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Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across different genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 different species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable differences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational efficiency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon in this large, commercially and environmentally important, class of marine invertebrates. Fields et al., 2014). Details about the data used for the different species are provided in Table S1 . Sequence data were processed as follows: predicted CDS from the fully sequenced genomes of C. gigas (release 9) and P. fucata were retrieved from http://oysterdb.cn and http://marinegenomics.oist.jp/pinctada fucata, respectively. De novo transcriptome assemblies were performed for all the other 62 bivalve species with the CLC Genomics Workbench (v.7.5, CLC Bio, Aarhus, Denmark) using the de novo assembly tool with "automatic word size" and "automatic bubble size" parameters selected, and setting the minimum allowed contig length to 300 bp. In all transcriptomes, ORFs (Open Reading Frames) longer than 100 codons were predicted with TransDecoder (http://transdecoder.sourceforge.net). We selected the predicted CDS of C. gigas, and of one representative species for the Imparidentia (R. decussatus), Protobranchia (S. velum) and Palaeoheterodonta (P. grandis) lineages to identify a subset of evolutionarily conserved protein-coding genes with a 1:1 orthology ratio across Bivalvia. This was achieved by performing reciprocal tBLASTx searches (the e-value threshold was set a 1 × 10 −10 and only hits displaying sequence identity >50% were considered). This procedure resulted in a selection of 2,846 conserved protein-coding genes, whose orthologous sequences were retrieved in the remaining 60 species. Due to the heterogeneous tissue and developmental stage origin, the different sequencing platforms and depth applied, several of these evolutionarily conserved sequences could not be identified or were fragmented in some transcriptomes. In order to ensure a minimum quality criteria, all the selected species had to display at least 25% of the sequences included in the dataset of evolutionarily conserved genes, with an average length >500 nucleotides.
Distributed under Creative Commons CC-BY 4.0 Analysis of synonymous codon usage patterns in sixty-four different bivalve species

Background: SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had experienced adaptive evolution, but whether other functional proteins of SARS have undergone adaptive evolution is not known. We employed several methods to investigate selective pressure among different SARS-CoV groups representing different epidemic periods and hosts. Our results suggest that most functional proteins of SARS-CoV have experienced a stepwise adaptive evolutionary pathway. Similar to previous studies, the spike protein underwent strong positive selection in the early and middle phases, and became stabilized in the late phase. In addition, the replicase experienced positive selection only in human patients, whereas assembly proteins experienced positive selection mainly in the middle and late phases. No positive selection was found in any proteins of bat SARS-like-CoV. Furthermore, specific amino acid sites that may be the targets of positive selection in each group are identified. This extensive evolutionary analysis revealed the stepwise evolution of different functional proteins of SARS-CoVs at different epidemic stages and different hosts. These results support the hypothesis that SARS-CoV originated from bats and that the spill over into civets and humans were more recent events.
Differential stepwise evolution of SARS coronavirus functional proteins in different host species

first two authors contribute equally. Zika virus can be passed from a pregnant woman to her fetus, thus leading to birth defects including more than microcephaly. It has been recently estimated that one-third of the world population will be infected by Zika, but unfortunately no vaccine or medicine is available so far. Zika NS2B-NS3pro is essential for its replication and thus represents an attractive target for drug discovery/design. Here we characterized conformation, Zika NS2B-NS3pro complexes by both experiments and MD simulations. The results unveil the unique properties of Zika NS2B-NS3pro which are very different from Dengue one. Particularly, CD and NMR studies indicate that unlike Dengue, the C-terminal region of Zika NS2B with a significant sequence variation is highly disordered in the open conformation. Indeed, MD simulations reveal that up to 100 ns, the Dengue NS2B C-terminus constantly has close contacts with its NS3pro domain. By a sharp contrast, the Zika NS2B C-terminus loses the contacts with its NS3pro domain after 10 ns, further forming a short β-sheet characteristic of the closed conformation at 30 ns. Furthermore, we found that a small molecule, previously identified as an active site inhibitor for other flaviviral NS2B-NS3pro, inhibited Zika NS2B-NS3pro potently in an allosteric manner. Our study provides the first insight into the dynamics of Zika NS2B-NS3pro and further deciphers that it is susceptible to allosteric inhibition, which thus bears critical implications for the future development of therapeutic allosteric inhibitors. author/funder. All rights reserved. No reuse allowed without permission.

Catalysis, inhibition and dynamics of Zika NS2B-NS3pro Unique properties of Zika NS2B-NS3pro complexes as decoded by experiments and MD simulations Catalysis, inhibition and dynamics of Zika NS2B-NS3pro