Journal of Heredity最新文献

The cactus moth, Cactoblastis cactorum, native to southern South America, has extended its range throughout Florida, north to coastal South Carolina and west to Texas in the United States and the Caribbean region, posing a threat to native Opuntia and also affecting the production of prickly pear-associated industries in both its native and non-native ranges. Past efforts to control the cactus moth have not been effective. However, promising biological control agents are currently under evaluation. Moreover, as genomic and transcriptomic data become available, emerging techniques, such as gene editing, offer promising avenues for developing alternative control strategies. In this study, we present novel transcriptomic data of adult male and female moths and larvae using RNA-Seq to gain new insights into the genetic repertoire of this cactus pest along its life cycle. The final assembly revealed 14,202 genes, of which 2,199 and 2,008 transcripts were differentially expressed between males and females, and between larvae and adults, respectively. Overall, functional analyses pointed to an enrichment of serine-type peptidase inhibitors, odorant-binding proteins, and glycoside hydrolases between life cycle stages (larvae vs. adults) and sex-specific biological functions. Our study provides the first report of differential gene expression across developmental stages, generating new and valuable genetic resources to guide future molecular and physiological research as well as pest management strategies in the cactus moth.

Diacylglycerol acyltransferases (DGAT) are key enzymes in fat storage, converting diacylglycerol and fatty acyl-CoA into triacylglycerol. In cattle (Bos taurus), the DGAT1 and DGAT2 genes are well known for their significant influence on milk production traits, particularly milk fat yield and percentage. However, the cattle genome contains twelve other DGAT gene family members that remain largely uncharacterized. This research examined the genetic makeup of these DGAT proteins, revealing differences in exon count, isoforms, amino acid composition, molecular weight, isoelectric points, and predicted SNP locations. The genes are distributed across five chromosomes (2, 14, 15, 25, and X), and the expansion of this gene family in cattle is likely the result of gene duplication events driven by specific motifs that favor such duplication. By identifying these distinctions, the study provides foundational insights into the lesser-known DGAT genes, which could be involved in regulating important traits like milk fat production. This comprehensive in silico analysis of the DGAT gene family offers valuable insights into the genetic and structural diversity of these enzymes in cattle. It also establishes a platform for future research into functional SNPs and their potential role in improving milk fat production traits, contributing to the advancement of cattle genetics and dairy production optimization. To this end, the identification of previously uncharacterized DGAT genes and their possible involvement in milk fat synthesis could pave the way for innovative breeding strategies focused on improving both milk yield and fat content in dairy cattle.

Genomic regions that influence sex are hypothesized to play a key role in evolutionary diversification, as sex determination mechanisms may promote or impede reproductive isolation between closely related species. Remarkably, these mechanisms are almost completely unknown in many taxa, especially in clades like fish with extremely variable sex determination. In Catostomus fishes, contemporary hybridization is extensive but variable, and factors influencing hybridization dynamics are not fully understood. We used genotyping-by-sequencing data from three Catostomus species (bluehead, white, and flannelmouth suckers) to identify regions of the genome associated with sex using a genome-wide association study. We identified a genomic region in bluehead suckers from Colorado on chromosome 4 that significantly associates with sex and is suggestive of a sex-determining region. This region is not significant in the other species studied here, or in a divergent lineage of bluehead suckers, implying that either the sex-determining region of the genome differs in these species and populations, or that technical limitations precluded identification of sex determination. These results provide the first description of sex determination systems in Catostomus species and suggest that further investigation of sex determination in the Catostomidae genus is needed to better characterize evolutionary turnover of sex determination in this species-rich group.

In the current era, many terrestrial carnivore populations confront a multitude of threats and are rapidly shifting their ranges in response to human-induced modifications. Monitoring changes in genetic diversity and structure of such species in response to changing environmental conditions is important for understanding species' responses and designing effective conservation management strategies. In this study, we investigated the genetic status of the golden jackal, a widely distributed canid inhabiting human-dominated landscapes and exhibiting high dispersal capability. We collected and analyzed 141 jackal samples from across the distribution range in India, employing a combination of mitochondrial DNA (mtDNA) (cytochrome b and control region) and nuclear microsatellite (n = 25) markers to investigate patterns of genetic diversity, gene flow, demographic history and phylogeography. Our analyses showed substantial levels of genetic diversity within India surpassing levels observed in other global populations. Bayesian and non-Bayesian clustering analyses revealed low levels of genetic differentiation among sampled populations, except for the Southern Indian population. Demographic analysis using both mtDNA and microsatellites revealed that golden jackals in India have not experienced significant bottlenecks, while estimates of past effective population size suggested declines during the last 2,500 generations, which corresponds to 7,500 to 10,000 years before present. Global phylogeographic analysis highlighted the distinctiveness of Indian jackals compared with other populations from across the species' distribution, with the highest number of haplotypes observed in Indian populations and no shared haplotypes observed between Indian and Middle Eastern populations, or Indian and European populations. These findings are indicative of a long evolutionary history and bring new insights to inform targeted conservation management strategies for golden jackals, both locally and globally.

