Examinando por Materia "Phylogeny"

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    Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
    (BioMed Central Ltd., 2018-01-17) Molano, E.P.L.; Cabrera, O.G.; Jose, J.; do Nascimento, L.C.; Carazzolle, M.F.; Teixeira, P.J.P.L.; Alvarez, J.C.; Tiburcio, R.A.; Tokimatu Filho, P.M.; de Lima, G.M.A.; Guido, R.V.C.; Corrêa, T.L.R.; Leme, A.F.P.; Mieczkowski, P.; Pereira, G.A.G.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
    Background: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. Results: We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Conclusion: Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity. © 2018 The Author(s).
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    Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
    (BioMed Central Ltd., 2018-01-17) Molano, E.P.L.; Cabrera, O.G.; Jose, J.; do Nascimento, L.C.; Carazzolle, M.F.; Teixeira, P.J.P.L.; Alvarez, J.C.; Tiburcio, R.A.; Tokimatu Filho, P.M.; de Lima, G.M.A.; Guido, R.V.C.; Corrêa, T.L.R.; Leme, A.F.P.; Mieczkowski, P.; Pereira, G.A.G.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)
    Background: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. Results: We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Conclusion: Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity. © 2018 The Author(s).
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    Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases
    (BioMed Central Ltd., 2014-01-01) Mosquera-Rendón, J.; Cárdenas-Brito, S.; Pineda, J.D.; Corredor, M.; Benítez-Páez, A.; Mosquera-Rendón, J.; Cárdenas-Brito, S.; Pineda, J.D.; Corredor, M.; Benítez-Páez, A.; Universidad EAFIT. Departamento de Ingeniería de Sistemas; I+D+I en Tecnologías de la Información y las Comunicaciones
    Background: RNA post-transcriptional modification is an exciting field of research that has evidenced this editing process as a sophisticated epigenetic mechanism to fine tune the ribosome function and to control gene expression. Although tRNA modifications seem to be more relevant for the ribosome function and cell physiology as a whole, some rRNA modifications have also been seen to play pivotal roles, essentially those located in central ribosome regions. RNA methylation at nucleobases and ribose moieties of nucleotides appear to frequently modulate its chemistry and structure. RNA methyltransferases comprise a superfamily of highly specialized enzymes that accomplish a wide variety of modifications. These enzymes exhibit a poor degree of sequence similarity in spite of using a common reaction cofactor and modifying the same substrate type. Results: Relationships and lineages of RNA methyltransferases have been extensively discussed, but no consensus has been reached. To shed light on this topic, we performed amino acid and codon-based sequence analyses to determine phylogenetic relationships and molecular evolution. We found that most Class I RNA MTases are evolutionarily related to protein and cofactor/vitamin biosynthesis methyltransferases. Additionally, we found that at least nine lineages explain the diversity of RNA MTases. We evidenced that RNA methyltransferases have high content of polar and positively charged amino acid, which coincides with the electrochemistry of their substrates. Conclusions: After studying almost 12,000 bacterial genomes and 2,000 patho-pangenomes, we revealed that molecular evolution of Class I methyltransferases matches the different rates of synonymous and non-synonymous substitutions along the coding region. Consequently, evolution on Class I methyltransferases selects against amino acid changes affecting the structure conformation. © 2014 Mosquera-Rendón et al.; licensee BioMed Central Ltd.
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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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    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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    A Revision of Philander (Marsupialia: Didelphidae), Part 1: P. quica, P. canus, and a New Species from Amazonia
    (American Museum of Natural History, 2018-01-31) Voss, R.S.; Díaz-Nieto, J.F.; Jansa, S.A.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
    This is the first installment of a revision of the didelphid marsupial genus Philander, commonly known as gray four-eyed opossums. Although abundant and widespread in lowland tropical forests from southern Mexico to northern Argentina, species of Philander are not well understood taxonomically, and the current literature includes many examples of conflicting species definitions and nomenclatural usage. Our revision is based on coalescent analyses of mitochondrial gene sequences, phylogenetic analyses of mitochondrial and nuclear genes, morphometric analyses, and firsthand examination of relevant type material. Based on these results, we provisionally recognize eight species, of which three are formally treated in this report: P. quica (Temminck, 1824), an Atlantic Forest endemic formerly known as P. frenatus (Olfers, 1818); P. canus (Osgood, 1913), a widespread species formerly treated as a synonym or subspecies of P. opossum (Linnaeus, 1758); and P. pebas, a new species endemic to Amazonia. The remaining, possibly valid, species of Philander can be allocated to two clades. The first is a cis-Andean complex that includes P. andersoni (Osgood, 1913); P. mcilhennyi Gardner and Patton, 1972; and P. opossum. The second is a trans-Andean complex that includes P. melanurus (Thomas, 1899) and P. pallidus (Allen, 1901). Among other nomenclatural acts, we designate a neotype for the long-problematic nominal taxon Didelphis superciliaris Olfers, 1818, and (in an appendix coauthored by Renate Angermann), we establish that Olfers' coeval binomen D. frenata is based on an eastern Amazonian type and is a junior synonym of P. opossum. © American Museum of Natural History 2018.
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    A REVISION OF THE DIDELPHID MARSUPIAL GENUS MARMOSA PART 2. SPECIES OF THE RAPPOSA GROUP (SUBGENUS MICOUREUS)
    (AMER MUSEUM NATURAL HISTORY, 2020-06-01) Voss, Robert S.; Giarla, Thomas C.; Diaz-Nieto, Juan F.; Jansa, Sharon A.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
    In this report, the second of a revisionary series on mouse opossums (Marmosa), we analyze cytochrome b sequence data from 166 specimens of the subgenus Micoureus and delimit putative species using the multirate Poisson Tree Processes (mPTP) method. That analysis identifies 21 putative species, many of which can be matched with available names, including alstoni, constantiae, demerarae, limae, germana, meridae, paraguayana, parda, perplexa, phaea, rapposa, and rutteri. However, some of these nominal taxa are not morphologically diagnosable, and in the absence of other corroborating evidence, we do not recommend that they all be recognized as valid. Phylogenetic analyses of a multigene dataset suggest that putative species of Micoureus belong to several wellsupported clades, one of which (the ``Rapposa Group'') is revised in this report. As defined herein, the Rapposa Group includes at least three valid species: M. rapposa Thomas, 1899 (including budini Thomas, 1920); M. parda Tate, 1931; and M. rutteri Thomas, 1924. Herein we document their ecogeographic distributions and diagnostic traits, comment on their taxonomic histories, and list the specimens we examined (including all relevant type material).