Draft Genome Sequences of Stenotrophomonas maltophilia Strains Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, Isolated from Different Manures in France: TABLE 1

International audienceStenotrophomonas maltophilia is a major opportunistic human pathogen responsible for nosocomial infections. Here, we report the draft genome sequences of Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, isolated from different manures in France, which provide insights into the genetic determinism of intrinsic or acquired antibiotic resistance in this species. Citation Bodilis J, Youenou B, Briolay J, Brothier E, Favre-Bonté S, Nazaret S. 2016. Draft genome sequences of Stenotrophomonas maltophilia strains Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, isolated from different manures in France

Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia

International audienceWe report the complete genome sequence of Bradyrhizobium sp. strain BDV5040, representative of Bradyrhizobium genospecies B, which symbiotically associates with legume hosts belonging to all three Fabaceae subfamilies across the Australian continent. The complete genome sequence provides a genetic reference for this Australian genospecies.Bradyrhizobium sp. strain BDV5040 was isolated in 1995 from a root nodule of Bossiaea ensata (Fabaceae, Faboideae, Bossiaeeae) collected in Ben Boyd National Park, New South Wales, Australia (37°12′S, 149°57′E; altitude, 140 m), in the course of a survey of rhizobia associated with native shrubby legumes in southeastern Australia (1). It is a representative of Bradyrhizobium genospecies B, which occurs under different climatic and edaphic conditions across the whole Australian continent and exhibits a broad host range encompassing all three Fabaceae subfamilies (1–4).Strain BDV5040 was grown from a lyophilized stock in 30 ml of yeast extract mannitol broth (5) at 25°C and 200 rpm for 5 days. Genomic DNA was prepared by successive phenol-chloroform extractions as described (6). DNA quantification and quality control were performed using a NanoDrop spectrophotometer, a Qubit 4 fluorometer, and agarose gel electrophoresis. The same DNA was used for Nanopore and Illumina sequencing. Illumina libraries were obtained using the Nextera XT kit following the manufacturer’s instructions, starting with 1 ng of genomic DNA, and were analyzed by paired-end 2 × 300-bp sequencing on a MiSeq instrument. Poor-quality regions (Q 1,500 bp) and quality (score of >8) using Nanofilt v2.5.0 (11), and adapters were removed using Porechop v0.2.4 (12). Long reads were further reduced to 800 Mbp as a target quantity using Filtlong v0.2.0 (13) (parameters: --min_length 2000 --keep_percent 90 --target_bases 800000000). Illumina and Nanopore reads were coassembled using Unicycler v0.4.8 (14) with default parameters, resulting in a single component with eight segments and incomplete status (length, 7,622,333 bp; N50, 7,339,313 bp). Completion was obtained by exporting the sequence path from Bandage v0.8.1 (15) and filling a last gap using Pilon v1.23 (16) and by manually comparing the sequence with Unicycler 003_long_read_assembly.fasta. The assembly and complete chromosome sequence were carefully inspected by visualizing the alignment of long and short reads using minimap2 v2.17 (17) and IGV v2.7.2 (18). Finally, the chromosome was rotated to start at dnaA.The circular chromosome is 7,622,528 bp long, with an average G+C content of 63.92%. The sequence was automatically annotated by the NCBI Prokaryote Genome Annotation Pipeline (PGAP) v4.13 (19). The genome consists of 7,092 protein-coding genes, 48 tRNAs, 1 copy each of the 5S, 16S, and 23S rRNA genes, and 88 pseudogenes.Data availability.The genome sequence of Bradyrhizobium genospecies B strain BDV5040 is available in NCBI GenBank under accession number CP061379. The raw sequence reads are available under SRA accession numbers SRX9514896 and SRX9514898 under BioProject number PRJNA662585 and BioSample number SAMN16089659

Complete genome of Bradyrhizobium sp. strain BDV5419, representative of Australian genospecies L

