The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Bowler, Chris; Allen, Andrew E.; Badger, Jonathan H.; Grimwood, Jane; Jabbari, Kamel; Kuo, Alan; Maheswari, Uma; Martens, Cindy; Maumus, Florian; Otillar, Robert; Rayko, Edda; Salamov, Asaf; Vandepoele, Klaas; Beszteri, Bánk; Gruber, Ansgar; Heijde, Marc; Katinka, Michaël; Möck, Thomas; Valentin, Klaus; Verret, Frédéric; Berges, John A.; Brownlee, Colin; Cadoret, Jean‐Paul; Chiovitti, Anthony; Choi, Chang Jae; Coesel, Sacha; Martino, Alessandra De; Detter, John C.; Durkin, Colleen A.; Falciatore, Angela; Fournet, Jérôme; Haruta, Miyoshi; Huysman, Marie J. J.; Jenkins, Bethany D.; Jiroutová, Kateřina; Jorgensen, Richard E.; Joubert, Yolaine; Kaplan, Aaron; Kröger, Nils; Kroth, Peter G.; Lindquist, Erica; Lommer, Markus; Martin‐Jézéquel, Véronique; Lopez, Pascal J.; Lucas, Susan; Mangogna, Manuela; McGinnis, Karen M.; Medlin, Linda K.; Montsant, Anton; Secq, Marie-Pierre Oudot–Le; Napoli, Carolyn A.; Oborník, Miroslav; Parker, Micaela S.; Petit, Jean-Louis; Porcel, Betina M.; Poulsen, Nicole; Robison, Matthew; Rychlewski, Leszek; Rynearson, Tatiana A.; Schmutz, Jeremy; Shapiro, Harris; Siaut, Magali; Stanley, Michele S.; Sussman, Michael R.; Taylor, Alison R.; Vardi, Assaf; Dassow, Peter von; Vyverman, Wim; Willis, Anusuya; Wyrwicz, Lucjan; Rokhsar, Daniel S.; Weissenbach, Jean; Armbrust, E. Virginia; Green, Beverley R.; Peer, Yves Van de; Grigoriev, Igor V.

doi:10.1038/nature07410

Cited by 1,439 publications

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“…To refine these results, we developed a stringent classification method which, starting from the clusters of orthologous proteins, generated > 9000 phylogenetic trees containing at least one P. multistriata protein and, based on the topology of each tree, predicted 252 genes of bacterial origin specifically within diatoms. This is < 50% of the number of genes reported to be of bacterial origin in P. tricornutum (587 genes) (Bowler et al ., 2008) and more than a previous estimate at lower resolution (Lommer et al ., 2012). Repeating the analysis considering HGT events within Stramenopiles and the SAR supergroup (Stramenopiles, Alveolates and Rhizaria), we predicted 353 and 438 P. multistriata genes of potential bacterial origin, respectively.…”

Section: Resultsmentioning

confidence: 63%

“…We confirmed an expansion of a gene family ( pseudouridine synthase ) (Fig. 3a) reported to be expanded in the P. tricornutum genome (Bowler et al ., 2008) and found specific expansion events within the order Bacillariales (Fig. 3a).…”

Section: Resultsmentioning

confidence: 91%

“…90–100 Ma (Perkins & Schall, 2002); Arabidopsis thaliana and Physcomitrella patens , with flowering plants reported to have diverged from the bryopsids c . 400–450 Ma (Rensing et al ., 2008)), confirming the rapid evolutionary rates in diatoms (Bowler et al ., 2008). …”

Section: Resultsmentioning

confidence: 99%

“…Approximately 26% (2886 singlets + 241 genes in 109 clusters) of the P. multistriata proteome was predicted to be orphan ( P. multistriata ‐specific) (Fig. S4), which is slightly less than that reported for other diatoms ( P. tricornutum , 35%, Bowler et al ., 2008; T. pseudonana , 29%, Armbrust et al ., 2004) and similar to estimates deriving from transcriptomic data (Di Dato et al ., 2015). Based on these data, we built a comprehensive species tree for 13 Stramenopiles by concatenating the alignments of 85 clusters of one‐to‐one orthologues conserved across the 13 species.…”

