International Joint Conference SOCO’16-CISIS’16-ICEUTE’16

This volume of Advances in Intelligent and Soft Computing contains accepted papers presented at SOCO 2016, CISIS 2016 and ICEUTE 2016, all conferences held in the beautiful and historic city of San Sebastián (Spain), in October 2016. Soft computing represents a collection or set of computational techniques in machine learning, computer science and some engineering disciplines, which investigate, simulate, and analyze very complex issues and phenomena. After a through peer-review process, the 11th SOCO 2016 International Program Committee selected 45 papers. In this relevant edition a special emphasis was put on the organization of special sessions. Two special session was organized related to relevant topics as: Optimization, Modeling and Control Systems by Soft Computing and Soft Computing Methods in Manufacturing and Management Systems. The aim of the 9th CISIS 2016 conference is to offer a meeting opportunity for academic and industry-related researchers belonging to the various, vast communities of Computational Intelligence, Information Security, and Data Mining. The need for intelligent, flexible behaviour by large, complex systems, especially in mission-critical domains, is intended to be the catalyst and the aggregation stimulus for the overall event. After a through peer-review process, the CISIS 2016 International Program Committee selected 20 papers. In the case of 7th ICEUTE 2016, the International Program Committee selected 14 papers

Additional file 6: Figure S2. of accD nuclear transfer of Platycodon grandiflorum and the plastid of early Campanulaceae

Phylogenetic trees generated from the DNA sequences of seven cp-genes using three algorithms. (A) single maximum parsimonious (MP) tree, (B) single neighbor-joining (NJ) tree, and (C) single maximum likelihood (ML) tree (HYK85 + G + I model). (PPTX 749 kb

Genome Information of <i>Methylobacterium oryzae</i>, a Plant-Probiotic Methylotroph in the Phyllosphere

<div><p>Pink-pigmented facultative methylotrophs in the <i>Rhizobiales</i> are widespread in the environment, and many <i>Methylobacterium</i> species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of <i>Methylobacterium oryzae</i> CBMB20^T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. <i>M. oryzae</i> is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B₁₂ biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of <i>M. oryzae</i>, we provide information on the full gene complement of <i>M. oryzae</i> that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of <i>M. oryzae</i> pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.</p></div

Methylotrophy and adaptation to the phyllosphere.

<p>Its genome contains an assortment of genes that may contribute to adaption to the phyllosphere, interaction with plants, and promotion of plant growth. H₄F, tetrahydrofolate; H₄MPT, tetrahydromethanopterin; MFR, methanofuran; PGA, phosphoglycerate; PEP, phosphoenolpyruvate; OAA, oxaloacetate; EMC, ethylmalonyl-CoA pathway; TCA, tricarboxylic acid cycle; ACC, 1-aminocyclopropane-1-carboxylate; AccD, 1-aminocyclopropane-1-carboxylate deaminase; DMAPP, dimethylallyl diphosphate; MiaA, tRNA isopentenylpyrophosphate transferase; PQQ, pyrroloquinoline quinone.</p

Circular representation of the five replicons of the <i>Methylobacterium oryzae</i> CBMB20^T genome.

<p>The first circle from inside is the color-coded COG functional category and next black circle indicates the scale bar. The third and fourth circles indicate the GC skew and the GC content. Next vertical red bars denote tRNAs and the green bars the rRNA operons. In the next circle are predicted CDSs represented by 25 colors according to COG functional classification (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106704#pone.0106704.s008" target="_blank">Table S4</a>), and outermost bars indicate genomic islands (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106704#pone.0106704.s005" target="_blank">Table S1</a>).</p

Comparison of the COG and subsystem assignments among completely sequenced <i>Methylobacterium</i> species.

<p>Color key indicates the relative abundance (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106704#pone.0106704.s008" target="_blank">Table S4</a>). Heat maps were constructed using R script.</p

Phylogenetic tree of the members of <i>Methylobacterium</i> whose genome sequences have been determined.

<p>The amino-acid sequences of 36 broadly conserved proteins were concatenated and aligned with MUSCLE, from which a neighbor-joining tree was constructed using MEGA 5. <i>Methylocella silvestris</i> BL2 (CP001280) was used as the out-group. Colored circles indicate the kinds of proteins that are known to promote plant growth.</p

Flower plot of the core genome and strain-specific genes of genome-sequenced <i>Methylobacterium</i> strains.

<p>The number in the center circle indicates the core genes of completely sequenced <i>Methylobacterium</i> strains and the numbers in the floral leafs indicate the number of strain specific CDSs, respectively.</p

COG and subsystem comparison of strain-specific CDSs.

<p>The numbers indicate the relative abundance of COG and subsystem assigned genes.</p><p>*, Coverage means the proportion of COG and subsystem assigned CDSs in strain specific CDSs.</p><p>COG and subsystem comparison of strain-specific CDSs.</p

<b>Table 2.</b> Number of shared genes and the pan-genome of <i>Methylobacterium</i> species.

<p>*, Shared groups are the CDS groups that encoded by at least two strains.</p>†<p>, Pan-genome is the sum of the number of shared groups and all strain specific CDSs in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106704#pone-0106704-g005" target="_blank">Figure 5</a>.</p><p><b>Table 2.</b> Number of shared genes and the pan-genome of <i>Methylobacterium</i> species.</p