High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

BACKGROUND: Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. METHODOLOGY/PRINCIPAL FINDINGS: Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. CONCLUSIONS/SIGNIFICANCE: The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly

In silico screening for pathogenesis related-2 gene candidates in Vigna uguiculata transcriptome

Plants evolved diverse mechanisms to struggle against pathogen attack, for example the activity of Pathogenesis-Related (PR) genes. Within this category PR-2 encodes a Beta-glucanase able to degrade the polysaccharides present in the pathogen cell wall. The aim of this work was to screen the NordEST database to identify PR-2 members in cowpea transcriptome and analyze the structure of the identified sequences as compared with data from public databases. After search for PR-2 sequences in NordEST; CLUSTALx and MEGA4 were used to align PR-2 orthologs and generate a dendrogram. CLUSTER program revealed the expression pattern trough differential display. A new tool was developed aiming to identify plant PR-2 proteins based in the HMMER analysis. Among results, a complete candidate from cowpea could be identified. Higher expression included all libraries submitted to biotic (cowpea severe mosaic virus, CPSMV) stress, as well as wounded and salinity stressed tissues, confirming PR expression under different kind of stresses. Dendrogram analysis showed two main clades, the outgroup and Magnoliopsida where monocots and dicots organisms were positioned as sister groups. The developed HMM model could identify PR-2 also in other important plant species, allowing the development of a bioinformatic routine that may help the identification not only of pathogenesis related genes but any other genes, classes that present similar conserved domains and motifs