Browsing by Author "Van de Peer, Yves"
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- Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plantsPublication . Xue, Jia-Yu; Dong, Shan-Shan; Wang, Ming-Qiang; Song, Tian-Qiang; Zhou, Guang-Can; Li, Zhen; Van de Peer, Yves; Shao, Zhu-Qing; Wang, Wei; Chen, Min; Zhang, Yan-Mei; Sun, Xiao-Qin; Chen, Hong-Feng; Zhang, Yong-Xia; Zhang, Shou-Zhou; Chen, Fei; Zhang, Liang-Sheng; Cox, Cymon; Liu, Yang; Wang, Qiang; Hang, Yue-YuThe early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon-sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon-usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony-informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.
- The genome of the seagrass Zostera marina reveals angiosperm adaptation to the seaPublication . Olsen, Jeanine L.; Rouze, Pierre; Verhelst, Brain; Lin, Yao-Cheng; Bayer, Till; Collen, Jonas; Dattolo, Emanuela; De Paoli, Emanuele; Dittami, Simon; Maumus, Florian; Michel, Gurvan; Kersting, Anna; Lauritano, Chiara; Lohaus, Rolf; Topel, Mats; Tonon, Thierry; Vanneste, Kevin; Amirebrahimi, Mojgan; Brakel, Janina; Bostrom, Christoffer; Chovatia, Mansi; Grimwood, Jane; Jenkins, Jerry W.; Jueterbock, Alexander; Mraz, Amy; Stam, Wytze T.; Tice, Hope; Bornberg-Bauer, Erich; Green, Pamela J.; Pearson, Gareth; Procaccini, Gabriele; Duarte, Carlos M.; Schmutz, Jeremy; Reusch, Thorsten B. H.; Van de Peer, YvesSeagrasses colonized the sea(1) on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet(2). Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes(3), genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae(4) and that is important for ion homoeostasis, nutrient uptake and O-2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming(5,6), to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants(7).