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Despite the considerable efforts to reconstruct the phylogeny of grasses, the relationships among the subfamilies Bambusoideae, Pooideae and Ehrhartoideae in the BEP clade remain unresolved. Here we completely sequenced three chloroplast genomes of representative species from Bambusoideae and Ehrhartoideae and obtained 19 additional chloroplast genome sequences of other grasses from GenBank. Using sequences of 76 chloroplast protein-coding genes from the 22 grass species, we fully resolved the phylogeny of the BEP clade. Our results strongly supported the (B,P)E hypothesis, i.e., Bambusoideae and Pooideae are more closely related than Ehrhartoideae. This result was not biased by systematic or sampling errors and was impervious to phylogenetic methods or model specification. The divergence time estimate suggests that the initial diversification of the BEP clade into three subfamilies happened within a short time period (≈ 4 MY). The presence of these short internal branches may explain the inability of previous studies to achieve a confident resolution of the BEP clade. The combination of the sequences of the entire chloroplast genomes provided sufficient phylogenetic information to resolve the BEP phylogeny fully. These results provide a valuable evolutionary framework for comparative and functional genomic studies using the grass family as a model system., (Copyright © 2011 Elsevier Inc. All rights reserved.)

An outbreak of hand foot and mouth disease occurred in Shang dong, China in 2009. Almost 20% of patient's swabs was positive for Coxsackie virus B5 (CVB5) identified by RT-PCR and sequencing. It was suggested that CVB5 may be another important pathogen for HFMD. Fifteen pairs of overlapping primers were designed and the genome sequence was sequenced. The genome of CVB5 was 7 399 nt in length, coding for 2 185aa. The genome displayed 80.6%-85.3% nucleotide sequence identity and 96.1%-96.9% amino acid sequence identity with another three CVB5 respectively. Phylogenetic analysis showed that different segment of genome underwent a distinct evolutionary and selective pressure. Simplot analysis displayed no evident recombination between genome of CVB5 and other HEV B viruses. The complete and characterized genome of CVB5/09 provides further insight into the genetics of CVB5 and other HEV B viruses, aiding in the surveillance and control of HFMD.

Thalictrum is a phylogenetically and economically important genus in the family Ranunculaceae, but is also regarded as one of the most challengingly difficult in plants for resolving the taxonomical and phylogenetical relationships of constituent taxa within this genus. Here, we sequenced the complete plastid genomes of two Thalictrum species using Illumina sequencing technology via de novo assembly. The two Thalictrum plastomes exhibited circular and typical quadripartite structure that was rather conserved in overall structure and the synteny of gene order. By updating the previously reported plastome annotation of other nine Thalictrum species, we found that the expansion or contraction of the inverted repeat region affect the boundary of the single-copy regions in Thalictrum plastome. We identified eight highly variable noncoding regions— infA-rps8 , ccsA-ndhD , trnSUGA-psbZ , trnHGUG-psbA , rpl16-rps3 , ndhG-ndhI , ndhD-psaC , and ndhJ-ndhK —that can be further used for molecular identification, phylogenetic, and phylogeographic in different species. Selective pressure and codon usage bias of all the plastid coding genes were also analyzed for the 11 species. Phylogenetic relationships showed Thalictrum is monophyly and divided into two major clades based on 11 Thalictrum plastomes. The availability of these plastomes offers valuable genetic information for accurate identification of species and taxonomy, phylogenetic resolution, and evolutionary studies of Thalictrum , and should assist with exploration and utilization of Thalictrum plants. [ABSTRACT FROM AUTHOR]

A new loach Oreonectes guilinensis sp. nov. is described from Guangxi Zhuang Autonomous Region, China. It is the second surface‐dwelling fish identified in the genus Oreonectes after the type species Oreonectes platycephalus. This new species can be distinguished from other species within the genus by the combination of the following features: a round caudal fin, 13–14 branched rays, an incomplete lateral line with 4–6 pores, a short pelvic fin located some distance from the anus, a scale‐covered body, a stout build (body width 14.0%–16.7% of standard length), a posterior chamber of well‐developed airbladder and a yellowish‐brown body with a lateral dark brown strip. The maximum likelihood phylogenetic analysis based on cytb gene recovered this new species in a well‐supported clade with the type species O. platycephalus, sister to the Lefua clade. Morphological comparisons as well as our phylogenetic tree support Oreonectes shuilongensis, Oreonectes daqikongensis, Oreonectes jiarongensis as species of Troglonectes. Based on our results there are 6 valid species in the genus Oreonectes. [ABSTRACT FROM AUTHOR]

Cuphea hyssopifolia is a small evergreen shrub of great economic and medicinal values. However, there are few studies on the ecological and genetic characteristics of this species. Chloroplast genomic analysis has been shown to resolve phylogenetic relationships. Here, we sequenced the complete chloroplast (cp) genome of C. hyssopifolia, which is the first complete cp genome reported in the genus Cuphea. The size of the whole cp genome is 158,821 bp, exhibiting the large (LSC, 89,064 bp) and small (SSC, 18,373 bp) single-copy regions and a pair of inverted repeats (IRs, 25,692 bp). The genome contained 111 unique genes, including 78 protein coding genes, 29 transfer RNAs (tRNA), and four ribosomal RNAs (rRNA). Neighbour-joining (NJ) phylogenetic analysis based on 43 genomes showed that C. hyssopifolia was closer to Heimia myrtifolia than Lagerstroemia species in the Lythraceae family. [ABSTRACT FROM AUTHOR]