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Capacity to cope with warming temperatures is a key determining factor of species' persistence under global climate change. Many successful invasive species have heightened thermal tolerance relative to their native counterparts, which may provide competitive advantages for habitat utilization and resource acquisition under warming scenarios, ultimately contributing to radically altered community composition. Enhanced transcriptional plasticity may be an important factor conferring superior abilities to cope with environmental stress, but the molecular mechanisms driving key differences of organismal traits in invasive versus native species are not well known. Although it is predicted that established invaders will evolve canalized phenotypes well‐adapted to new environments, it is not clear whether the same expectations are true for invaders of variable thermal environments or under climate warming scenarios where abilities to cope with fluctuating and increasing temperatures may provide fitness advantages. Here, we compare a highly successful invasive fish and a sympatric endangered native fish living in a dynamic estuarine environment that is projected to warm under climate change. We linked organismal physiological limits with global transcriptional responses at multiple common relative and absolute temperature thresholds and determined that heightened thermal tolerance of invasive Inland Silversides (Menidia beryllina) is associated with transcriptional changes that are greater both in the number of genes and the magnitude of response relative to native Delta Smelt (Hypomesus transpacificus). Modulated genes contributed to the enrichment of biological processes that differed between species and generally increased with temperature. These results are in concordance with the hypothesis that transcriptional plasticity may play a key role in determining population persistence, species interactions, and shaping community assemblages under climate change. Future studies encompassing a wider range of species and taxa are needed to determine whether this is a general pattern found between native and invasive species more broadly.

 

Abstract The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management. 

Abstract Background The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. Findings Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. Conclusion Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.