomes suggests that these genes had different evolutionary rates prior to their incorporation into the differentiated ZZ/ZW sex chromosomes of the Furcifer genus. The results highlight the need to control for differences in the evolutionary rates of individual genes when testing for the faster-X/Z effect.

Predatory species who hunt for their prey rely on a suite of integrated characters, including sensory traits that are also used for nonpredatory behaviors. Linking the evolution of sensory traits to specific selection pressures therefore requires a deep understanding of the underlying genetics and molecular mechanisms producing these complex phenotypes. However, this relationship remains poorly understood for complex sensory systems that consist of proteins encoded by large gene families. The chemosensory repertoire of rattlesnakes includes hundreds of type-2 vomeronasal receptors and olfactory receptors, representing the two largest gene families found in the genome. To investigate the biological importance of this chemoreceptor diversity, we assessed gene expression in the eastern diamondback rattlesnake (Crotalus adamanteus) and identified sex- and age-biased genes. We found type-2 vomeronasal receptor expression in the vomeronasal epithelium was limited to juvenile snakes, suggesting the sensory programming of this tissue may be correlated with early life development. In the olfactory epithelium, we found subtle expression biases that were more indicative of life history rather than development. We also found transcriptional evidence for dosage compensation of sex-linked genes and trait integration in the expression of transcription factors. We overlay our molecular characterizations in Crotalus adamanteus onto updated olfactory receptor and type-2 vomeronasal receptor phylogenies, providing a genetic road map for future research on these receptors. Finally, we investigated the deeper macroevolutionary context of the most highly expressed type-2 vomeronasal receptor gene spanning the rise of tetrapods and estimated the strength of positive selection for individual amino acid residues in the predicted protein structure. We hypothesize that this gene may have evolved as a conserved signaling subunit to ensure consistent G-protein coupled receptor functionality, potentially relaxing signaling constraints on other type-2 vomeronasal receptor paralogs and promoting ligand binding specificity.