Section: Resultsmentioning

confidence: 99%

“…The genome size, N50 value and GC content were taken from the respective publications (Armbrust et al ., 2004; Bowler et al ., 2008; Cock et al ., 2010; Lévesque et al ., 2010; Lommer et al ., 2012; Tanaka et al ., 2015; Mock et al ., 2017). …”

Section: Methodsmentioning

confidence: 99%

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Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

et al. 2017

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Summary Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo‐nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics.We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex‐related genes. We also identified a small number of conserved noncoding elements.Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein‐coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis‐related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient‐replete conditions.The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.

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Section: Resultsmentioning

confidence: 63%

Section: Resultsmentioning

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

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Diatoms

Theriot¹

2012

Encyclopedia of Life Sciences

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Diatoms are single‐celled autotrophic organisms with highly ornate siliceous walls. They account for more than 20% of the world's primary production, are responsible for much of the petroleum humans use, and deposits of their shells are mined for numerous uses. The most taxonomically diverse groups of photosynthetic protists, diatoms are of ecological importance in nearly every freshwater and marine habitat. Their closest relatives are a poorly known group of microflagellates, some silicified and some not. Efforts to reconstruct diatom phylogeny are hampered by the fact that their true diversity and that of their closest relatives remains unknown. Genomic studies are creating tremendous new opportunities for study of this important group. Perhaps as much as a third of the diatom nuclear genome is now thought to be recently laterally transferred from bacteria. Diatom adaptation to such a wide range of environments may be a result of the resulting novel gene combinations. Key Concepts: Diatoms are a highly diverse group of protists, with perhaps more than 200 000 species, most of which remain undescribed. There are four major structural groups, radial centrics, polar centrics, araphid pennates and raphid pennates. Among the four major structural groups of diatoms, only the raphid pennates are robustly supported as monophyletic. Diatoms dominate the world's oceans, lakes and streams, conducting more than 20% of the world's photosynthesis. Diatoms are critical indicators of aquatic ecosystem conditions, past and present. Fossil diatoms have significant economic importance as stratigraphic indicators for mineral exploration, particularly petroleum and as a source of diatomite, which is used in numerous industrial applications. Diatoms make a diverse number of nanoscale siliceous structures, an order of magnitude smaller than that presently attainable by human technology. Understanding how diatoms make their shells may lead to breakthroughs in nanotechnology. Nearly a third of the diatom nuclear genome appears to be the result of relatively recent horizontal gene transfer from bacteria. Horizontal gene transfer may play a role in the apparent rapid adaptation and diversification of diatoms.

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Silica

Perry¹

2010

Encyclopedia of Life Sciences

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The element silicon (Si) is used by all living organisms either in molecular processes or in the formation of the mineral silica. The mineral is found in single cell organisms (e.g. radiolarian, diatoms, dinoflagellates and algae) through molluscs (e.g. limpets) to higher plants and primitive animals such as sponges. It is formed from an environment that is undersaturated with respect to Si and under conditions of around neutral pH and low temperature, c . 4–40°C. The mineral can be formed both intra‐ or extracellularly and specific biochemicals involved with mineral deposition include lipids, proteins (including heavily posttranslationally modified proteins), long‐change polyamines and carbohydrates. Knowledge of the complete genome for some species is providing opportunities to uncover the precise mechanisms of element uptake, transport and deposition although much still remains to be understood. Key Concepts: Silicon is an essential element for many if not all organisms. A range of biomolecules/biopolymers are used to control and regulate silica precipitation in the natural environment. The presence of biogenic silica in an organism confers functional properties on that organism which may include structural/mechanical support and/or defence against biotic or abiotic environmental stresses. Much remains to be understood in respect of how the element is transported, concentrated and spatially organised within organisms as well as the effect the presence of the element/mineral has on other cellular functions.

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The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Cited by 1,439 publications

References 31 publications

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

Diatoms

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