Percorrer por autor "Raimondi, Peter"
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- Past climate-driven range shifts structuring intraspecific biodiversity levels of the giant kelp (Macrocystis pyrifera) at global scalesPublication . Assis, Jorge; Alberto, Filipe; Macaya, Erasmo C.; Coelho, Nelson; Faugeron, Sylvain; Pearson, Gareth; Ladah, Lydia; Reed, Daniel C.; Raimondi, Peter; Mansilla, Andrés; Brickle, Paul; Zuccarello, Giuseppe C.; Serrao, EsterThe paradigm of past climate-driven range shifts structuring the distribution of marine intraspecific biodiversity lacks replication in biological models exposed to comparable limiting conditions in independent regions. This may lead to confounding effects unlinked to climate drivers. We aim to fill in this gap by asking whether the global distribution of intraspecific biodiversity of giant kelp (Macrocystis pyrifera) is explained by past climate changes occurring across the two hemispheres. We compared the species' population genetic diversity and structure inferred with microsatellite markers, with range shifts and long-term refugial regions predicted with species distribution modelling (SDM) from the last glacial maximum (LGM) to the present. The broad antitropical distribution of Macrocystis pyrifera is composed by six significantly differentiated genetic groups, for which current genetic diversity levels match the expectations of past climate changes. Range shifts from the LGM to the present structured low latitude refugial regions where genetic relics with higher and unique diversity were found (particularly in the Channel Islands of California and in Peru), while post-glacial expansions following similar to 40% range contraction explained extensive regions with homogenous reduced diversity. The estimated effect of past climate-driven range shifts was comparable between hemispheres, largely demonstrating that the distribution of intraspecific marine biodiversity can be structured by comparable evolutionary forces across the global ocean. Additionally, the differentiation and endemicity of regional genetic groups, confers high conservation value to these localized intraspecific biodiversity hotspots of giant kelp forests.
- The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeanaPublication . Alves-Lima, Cicero; Montecinos, Gabriel; Escalona, Merly; Calhoun, Sara; Marimuthu, Mohan; Nguyen, Oanh; Beraut, Eric; Lipzen, Anna; Grigoriev, Igor V; Raimondi, Peter; Nuzhdin, Sergey; Alberto, FilipeBull 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 1,562 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 Mb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 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.