Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.
Jonas Collén,Betina M. Porcel,Betina M. Porcel,Wilfrid Carré,Steven G. Ball,Cristian Chaparro,Thierry Tonon,Tristan Barbeyron,Gurvan Michel,Benjamin Noel,Klaus Valentin,Marek Eliáš,François Artiguenave,François Artiguenave,Alok Arun,Jean-Marc Aury,Jose Fernandes Barbosa-Neto,John H. F. Bothwell,François-Yves Bouget,François-Yves Bouget,Loraine Brillet,Francisco Cabello-Hurtado,Salvador Capella-Gutierrez,Bénédicte Charrier,Lionel Cladière,J. Mark Cock,Susana M. Coelho,Christophe Colleoni,Mirjam Czjzek,Corinne Da Silva,Ludovic Delage,Philippe Deschamps,Simon M. Dittami,Simon M. Dittami,Toni Gabaldón,Claire M. M. Gachon,Agnès Groisillier,Cécile Hervé,Kamel Jabbari,Kamel Jabbari,Michael Katinka,Michael Katinka,Bernard Kloareg,Nathalie Kowalczyk,Karine Labadie,Catherine Leblanc,Pascal J. Lopez,Deirdre H. McLachlan,Laurence Meslet-Cladiere,Ahmed A. Moustafa,Zofia Nehr,Pi Nyvall Collén,Olivier Panaud,Frédéric Partensky,Frédéric Partensky,Julie Poulain,Stefan A. Rensing,Sylvie Rousvoal,Gaelle Samson,Aikaterini Symeonidi,Aikaterini Symeonidi,Jean Weissenbach,Jean Weissenbach,Antonios Zambounis,Patrick Wincker,Patrick Wincker,Catherine Boyen +66 more
TLDR
An evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA is proposed; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.Abstract:
Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.read more
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Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation
Koichi Hori,Fumito Maruyama,Takatomo Fujisawa,Tomoaki Togashi,Nozomi Yamamoto,Mitsunori Seo,Syusei Sato,Takuji Yamada,Hiroshi Mori,Naoyuki Tajima,Takashi Moriyama,Masahiko Ikeuchi,Mai Watanabe,Hajime Wada,Koichi Kobayashi,Masakazu Saito,Tatsuru Masuda,Yuko Sasaki-Sekimoto,Kiyoshi Mashiguchi,Koichiro Awai,Mie Shimojima,Shinji Masuda,Masako Iwai,Takashi Nobusawa,Takafumi Narise,Satoshi Kondo,Hikaru Saito,Ryoichi Sato,Masato Murakawa,Yuta Ihara,Yui Oshima-Yamada,Kinuka Ohtaka,Masanori Satoh,Kohei Sonobe,Midori Ishii,Ryosuke Ohtani,Miyu Kanamori-Sato,Rina Honoki,Daichi Miyazaki,Hitoshi Mochizuki,Jumpei Umetsu,Kouichi Higashi,Daisuke Shibata,Yuji Kamiya,Naoki Sato,Yasukazu Nakamura,Satoshi Tabata,Shigeru Ida,Ken Kurokawa,Hiroyuki Ohta +49 more
TL;DR: The draft genome sequence of the filamentous terrestrial alga Klebsormidium flaccidum is reported to elucidate the early transition step from aquatic algae to land plants and suggests that, during evolution, this alga acquired the fundamental machinery required for adaptation to terrestrial environments.
Journal ArticleDOI
The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea
Jeanine L. Olsen,Pierre Rouzé,Bram Verhelst,Yao-Cheng Lin,Till Bayer,Jonas Collén,Emanuela Dattolo,Emanuele De Paoli,Simon M. Dittami,Florian Maumus,Gurvan Michel,Anna R. Kersting,Anna R. Kersting,Chiara Lauritano,Rolf Lohaus,Mats Töpel,Thierry Tonon,Kevin Vanneste,Mojgan Amirebrahimi,Janina Brakel,Christoffer Boström,Mansi Chovatia,Jane Grimwood,Jerry Jenkins,Alexander Jueterbock,Amy Mraz,Wytze T. Stam,Hope Tice,Erich Bornberg-Bauer,Pamela J. Green,Gareth A. Pearson,Gabriele Procaccini,Carlos M. Duarte,Jeremy Schmutz,Thorsten B. H. Reusch,Thorsten B. H. Reusch,Yves Van de Peer,Yves Van de Peer +37 more
TL;DR: The genome of Zostera marina, the first, to the authors' knowledge, marine angiosperm to be fully sequenced, reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle.
Journal ArticleDOI
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.
