The Evolutionary History and Polyploid Origin of Coast Redwood (Sequoia sempervirens

The majestic coast redwood (Sequoia sempervirens) is a California endemic tree of economic, ecological, and cultural value. Coast redwoods are also noteworthy due to their genomic composition; they are polyploid, having six copies of each chromosome rather than the two copies seen in almost all other conifers. It is known that polyploidy in Sequoia arose at least 34 millions years ago (Ma) because fossils from this era have stomatal guard-cells (known proxies for ploidy) whose size indicates polyploidy. Diverse mechanisms have been proposed to explain the origin of polyploidy in the coast redwood, and some authors have argued hybridization among multiple redwood lineages played a role. We sequenced leaf-expressed genes (a transcriptome) from all three redwood species and a close relative and used statistical analysis to show that polyploidy in coast redwood is unlikely to have involved hybridization. To further test this finding, we then sequenced a targeted subset of the genome for 8 redwood accessions and two outgroups. These data support the same conclusion: polyploidy did not involve hybridization among divergent species. We also used the sequences, combined with the fossil record, to infer the divergence dates of Sequoia from its sister group, giant sequoia (Sequoiadendron giganteum), and to determine when the different chromosomal copies of Sequoia genes last shared common ancestry. We found that the Sequoia and Sequoiadendron lineages diverged ~ 51 Ma, whereas most Sequoia gene copies diverged from one another ~13Ma. The latter date is noticeably much more recent than the polyploidy event itself (>34 Ma). We argued that this finding can be explained by inferring that the three pairs of genes (homeologs) in Sequoia exchanged genetic information long after polyploidization. This inference is consistent with observations that, even today, Sequoia chromosomes do not consistently pair up during cell division. Our elucidation of the complex genetics and genome history of the coast redwood provides important background information for efforts to ensure the long-term survival of this magnificent and iconic tree species in the face of rapid changes in the California climate.