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Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii ArchiMer
Marcelino, Vanessa R.; Cremen, Ma Chiela M.; Jackson, Chistopher J.; Larkum, Anthony A. W.; Verbruggen, Heroen.
Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species' genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation...
Tipo: Text Palavras-chave: Genome streamlining; Photosynthesis; Rates of evolution; Boring algae; Stoichiogenomics.
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00659/77094/78418.pdf
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Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae ArchiMer
Marcelino, Vanessa Rossetto; Verbruggen, Heroen.
Bacteria, fungi and green algae are common inhabitants of coral skeletons. Their diversity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the biodiversity. We used a cost-effective protocol and a combination of markers (tufA, 16S rDNA, 18S rDNA and 23S rDNA) to characterize the microbiome of 132 coral skeleton samples. We identified a wide range of prokaryotic and eukaryotic organisms, many never reported in corals before. We additionally investigated the phylogenetic diversity of the green algae-the most abundant eukaryotic member of this community, for which previous literature recognizes only a handful...
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Ano: 2016 URL: https://archimer.ifremer.fr/doc/00659/77095/78416.pdf
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Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data ArchiMer
Verbruggen, Heroen; Marcelino, Vanessa R.; Guiry, Michael D.; Cremen, Ma. Chiela M.; Jackson, Christopher J..
The green algal genus Ostreobium is an important symbiont of corals, playing roles in reef decalcification and providing photosynthates to the coral during bleaching events. A chloroplast genome of a cultured strain of Ostreobium was available, but low taxon sampling and Ostreobium's early-branching nature left doubt about its phylogenetic position. Here, we generate and describe chloroplast genomes from four Ostreobium strains as well as Avrainvillea mazei and Neomeris sp., strategically sampled earlybranching lineages in the Bryopsidales and Dasycladales respectively. At 80,584 bp, the chloroplast genome of Ostreobium sp. HV05042 is the most compact yet found in the Ulvophyceae. The Avrainvillea chloroplast genome is similar to 94 kbp and contains...
Tipo: Text Palavras-chave: Bryopsidales; Chloroplast genome; Coral symbiosis; Dasycladales; Molecular phylogenetics; Ostreobium; Phylogenomics.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00659/77091/78412.pdf
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Outstanding Challenges in the Transferability of Ecological Models ArchiMer
Yates, Katherine L.; Bouchet, Phil J.; Caley, M. Julian; Mengersen, Kerrie; Randin, Christophe F.; Parnell, Stephen; Fielding, Alan H.; Bamford, Andrew J.; Ban, Stephen; Marcia Barbosa, A.; Dormann, Carsten F.; Elith, Jane; Embling, Clare B.; Ervin, Gary N.; Fisher, Rebecca; Gould, Susan; Graf, Roland F.; Gregr, Edward J.; Halpin, Patrick N.; Heikkinen, Risto K.; Heinanen, Stefan; Jones, Alice R; Krishnakumar, Periyadan K.; Lauria, Valentina; Lozano-montes, Hector; Mannocci, Laura; Mellin, Camille; Mesgaran, Mohsen B.; Moreno-amat, Elena; Mormede, Sophie; Novaczek, Emilie; Oppel, Steffen; Crespo, Guillermo Ortuno; Peterson, A. Townsend; Rapacciuolo, Giovanni; Roberts, Jason J.; Ross, Rebecca E.; Scales, Kylie L.; Schoeman, David; Snelgrove, Paul; Sundblad, Goran; Thuiller, Wilfried; Torres, Leigh G.; Verbruggen, Heroen; Wang, Lifei; Wenger, Seth; Whittingham, Mark J.; Zharikov, Yuri; Zurell, Damaris; Sequeira, Ana M. M..
Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their 'transferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability...
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Ano: 2018 URL: https://archimer.ifremer.fr/doc/00466/57728/59909.pdf
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