Jaime Huerta-Cepas,Salvador Capella-Gutierrez,Leszek P. Pryszcz,Marina Marcet-Houben,Toni Gabaldón +4 more
TL;DR: A benchmark of the orthology predictions provided by the database is discussed, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes are discussed.
Journal ArticleDOI
Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits
Dongmei Wang,Kang Ning,Jing Li,Jianqiang Hu,Danxiang Han,Hui Wang,Xiaowei Zeng,Xiaoyan Jing,Qian Zhou,Xiaoquan Su,Xingzhi Chang,A.M. Wang,Wei Wang,Jing Jia,Li Wei,Yi Xin,Yinghe Qiao,Ranran Huang,Jie Chen,Bo Han,Kangsup Yoon,Russell T. Hill,Yonathan Zohar,Feng Chen,Qiang Hu,Jian Xu +25 more
TL;DR: Multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis.
Journal ArticleDOI
Seaweed–microbial interactions: key functions of seaweed‐associated bacteria
TL;DR: The role of extracellular polymeric substances in growth and settlement of seaweeds spores is highlighted and the molecular mechanisms underlying reported ecological phenomena in seaweeds requires a combined ecological, microbiological and biochemical approach.
References
More filters
Journal ArticleDOI
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D
Motomichi Matsuzaki,Osami Misumi,Tadasu Shin-I,Shinichiro Maruyama,Manabu Takahara,Shin-ya Miyagishima,Toshiyuki Mori,Keiji Nishida,Fumi Yagisawa,Keishin Nishida,Yamato Yoshida,Yoshiki Nishimura,Shunsuke Nakao,Tamaki Kobayashi,Yu Momoyama,Tetsuya Higashiyama,Ayumi Minoda,Masako Sano,Hisayo Nomoto,Kazuko Oishi,Hiroko Hayashi,Fumiko Ohta,Satoko Nishizaka,Shinobu Haga,Sachiko Miura,Tomomi Morishita,Yukihiro Kabeya,Kimihiro Terasawa,Yutaka Suzuki,Yasuyaki Ishii,Shuichi Asakawa,Hiroyoshi Takano,Niji Ohta,Haruko Kuroiwa,Kan Tanaka,Nobuyoshi Shimizu,Sumio Sugano,Naoki Sato,Hisayoshi Nozaki,Naotake Ogasawara,Yuji Kohara,Tsuneyoshi Kuroiwa +41 more
TL;DR: The results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.
Journal ArticleDOI
A molecular timeline for the origin of photosynthetic eukaryotes
TL;DR: An ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae from the opisthokonts sometime before 1,558 MYA is supported.
Journal ArticleDOI
The Ectocarpus genome and the independent evolution of multicellularity in brown algae
J. Mark Cock,Lieven Sterck,Pierre Rouzé,Delphine Scornet,Andrew E. Allen,Grigoris D. Amoutzias,Véronique Anthouard,François Artiguenave,Jean-Marc Aury,Jonathan H. Badger,Bank Beszteri,Kenny Billiau,Eric Bonnet,John H. F. Bothwell,Chris Bowler,Catherine Boyen,Colin Brownlee,Carl J. Carrano,Bénédicte Charrier,Ga Youn Cho,Susana M. Coelho,Jonas Collén,Erwan Corre,Corinne Da Silva,Ludovic Delage,Nicolas Delaroque,Simon M. Dittami,Sylvie Doulbeau,Marek Eliáš,Garry Farnham,Claire M. M. Gachon,Bernhard Gschloessl,Svenja Heesch,Kamel Jabbari,Claire Jubin,Hiroshi Kawai,Kei Kimura,Bernard Kloareg,Frithjof C. Küpper,Daniel Lang,Aude Le Bail,Catherine Leblanc,Patrice Lerouge,Martin Lohr,Pascal J. Lopez,Cindy Martens,Florian Maumus,Gurvan Michel,Diego Miranda-Saavedra,Julia Morales,Hervé Moreau,Taizo Motomura,Chikako Nagasato,Carolyn A. Napoli,David R. Nelson,Pi Nyvall-Collén,Akira F. Peters,Cyril Pommier,Philippe Potin,Julie Poulain,Hadi Quesneville,Betsy Read,Stefan A. Rensing,Andrés Ritter,Sylvie Rousvoal,Manoj P. Samanta,Gaelle Samson,Declan C. Schroeder,Béatrice Segurens,Martina Strittmatter,Thierry Tonon,James W. Tregear,Klaus Valentin,Peter von Dassow,Takahiro Yamagishi,Yves Van de Peer,Patrick Wincker +76 more
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A three-dimensional view of the molecular machinery of RNA interference
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TL;DR: A new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads, which has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links, and detection of repeat contigs by forward- reverse link inconsistency.
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