International audienceWe report the complete genome sequence of Bradyrhizobium sp. strain BDV5419, representative of Bradyrhizobium genospecies L, which symbiotically associates with the Australian native legume Hardenbergia violaceae and is expected to represent a novel Bradyrhizobium species. The complete genome sequence provides a genetic reference for this Australian genospecies

Lipid modulation of skeletal muscle mass and function

Loss of skeletal muscle mass is a characteristic feature of various pathologies including cancer, diabetes, and obesity, as well as being a general feature of ageing. However, the processes underlying its pathogenesis are not fully understood and may involve multiple factors. Importantly, there is growing evidence which supports a role for fatty acids and their derived lipid intermediates in the regulation of skeletal muscle mass and function. In this review, we discuss evidence pertaining to those pathways which are involved in the reduction, increase and/or preservation of skeletal muscle mass by such lipids under various pathological conditions, and highlight studies investigating how these processes may be influenced by dietary supplementation as well as genetic and/or pharmacological intervention

Reconciling the biogeography of an invader through recent and historic genetic patterns: the case of topmouth gudgeon Pseudorasbora parva

© 2018 The Author(s) The genetic variability and population structure of introduced species in their native range are potentially important determinants of their invasion success, yet data on native populations are often poorly represented in relevant studies. Consequently, to determine the contribution of genetic structuring in the native range of topmouth gudgeon Pseudorasbora parva to their high invasion success in Europe, we used a dataset comprising of 19 native and 11 non-native populations. A total of 666 samples were analysed at 9 polymorphic microsatellite loci and sequenced for 597 bp of mitochondrial DNA. The analysis revealed three distinct lineages in the native range, of which two haplogroups were prevalent in China (100%), with a general split around the Qinling Mountains. Dating of both haplogroups closely matched past geological events. More recently, its distribution has been influenced by fish movements in aquaculture, resulting in gene flow between previously separated populations in Northern and Southern China. Their phylogeography in Europe indicate as few as two introductions events and two dispersal routes. Microsatellite data revealed native populations had higher genetic diversity than those in the invasive range, a contrast to previous studies on P. parva. This study confirms the importance of extensive sampling in both the native and non-native range of invasive species in evaluating the influence of genetic variability on invasion success

Historical biogeography of european leuciscins (Cyprinidae): Evaluating the Lago Mare dispersal hypothesis

ABSTRACT Aim To test the importance of the Lago Mare stage of the Messinian Salinity Crisis for the dispersal and diversification of European leuciscins (Cyprinidae: Leuciscinae). Location Europe. Methods Cytochrome b sequences of European leuciscins were employed to investigate phylogenetic relationships among species, using Bayesian inference, and to estimate times of diversification, using a relaxed molecular clock. The distributions of 190 European leuciscins were compiled, and regional species compositions were compared using a taxonomic similarity index and an area cladogram. Results Leuciscins restricted to the Iberian and Italian peninsulas and the West and South Balkan regions are phylogenetically more closely related to northern European species than to species from another southern European area. Application of a relaxed molecular clock to a Bayesian phylogeny indicates that most southern clades originated and diversified prior to the Messinian. Southern European regions are taxonomically distinct from one another, and from a more taxonomically homogeneous group of areas that includes Anatolia, East Balkans, Middle East, North Europe and West Russia. Main conclusions The scenario of a Messinian period of dispersal of Paratethyan fauna into Mediterranean regions, via the Lago Mare, predicts a rapid period of diversification and a pattern of close association among southern European faunas. Phylogenetic relationships among leuciscins, the timing of cladogenic events, and the taxonomic similarity among geographical regions do not conform to this expectation. The depth of clades endemic to southern Europe, together with the high levels of endemism in these regions, suggests that the faunas in these regions diverged prior to the Messinian and have evolved largely in isolation from one another. Our results support a model of gradual colonization of Mediterranean regions since the Oligocene. Subsequent connections between adjacent areas may have occurred in the Messinian or Pleistocene