Secondary and Tertiary Endosymbiosis and Kleptoplasty

Alga is an informal name that refers to a diverse group of photosynthetic eukaryotes that have a polyphyletic origin in the tree of life. Although genomics has provided powerful tools for understanding the evolution of algal photosynthesis many issues remain unresolved. These include explaining the intermingling of plastid-lacking taxa such as ciliates and oomycetes among plastid-containing groups of chromalveolates. Does this pattern reflect a single ancient endosymbiosis in the chromalveolate ancestor followed by independent plastid losses or multiple secondary endosymbioses? Here we review current knowledge about chromalveolate evolution and phylogeny with a focus on secondary and tertiary endosymbiosis and survey recent genome-wide analyses to assess the potentially broad and lasting impacts of plastid transfer on eukaryote evolution. We assess the evidence for ‘footprints’ of photosynthetic pasts that remain even when the plastid is lost. These data comprise remnant algal genes in the nucleus of plastid-lacking taxa that have putatively originated via intracellular gene transfer from the former endosymbiont. We also provide a survey of recent work done in the field of protein import (i.e., via translocons) into chromalveolate and other plastids derived from secondary endoysmbiosis. We contrast the similarities and differences between primary and secondary plastid protein import machineries and speculate on the key innovations that led to their establishment. And finally, we take a careful look at the remarkable case of sea slug (Elysia chlorotica) kleptoplasty and photosynthesis and review recent work aimed at explaining this phenomenon in different metazoa. In particular, we critically assess support for the hypothesis that sea slug photosynthesis is explained by massive horizontal gene transfer (HGT) from the genome of the captured alga.