BraunPhillips2008.JPhycol - J. Phycol. 44, 26 (2008) 2008...

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PHYLOGENOMICS AND SECONDARY PLASTIDS:ALOOKBACKANDALOOKAHEAD 1 Edward L. Braun 2 Department of Zoology, University of Florida, Gainesville, Florida 32611, USA and Naomi Phillips Biology Department, Arcadia University, 450 S. Easton Rd., Glenside, Pennsylvania 19038, USA Despite their importance to evolution, ecology, and cell biology, eukaryotes that acquired plastids through secondary endosymbiosis remain poorly studied from a genomic standpoint. Chromalveolata, a eukaryotic supergroup proposed to have des- cended from a heterotrophic eukaryote that acquired a red algal plastid by secondary endosymbi- osis, includes four major lineages (alveolates, cryp- tophytes, haptophytes, and heterokonts). The chromalveolates exhibit remarkable diversity of cellular organization, and the available data suggest that they exhibit equal diversity in their genome organization. One of the most obvious differences in cellular organization is the retention of a highly reduced red algal nucleus in cryptophytes (also known as cryptomonads), but there are other major differences among chromalveolate lineages, includ- ing the loss of photosynthesis in multiple lineages. Although the hypothesis of chromalveolate mono- phyly is appealing, there is limited support for the hypothesis from nuclear genes, and questions have even been raised about the monophyly of chromal- veolate plastids. Evidence for the chromalveolate hypothesis from large-scale nuclear data sets is reviewed, and alternative hypotheses are described. The potential for integrating information from chromalveolate genomics into functional genomics is described, emphasizing both the methodological challenges and the opportunities for future phyloge- nomic analyses of these groups. Key index words: alveolates; chromists; crypto- phytes; haptophytes; heterokonts; phylogenomics Abbreviation: EST, expressed sequence tag Chromalveolata is a proposed eukaryote super- group that has emerged in recent large-scale molec- ular phylogenies (e.g., Delsuc et al. 2005). Although Chromalveolata has been included in only one for- mal taxonomy (see Parfrey et al. 2006), the group was proposed to provide a very plausible and parsi- monious explanation for the presence of plastids in both chromists and alveolates (Cavalier-Smith 1999). Thus, the de±nition of the chromists and alveolates and the origin of plastids in these groups are closely linked to the de±nition of the supergroup. Chromalveolate plastids are proposed to have an origin that is distinct from the plastids in the Plan- tae (also called Archaeplastida, see Parfrey et al. 2006). Plastids in the Plantae arose directly from a cyanobacterial ancestor by endosymbiosis (primary), while the plastids in chromalveolates arose by a sec- ondary endosymbiotic event of a red algal ancestor. Chromalveolate plastids have the same cyanobacteri-
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This note was uploaded on 04/17/2008 for the course PCB 3063 taught by Professor Marta during the Spring '08 term at University of Florida.

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BraunPhillips2008.JPhycol - J. Phycol. 44, 26 (2008) 2008...

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