Examinando por Autor "Franco-Sierra, N.D."

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    Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture
    (Springer, 2020-01-01) Franco-Sierra, N.D.; Posada, L.F.; Santa-María, G.; Romero-Tabarez, M.; Villegas-Escobar, V.; Álvarez, J.C.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
    Bacillus subtilis is a remarkably diverse bacterial species that displays many ecological functions. Given its genomic diversity, the strain Bacillus subtilis EA-CB0575, isolated from the rhizosphere of a banana plant, was sequenced and assembled to determine the genomic potential associated with its plant growth promotion potential. The genome was sequenced by Illumina technology and assembled using Velvet 1.2.10, resulting in a whole genome of 4.09 Mb with 4332 genes. Genes involved in the production of indoles, siderophores, lipopeptides, volatile compounds, phytase, bacilibactin, and nitrogenase were predicted by gene annotation or by metabolic pathway prediction by RAST. These potential traits were determined using in vitro biochemical tests, finding that B. subtilis EA-CB0575 produces two families of lipopeptides (surfactin and fengycin), solubilizes phosphate, fixes nitrogen, and produces indole and siderophores compounds. Finally, strain EA-CB0575 increased 34.60% the total dry weight (TDW) of tomato plants with respect to non-inoculated plants at greenhouse level. These results suggest that the identification of strain-specific genes and predicted metabolic pathways might explain the strain potential to promote plant growth by several mechanisms of action, accelerating the development of plant biostimulants for sustainable agricultural. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.
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    Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture
    (Springer, 2020-01-01) Franco-Sierra, N.D.; Posada, L.F.; Santa-María, G.; Romero-Tabarez, M.; Villegas-Escobar, V.; Álvarez, J.C.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)
    Bacillus subtilis is a remarkably diverse bacterial species that displays many ecological functions. Given its genomic diversity, the strain Bacillus subtilis EA-CB0575, isolated from the rhizosphere of a banana plant, was sequenced and assembled to determine the genomic potential associated with its plant growth promotion potential. The genome was sequenced by Illumina technology and assembled using Velvet 1.2.10, resulting in a whole genome of 4.09 Mb with 4332 genes. Genes involved in the production of indoles, siderophores, lipopeptides, volatile compounds, phytase, bacilibactin, and nitrogenase were predicted by gene annotation or by metabolic pathway prediction by RAST. These potential traits were determined using in vitro biochemical tests, finding that B. subtilis EA-CB0575 produces two families of lipopeptides (surfactin and fengycin), solubilizes phosphate, fixes nitrogen, and produces indole and siderophores compounds. Finally, strain EA-CB0575 increased 34.60% the total dry weight (TDW) of tomato plants with respect to non-inoculated plants at greenhouse level. These results suggest that the identification of strain-specific genes and predicted metabolic pathways might explain the strain potential to promote plant growth by several mechanisms of action, accelerating the development of plant biostimulants for sustainable agricultural. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.
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    Mitochondrial genome characterization of Tecia solanivora (Lepidoptera: Gelechiidae) and its phylogenetic relationship with other lepidopteran insects
    (Elsevier, 2016-05-01) Ramírez-Ríos, V.; Franco-Sierra, N.D.; Alvarez, J.C.; Saldamando-Benjumea, C.I.; Villanueva, Diego Fernando; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
    The complete mitogenome of the potato tuber moth Tecia solanivora (Lepidoptera: Gelechiidae) was sequenced, annotated, characterized and compared with 140 species of the order Lepidoptera. The circular genome is 15,251 bp, containing 37 genes (13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region). The gene arrangement was identical to other lepidopteran mitogenomes but different from the ancestral arrangement found in most insects for the tRNA-Met gene (A + T-region, tRNA-I, tRNA-Q, tRNA-M). The mitogenome of T. solanivora is highly A + T-biased (78.2%) and exhibits negative AT- and GC-skews. All PCGs are initiated by canonical ATN start codons, except for Cytochrome Oxidase subunit 1 (COI), which is initiated by CGA. Most PCGs have a complete typical stop codon (TAA). Only NAD1 has a TAG stop codon and the COII and NAD5 genes have an incomplete stop codon consisting of just a T. The A + T-rich region is 332 bp long and contains common features found in lepidopteran mitogenomes, including the `ATAGA' motif, a 17 bp poly (T) stretch and a (AT)(8) element preceded by the `ATTTA' motif. Other tandem repeats like (TAA)(4) and (TAT), were found, as well as (T)(6) and (A)(10) mononucleotide repeat elements. Finally, this mitogenome has 20 intergenic spacer regions. The phylogenetic relationship of T. solanivora with 28 other lepidopteran families (12 superfamilies) showed that taxonomic classification by morphological features coincides with the inferred phylogeny. Thus, the Gelechiidae family represents a monophyletic group, suggesting that T. solanivora and Pectinophora gossypiella have a recent common ancestor. (C) 2016 Elsevier B.V. All rights reserved.
