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The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe. [ABSTRACT FROM AUTHOR]

Retrophyllum piresii (Podocarpaceae) is an endemic conifer species from the Brazilian Amazonian Region, and very few data related to ecological and genetic characteristics of this species are available. Plastome sequencing is an efficient tool to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as to probe the structural and functional evolution of plants. Usually, the plastome of photosynthetic land plants is quadripartite, with two copies of the inverted repeats (IRs) separating the small and large single-copy regions. However, in gymnosperms, IR can vary from large in size to completely absent, being constituted principally by transfer RNA (tRNA) genes, or a part of sequence of other genes. Here, we sequenced and characterized the complete plastome of R. piresii. This plastome was determined to be 133,291 bp (~480-fold coverage), presenting a total of 120 identified genes, of which 118 were single copy and two genes, trnN-GUU and trnD-GUC, were found to be duplicated and occurring as inverted and directed repeat (DR) sequences, respectively. These repeated regions presented recombinationally active sites, resulting in an IR-mediated inversion and a DR-mediated deletion. However, the isoform resulted from DR-mediated deletion may result in unviable plastome, with deletion of photosynthetic and expression machinery-related genes. [ABSTRACT FROM AUTHOR]

Rice is staple food of nearly half the world's population. Rice yields must therefore increase to feed ever larger populations. By colonising rice and other plants, Herbaspirillum spp. stimulate plant growth and productivity. However the molecular factors involved are largely unknown. To further explore this interaction, the transcription profiles of Nipponbare rice roots inoculated with Herbaspirillum seropedicae were determined by RNA-seq. Mapping the 104 million reads against the Oryza sativa cv. Nipponbare genome produced 65 million unique mapped reads that represented 13,840 transcripts each with at least two-times coverage. About 7.4% (1,014) genes were differentially regulated and of these 255 changed expression levels more than two times. Several of the repressed genes encoded proteins related to plant defence (e.g. a putative probenazole inducible protein), plant disease resistance as well as enzymes involved in flavonoid and isoprenoid synthesis. Genes related to the synthesis and efflux of phytosiderophores (PS) and transport of PS-iron complexes were induced by the bacteria. These data suggest that the bacterium represses the rice defence system while concomitantly activating iron uptake. Transcripts of H. seropedicae were also detected amongst which transcripts of genes involved in nitrogen fixation, cell motility and cell wall synthesis were the most expressed. [ABSTRACT FROM AUTHOR]