Characterizing functional connectivity is an important challenge in the face of ongoing environmental change. Approaches combining landscape-genetic and network methodologies have shown promise in allowing for simultaneous identification of strong and vulnerable populations, and the landscape factors that may inhibit or facilitate population connectivity. Here we leverage these tools to assess the genetic structure and functional connectivity of Parnassius clodius butterflies in three protected regions in the United States, North Cascades National Park (WA), Grand Teton National Park (WY), and Yosemite National Park (CA), and determine whether these metrics vary with differences in sampling scale among regions. We also test the resilience of population connectivity to extirpation using graph-theoretic analyses (e.g. network analyses) and test the relative importance of isolation-by-distance, isolation-by-resistance, and isolation-by-environment in limiting population connectivity, using butterfly habitat suitability, host plant data, terrain roughness, percent forest cover, and climate variables. Both traditional genetic clustering analyses and network analyses revealed fine-scale genetic structure across all three regions. Our network analyses revealed similarity in topology across regions despite significant landscape variation, and network sensitivity analyses revealed that P. clodius subpopulations within the Grand Teton and Yosemite NP regions are more vulnerable to perturbations. Our landscape-genetic analyses suggest that environmental variation has an important impact on genetic differentiation in addition to geographical distance, but the contribution of specific variables varies across replicate landscapes.

The white perch, Morone americana, is a widely distributed and ecologically important teleost native to the east coast of North America. Due to its ease of capture and high abundance across a range of ecological conditions, the white perch has been used - and continues to be developed - as a bioindicator of contaminant exposure. Outside of its native range, the white perch is invasive, negatively impacting local ecology and hybridizing with congeneric species. Using PacBio HiFi data, we present two (female and male) highly contiguous genome assemblies. The female assembly spans 694 Mb (264 contigs, N50: 24.9 Mb), with 85% of the total assembly size captured in the largest 24 contigs (the karyotype for the species is 2n = 48). The male assembly spans 688 Mb (265 contigs, N50: 26.4 Mb), with 89% of the total assembly size captured in the largest 24 contigs. Both assemblies have high BUSCO completeness scores of 98.7% (female) and 98.8% (male), and a high k-mer completeness (>98% for both genomes). Combining evidence derived from transcriptomic data and a large protein database, we constructed a high-quality annotation for the female assembly (99% BUSCO completeness, 87% OMArk completeness), including 20,699 predicted protein-coding genes, of which 20,406 have a functional annotation and 16,187 have an associated gene name. These reference genomes will support the development of the white perch as a bioindicator and will serve as an important resource for studying the species' invasiveness and monitoring intraspecific hybridization using genomic tools.

Genome-structural evolution on a large scale is prevalent in various organisms. The role of genome-structural rearrangements, including chromosome fusions, has been revealed in genome evolution and species divergence. However, the empirical evidence in adaptation remains debated at the current time. We investigated the phylogenetic relationship, genomic divergence, and environmental associations of closely related Asian clams: the freshwater species Corbicula fluminea and brackish-freshwater species Corbicula mortoni. The chromosome-level genome assembly of brackish-freshwater C. mortoni using single-molecule and Hi-C sequencing revealed a chromosome-scale rearrangement relative to freshwater C. fluminea. Strikingly, genomic characterization studies including outgroup species Archivesica marissinica indicated two independent fusion events in these closely related species. Transcriptome analysis under salinity stress identified differentially expressed genes (DEGs) and revealed a significant enrichment of significantly down-regulated genes (SDGs) on the fused chromosome of C. mortoni, suggesting possible regulatory shifts associated with fusion. In summary, our genomic and transcriptomic analyses document important chromosome-scale evolutionary events during Corbicula speciation and provides insights into the relationship between genomic reorganization and gene regulation in response to environmental variation.

Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures > 97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.

Few genomic resources currently exist for the American endemic family Cactaceae, a group of around 1850 species, which are world renowned for their amazing growth forms and succulent habits. These icons of arid landscapes across the Americas are threatened in many parts of their range, including in parts of California, and developing more comprehensive genomic data will aid efforts to better understand and preserve these plants. We sequenced and assembled the genome of the beavertail cactus, Opuntia basilaris, which is represented by three varieties in California, one of which is threatened and another endangered. The genome assembly has a BUSCO complete score of 98.1%, and a total scaffold length of 980 Mb, with a scaffold N50 length of 83 Mb. The genome size of diploid O. basilaris is markedly smaller than other diploid members of Cactaceae that have been assembled to date. This is the first nuclear genome sequenced in subfamily Opuntioideae and the most complete nuclear genome for Cactaceae to date and will lay the foundation for future genomic work across the biologically and taxonomically complicated prickly pear cacti.