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    Mitochondrial genome characterization of Tecia solanivora (Lepidoptera: Gelechiidae) and its phylogenetic relationship with other lepidopteran insects
    (Elsevier, 2016-05-01) Ramírez-Ríos, V.; Franco-Sierra, N.D.; Alvarez, J.C.; Saldamando-Benjumea, C.I.; Villanueva, Diego Fernando; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)
    The complete mitogenome of the potato tuber moth Tecia solanivora (Lepidoptera: Gelechiidae) was sequenced, annotated, characterized and compared with 140 species of the order Lepidoptera. The circular genome is 15,251 bp, containing 37 genes (13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region). The gene arrangement was identical to other lepidopteran mitogenomes but different from the ancestral arrangement found in most insects for the tRNA-Met gene (A + T-region, tRNA-I, tRNA-Q, tRNA-M). The mitogenome of T. solanivora is highly A + T-biased (78.2%) and exhibits negative AT- and GC-skews. All PCGs are initiated by canonical ATN start codons, except for Cytochrome Oxidase subunit 1 (COI), which is initiated by CGA. Most PCGs have a complete typical stop codon (TAA). Only NAD1 has a TAG stop codon and the COII and NAD5 genes have an incomplete stop codon consisting of just a T. The A + T-rich region is 332 bp long and contains common features found in lepidopteran mitogenomes, including the `ATAGA' motif, a 17 bp poly (T) stretch and a (AT)(8) element preceded by the `ATTTA' motif. Other tandem repeats like (TAA)(4) and (TAT), were found, as well as (T)(6) and (A)(10) mononucleotide repeat elements. Finally, this mitogenome has 20 intergenic spacer regions. The phylogenetic relationship of T. solanivora with 28 other lepidopteran families (12 superfamilies) showed that taxonomic classification by morphological features coincides with the inferred phylogeny. Thus, the Gelechiidae family represents a monophyletic group, suggesting that T. solanivora and Pectinophora gossypiella have a recent common ancestor. (C) 2016 Elsevier B.V. All rights reserved.
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    Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification
    (John Wiley and Sons Ltd, 2020-01-01) Franco-Sierra, N.D.; Díaz-Nieto, J.F.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
    Molecular information is crucial for species identification when facing challenging morphology-based specimen identifications. The use of DNA barcodes partially solves this problem, but in some cases when PCR is not an option (i.e., primers are not available, problems in reaction standardization), amplification-free approaches could be an optimal alternative. Recent advances in DNA sequencing, like the MinION device from Oxford Nanopore Technologies (ONT), allow to obtain genomic data with low laboratory and technical requirements, and at a relatively low cost. In this study, we explore ONT sequencing for molecular species identification from a total DNA sample obtained from a neotropical rodent and we also test the technology for complete mitochondrial genome reconstruction via genome skimming. We were able to obtain “de novo” the complete mitogenome of a specimen from the genus Melanomys (Cricetidae: Sigmodontinae) with average depth coverage of 78X using ONT-only data and by combining multiple assembly routines. Our pipeline for an automated species identification was able to identify the sample using unassembled sequence data (raw) in a reasonable computing time, which was substantially reduced when a priori information related to the organism identity was known. Our findings suggest ONT sequencing as a suitable candidate to solve species identification problems in metazoan nonmodel organisms and generate complete mtDNA datasets. © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.