Comparative genomics of the pennate diatom Phaeodactylum tricornutum.
Reads0
Chats0
TLDR
A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism.Abstract:
Diatoms are one of the most important constituents of phytoplankton communities in aquatic environments, but in spite of this, only recently have large-scale diatom-sequencing projects been undertaken. With the genome of the centric species Thalassiosira pseudonana available since mid-2004, accumulating sequence information for a pennate model species appears a natural subsequent aim. We have generated over 12,000 expressed sequence tags (ESTs) from the pennate diatom Phaeodactylum tricornutum, and upon assembly into a nonredundant set, 5,108 sequences were obtained. Significant similarity (E < 1E-04) to entries in the GenBank nonredundant protein database, the COG profile database, and the Pfam protein domains database were detected, respectively, in 45.0%, 21.5%, and 37.1% of the nonredundant collection of sequences. This information was employed to functionally annotate the P. tricornutum nonredundant set and to create an internet-accessible queryable diatom EST database. The nonredundant collection was then compared to the putative complete proteomes of the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the centric diatom T. pseudonana. A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism. Finally, codon usage and utilization of C and G relative to gene expression (as measured by EST redundance) were studied, and preferences for utilization of C and CpG doublets were noted among the P. tricornutum EST coding sequences.read more
Citations
More filters
Journal ArticleDOI
Carbon Concentrating Mechanisms in Eukaryotic Marine Phytoplankton
TL;DR: The energetic and nutrient costs of CCMs may modulate how variable CO2 affects primary production, element composition, and species composition of phytoplankton in the ocean.
Journal ArticleDOI
In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning
TL;DR: The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase, linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin.
Journal ArticleDOI
Diatoms—From Cell Wall Biogenesis to Nanotechnology
Nils Kröger,Nicole Poulsen +1 more
TL;DR: Analysis of the organic components associated with diatom silica, the development of techniques for molecular genetic manipulation of diatoms, and two diatom genome sequencing projects are providing insight into the composition and mechanism of the remarkable biosilica-forming machinery.
Journal ArticleDOI
Diatoms, Biomineralization Processes, and Genomics
TL;DR: Diatoms are eukaryotic unicellular microalgae with cell walls made of a composite of organic material, and silica which is often intricately and ornately shaped, which is indicative of the molecular control of intracellular processes by which organics facilitate mineral formation.
Journal ArticleDOI
Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum.
Magali Siaut,Marc Heijde,Manuela Mangogna,Anton Montsant,Sacha Coesel,Andrew E. Allen,Alessandro Manfredonia,Angela Falciatore,Chris Bowler,Chris Bowler +9 more
TL;DR: The identification of several reference genes that can be used as internal standards for gene expression studies by quantitative real-time PCR (qRT-PCR) in P. tricornutum cells grown over a diel cycle are reported.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Journal ArticleDOI
CAP3: A DNA Sequence Assembly Program
Xiaoqiu Huang,Anup Madan +1 more
TL;DR: The third generation of the CAP sequence assembly program is described, which has a capability to clip 5' and 3' low-quality regions of reads and uses forward-reverse constraints to correct assembly errors and link contigs.
Journal ArticleDOI
The COG database: a tool for genome-scale analysis of protein functions and evolution
TL;DR: The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes.
Related Papers (5)
The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism
E. Virginia Armbrust,John A. Berges,Chris Bowler,Beverley R. Green,Diego Martinez,Nicholas H. Putnam,Shiguo Zhou,Andrew E. Allen,Andrew E. Allen,Kirk E. Apt,Michael Bechner,Mark A. Brzezinski,Balbir K. Chaal,Anthony Chiovitti,Aubrey K. Davis,Mark S. Demarest,J. Chris Detter,Tijana Glavina,David Goodstein,Masood Z. Hadi,Uffe Hellsten,Mark Hildebrand,Bethany D. Jenkins,Jerzy Jurka,Vladimir V. Kapitonov,Nils Kröger,Winnie W. Y. Lau,Todd W. Lane,Frank W. Larimer,J. Casey Lippmeier,J. Casey Lippmeier,Susan Lucas,Mónica Medina,Anton Montsant,Miroslav Oborník,Miroslav Oborník,Micaela S. Parker,Brian Palenik,Gregory J. Pazour,Paul G. Richardson,Tatiana A. Rynearson,Mak A. Saito,David C. Schwartz,Kimberlee Thamatrakoln,Klaus Valentin,Assaf Vardi,Frances P. Wilkerson,Daniel S. Rokhsar +47 more
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
Chris Bowler,Andrew E. Allen,Andrew E. Allen,Jonathan H. Badger,Jane Grimwood,Kamel Jabbari,Alan Kuo,Uma Maheswari,Cindy Martens,Florian Maumus,Robert Otillar,Edda Rayko,Asaf Salamov,Klaas Vandepoele,Bank Beszteri,Ansgar Gruber,Marc Heijde,Michael Katinka,Thomas Mock,Klaus Valentin,Frédéric Verret,John A. Berges,Colin Brownlee,Jean-Paul Cadoret,Anthony Chiovitti,Chang Jae Choi,Sacha Coesel,Alessandra De Martino,J. Chris Detter,Colleen A. Durkin,Angela Falciatore,Jérome Fournet,Miyoshi Haruta,Marie J. J. Huysman,Bethany D. Jenkins,Katerina Jiroutova,Richard E. Jorgensen,Yolaine Joubert,Aaron Kaplan,Nils Kröger,Peter G. Kroth,Erica Lindquist,Markus Lommer,Véronique Martin-Jézéquel,Pascal J. Lopez,Susan Lucas,Manuela Mangogna,Karen M. McGinnis,Linda K. Medlin,Anton Montsant,Anton Montsant,Marie-Pierre Oudot-Le Secq,Carolyn A. Napoli,Miroslav Oborník,Micaela S. Parker,Jean-Louis Petit,Betina M. Porcel,Nicole Poulsen,Matthew Robison,Leszek Rychlewski,Tatiana A. Rynearson,Jeremy Schmutz,Jeremy Schmutz,Harris Shapiro,Magali Siaut,Michele S. Stanley,Michael R. Sussman,Alison Taylor,Assaf Vardi,Peter von Dassow,Wim Vyverman,Anusuya Willis,Lucyan S. Wyrwicz,Daniel S. Rokhsar,Jean Weissenbach,E. Virginia Armbrust,Beverley R. Green,Yves Van de Peer,Igor V. Grigoriev +78 more