Genomics of Algae

Abstract

Algae are dominant contributors to primary production and have a major impact on biogeochemical cycles because of their unique metabolisms. Few algal genomes have so far been characterized, although whole genome sequences have now been generated from representatives of the green, red and brown algae. In addition, numerous projects are progressing to define algal transcriptomes using expressed sequence tags (ESTs) and microarrays. Multiple efforts based on comparative and functional genomics approaches have already generated an influx of exciting data about evolutionary origins and functional innovations of different algal species dispersed throughout the eukaryotic tree of life. Key concepts: Algal species have little common phylogeny and are widely dispersed throughout the eukaryotic tree of life. Red and green algae lie within the Archaeplastida whereas brown algae lie within the Stramenopile and Alveolata lineages. Brown algae have secondary plastids, thought to be derived from secondary endosymbiosis. Chlamydomonas reinhardtii represents the best‐studied experimental system for algae. Diatom genomes are highly chimeric in nature, with genes derived from both partners of the secondary endosymbiosis, as well as large numbers of bacterial genes acquired by horizontal gene transfer. The existence of C4 photosynthesis in algae has not yet been conclusively demonstrated. Distinct algal species often comprise ecotypes optimized for growth in specific environmental conditions.

Do Red and Green Make Brown?: Perspectives on Plastid Acquisitions within Chromalveolates

“…Furthermore, an "endosymbiotic mosaic" of red, green, and chromalveolate-derived genes could have provided the genetic diversity to allow extant chromalveolates to dominate post-Permian algal communities. Many of these hypotheses will be resolved through broader, more balanced taxonomic sampling in phylogenetic data sets and from current genome sequencing projects such as that of the photosynthetic apicomplexan relative Chromera velia, the model rhizarian Bigelowiella natans, the relatively slow-evolving red algae Chrondrus crispus and Porphyra yezoensis, and the glaucophyte Cyanophora paradoxa (45). In parallel, it will be essential to gain a better understanding of the physiological properties of different endosymbiont lineages, including whether the red chloroplast lineage mitigates CO 2 and nutrient limitation and whether the retention of specific green genes confers enhanced selective fitness on chromalveolates.…”

“…These algae are characterized by the presence of chlorophyll c and specific accessory xanthophyll pigments in the light-harvesting antennae-hence, the common term for many of these species is "brown algae" (21,45). Brown algae are distributed in four major phyla (for detailed reviews, see references 1 and 123), commonly grouped as the "chromalveolates."…”