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Title: The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism

Abstract

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in the marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature ofmore » diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different evolutionary history from the higher plants that dominate photosynthesis on land. Higher plants and green, red and glaucophyte algae are derived from a primary endosymbiotic event in which a non-photosynthetic eukaryote acquired a chloroplast by engulfing (or being invaded by) a prokaryotic cyanobacterium. In contrast, dominant bloom-forming eukaryotic phytoplankton in the ocean, such as diatoms and haptophytes, were derived by secondary endosymbiosis whereby a non-photosynthetic eukaryote acquired a chloroplast by engulfing a photosynthetic eukaryote, probably a red algal endosymbiont (Fig. 1). Each endosymbiotic event led to new combinations of genes derived from the hosts and endosymbionts (7). Prior to this project, relatively few diatom genes had been sequenced, few chromosome numbers were known, and genetic maps did not exist (8). The ecological and evolutionary importance of diatoms motivated our sequencing and analysis of the nuclear, plastid, and mitochondrial genomes of the marine centric diatom Thalassiosira pseudonana.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Director. Office of Science. Office of Biological andEnvironmental Research
OSTI Identifier:
860384
Report Number(s):
LBNL-58730
Journal ID: ISSN 0193-4511; SCEHDK; R&D Project: 626879; BnR: KP1103010; TRN: US200524%%127
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Science
Additional Journal Information:
Journal Volume: 306; Journal Issue: 5693; Related Information: Journal Publication Date: October 1,2004; Journal ID: ISSN 0193-4511
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; BIOSYNTHESIS; CARBON DIOXIDE; CARBOXYLIC ACIDS; CELL WALL; CHLOROPLASTS; CHROMOSOMES; DIATOMS; ECOLOGY; ENZYMES; METABOLISM; OPTICAL MICROSCOPES; PHOTOSYNTHESIS; PHYTOPLANKTON; SILICIC ACID; UNICELLULAR ALGAE

Citation Formats

Ambrust, E V, Berges, J, Bowler, C, Green, B, Martinez, D, Putnam, N, Zhou, S, Allen, A, Apt, K, Bechner, M, Brzezinski, M, Chaal, B, Chiovitti, A, Davis, A, Goodstein, D, Hadi, M, Hellsten, U, Hildebrand, M, Jenkins, B, Jurka, J, Kapitonov, V, Kroger, N, Lau, W, Lane, T, Larimer, F, Lippmeier, J, Lucas, S, Medina, M, Montsant, A, Obornik, M, Parker, M Schnitzler, Palenik, B, Pazour, G, Richardson, P, Rynearson, T, Saito, M, Schwartz, D, Thamatrakoln, K, Valentin, K, Vardi, A, Wilkerson, F, Rokhsar, D, Vardi, A, Wilkerson, F P, and Rokhsar, D S. The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism. United States: N. p., 2004. Web.
Ambrust, E V, Berges, J, Bowler, C, Green, B, Martinez, D, Putnam, N, Zhou, S, Allen, A, Apt, K, Bechner, M, Brzezinski, M, Chaal, B, Chiovitti, A, Davis, A, Goodstein, D, Hadi, M, Hellsten, U, Hildebrand, M, Jenkins, B, Jurka, J, Kapitonov, V, Kroger, N, Lau, W, Lane, T, Larimer, F, Lippmeier, J, Lucas, S, Medina, M, Montsant, A, Obornik, M, Parker, M Schnitzler, Palenik, B, Pazour, G, Richardson, P, Rynearson, T, Saito, M, Schwartz, D, Thamatrakoln, K, Valentin, K, Vardi, A, Wilkerson, F, Rokhsar, D, Vardi, A, Wilkerson, F P, & Rokhsar, D S. The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism. United States.
Ambrust, E V, Berges, J, Bowler, C, Green, B, Martinez, D, Putnam, N, Zhou, S, Allen, A, Apt, K, Bechner, M, Brzezinski, M, Chaal, B, Chiovitti, A, Davis, A, Goodstein, D, Hadi, M, Hellsten, U, Hildebrand, M, Jenkins, B, Jurka, J, Kapitonov, V, Kroger, N, Lau, W, Lane, T, Larimer, F, Lippmeier, J, Lucas, S, Medina, M, Montsant, A, Obornik, M, Parker, M Schnitzler, Palenik, B, Pazour, G, Richardson, P, Rynearson, T, Saito, M, Schwartz, D, Thamatrakoln, K, Valentin, K, Vardi, A, Wilkerson, F, Rokhsar, D, Vardi, A, Wilkerson, F P, and Rokhsar, D S. 2004. "The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism". United States. https://www.osti.gov/servlets/purl/860384.
@article{osti_860384,
title = {The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism},
author = {Ambrust, E V and Berges, J and Bowler, C and Green, B and Martinez, D and Putnam, N and Zhou, S and Allen, A and Apt, K and Bechner, M and Brzezinski, M and Chaal, B and Chiovitti, A and Davis, A and Goodstein, D and Hadi, M and Hellsten, U and Hildebrand, M and Jenkins, B and Jurka, J and Kapitonov, V and Kroger, N and Lau, W and Lane, T and Larimer, F and Lippmeier, J and Lucas, S and Medina, M and Montsant, A and Obornik, M and Parker, M Schnitzler and Palenik, B and Pazour, G and Richardson, P and Rynearson, T and Saito, M and Schwartz, D and Thamatrakoln, K and Valentin, K and Vardi, A and Wilkerson, F and Rokhsar, D and Vardi, A and Wilkerson, F P and Rokhsar, D S},
abstractNote = {Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in the marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different evolutionary history from the higher plants that dominate photosynthesis on land. Higher plants and green, red and glaucophyte algae are derived from a primary endosymbiotic event in which a non-photosynthetic eukaryote acquired a chloroplast by engulfing (or being invaded by) a prokaryotic cyanobacterium. In contrast, dominant bloom-forming eukaryotic phytoplankton in the ocean, such as diatoms and haptophytes, were derived by secondary endosymbiosis whereby a non-photosynthetic eukaryote acquired a chloroplast by engulfing a photosynthetic eukaryote, probably a red algal endosymbiont (Fig. 1). Each endosymbiotic event led to new combinations of genes derived from the hosts and endosymbionts (7). Prior to this project, relatively few diatom genes had been sequenced, few chromosome numbers were known, and genetic maps did not exist (8). The ecological and evolutionary importance of diatoms motivated our sequencing and analysis of the nuclear, plastid, and mitochondrial genomes of the marine centric diatom Thalassiosira pseudonana.},
doi = {},
url = {https://www.osti.gov/biblio/860384}, journal = {Science},
issn = {0193-4511},
number = 5693,
volume = 306,
place = {United States},
year = {2004},
month = {9}
}