10 documents found, page 1 of 1
First release of the European marine omics biodiversity observation network (EM...
Pavloudi, Christina; Santi, Ioulia; Azua, Iñigo; Baña, Zuriñe; Bastianini, Mauro; Belser, Caroline; Bilbao, Jone; Bitz-Thorsen, Julie; Broudin, CarolineThe European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (A...
Batch studies on the biodegradation of paracetamol and 1,4-hydroquinone by nove...
Lara-Moreno, Alba; Fatma El-Sayed; Cox, Cymon; Costa, Maria Clara; Carlier, JorgeThe emerging pollutant paracetamol (APAP) is one of the most prescribed drugs worldwide. In addition, APAP and its main metabolites, namely, 4-aminophenol (4-AP), hydroquinone (H2Q), benzoquinone (BQ), and 2,5-dihydroxy-1,4-benzoquinone (2,5-OH-BQ), among others, are frequently detected in wastewater treatment plants (WWTPs) influents, effluents, and the environment. Thus, continuous release into the environmen...
A low‐latitude species pump: Peripheral isolation, parapatric speciation and ma...
Almeida, Susana C.; Neiva, João; Sousa, Filipe; Martins, Neusa; Cox, Cymon; Melo‐Ferreira, José; Guiry, Michael D.; Serrao, Ester; Pearson, GarethGeologically recent radiations can shed light on speciation processes, but incomplete lineage sorting and introgressive gene flow render accurate evolutionary reconstruction and interpretation challenging. Independently evolving metapopulations of low dispersal taxa may provide an additional level of phylogeographic information, given sufficiently broad sampling and genome-wide sequencing. Evolution in the mari...
Recoding amino acids to a reduced alphabet may increase or decrease phylogeneti...
Foster, Peter G; Schrempf, Dominik; Szöllősi, Gergely J; Williams, Tom A; Cox, Cymon; Embley, T MartinCommon molecular phylogenetic characteristics such as long branches and compositional heterogeneity can be problematic for phylogenetic reconstruction when using amino acid data. Recoding alignments to reduced alphabets before phylogenetic analysis has often been used both to explore and potentially decrease the effect of such problems. We tested the effectiveness of this strategy on topological accuracy using ...
Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inf...
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, MinThe 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 f...
A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)
Louro, Bruno; De Moro, Gianluca; Garcia, Carlos; Cox, Cymon; Veríssimo, Ana; Sabatino, Stephen J.; Santos, António M.; Canario, A.V.M.The European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, struct...
Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant an...
Karimi, Elham; Keller-Costa, Tina; Slaby, Beate M; Cox, Cymon; da Rocha, Ulisses N; Hentschel, Ute; da Silva Costa, RodrigoMarine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sph...
Resolution of the ordinal phylogeny of mosses using targeted exons from organel...
Liu, Yang; Johnson, Matthew G.; Cox, Cymon; Medina, Rafael; Devos, Nicolas; Vanderpoorten, Alain; Hedenäs, Lars; Bell, Neil E.; Shevock, James R.Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nu...
Improved phylogeny of brown algae Cystoseira (Fucales) from the Atlantic-Medite...
Bruno De Sousa, Carolina; Cox, Cymon; Brito, Luís; Pavão, Maria Madalena; Pereira, Hugo; Ferreira, Ana; Ginja, Catarina; Campino, LeneaCystoseira is a common brown algal genus widely distributed throughout the Atlantic and Mediterranean regions whose taxonomical assignment of specimens is often hampered by intra- and interspecific morphological variability. In this study, three mitochondrial regions, namely cytochrome oxidase subunit 1 (COI), 23S rDNA (23S), and 23S-tRNAVal intergenic spacer (mt-spacer) were used to analyse the phylogenetic re...
A 20-state empirical amino-acid substitution model for green plant chloroplasts
Cox, Cymon; Foster, P. G.We introduce a new empirical amino-acid substitution model intended for use with for green plant (Viridiplantae) chloroplast protein data, which we call gcpREV (green chloroplast reversible model). Relative exchange rates and base composition frequencies among amino-acids were calculated using a Markov-chain Monte Carlo analysis on a combined data set of 34 proteins sampled among 27 taxa of green plants. The gc...