Papers by Marco Cristancho
Ingeniería Investigación y Tecnología, Oct 1, 2017
El uso de supercomputación en la ciencia es necesario, debido a las grandes cantidades de datos q... more El uso de supercomputación en la ciencia es necesario, debido a las grandes cantidades de datos que se analizan para obtener resultados impactantes. Las tecnologías many-core como Intel Xeon Phi aparecen como una alternativa de acelerar estos análisis y su uso en la supercomputación, en especial, dentro de la bioinformática, donde es más común, pero los resultados no son los esperados al ejecutar software altamente demandante en clústeres heterogéneos. En la siguiente investigación se muestra un wrapper encargado de paralelizar óptimamente NCBI-Blast sobre varios nodos de CPUs y Xeon Phi, con el objetivo de reducir al máximo los tiempos de ejecución y demostrar la utilidad que pueden tener las tecnologías many-core en las ciencias aplicadas.
La biota marina juega un rol fundamental a nivel sistemico de los ambientes marinos, ya que regul... more La biota marina juega un rol fundamental a nivel sistemico de los ambientes marinos, ya que regula el equilibrio entre los factores bioticos y abioticos y cumplen servicios de alimentacion, proteccion costera, recreacion, entre otros, para las comunidades humanas que se sustentan de estos recursos. Los microorganismos marinos, en particular, son fundamentales para el funcionamiento y salud de estos ecosistemas y de la macrobiota, debido a que contribuyen de manera integral a los flujos, procesos y ciclos biogeoquimicos del carbono, nitrogeno y azufre, y representan el 90% de la biomasa de los oceanos. Se estima que pueden existir 1.2 x 1029 microorganismos en habitats acuaticos y hasta 3.5 x 1030 en la sub-‐ superficie oceanica; ademas, el numero de virus en el oceano se estima en ordenes de magnitud mayores a 1030. Por tanto, por su alta abundancia y diversidad, los microorganismos marinos representan un recurso biologico de gran importancia, cuyas fluctuaciones puede generar un impacto significativo en todo el sistema.
Advances in intelligent systems and computing, 2014
We have implemented a web-based Bioinformatics platform that functions as a genomics information ... more We have implemented a web-based Bioinformatics platform that functions as a genomics information resource for coffee and other organisms studied at the Colombia National Coffee Research Center-CENICAFE. The Bioinformatics platform includes a Laboratory Integrated Management System (LIMS), the implementation of wEMBOSS, home-developed perl tools for data analysis, InterproScan for annotation of sequence domains, and the implementation of wBLAST and wNetBLAST among other tools available. The main backbone of the system is an adaptation of the SOL Genomics Network (SGN) databases developed at Cornell University for ESTs, molecular markers and BAC sequences storage and analysis (http://sgn.cornell.edu). The system is based on the postgresQL relational database, the use of perl scripts for the manipulation of data, the Apache Web server with the mod_perl integrated perl interpreter, and the servers run the Debian distribution of the GNU/Linux operating system. Although SGN has mainly developed as a plant genomics oriented resource, the Cenicafe platform has implemented several new tools and databases for the analysis of other organisms sequence data such as fungi and insects. The Cenicafe databases contain to date 32.000 coffee EST sequences from 22 libraries organized in 9.257 C. arabica and 1.239 C. liberica unigenes, 6.000 Beauveria bassiana EST sequences organized in 2.404 unigenes, and 4.000 Hypothenemus hampei (coffee berry borer) EST sequences organized in 885 unigenes, besides the more than 100.000 Solanaceae unigene sequences annotated at SGN. The sequences are annotated based on Solanaceae, Arabidopsis, Swissprot and Genbank sequence comparisons using BLAST homology searches, aminoacids are predicted using ESTScan, the domains are annotated using InterproScan and Gene families are annotated using a perl script developed at SGN. The system will implement in the near future a database of coffee genetics resources developed at Cenicafe, a proteomics platform, and a Microarray database. We will also be incorporating other components to the platform specially for the visualization of genetic maps from the Gmod project (Gbrowse), the SGN system, TIGR, and other open source projects.
This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Bi... more This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Biology and Bioinformatics Congress CCBCOL, after a rigorous review process in which 54 papers were accepted for publication from 119 submitted contributions. Bioinformatics and Computational Biology are areas of knowledge that have emerged due to advances that have taken place in the Biological Sciences and its integration with Information Sciences. The expansion of projects involving the study of genomes has led the way in the production of vast amounts of sequence data which needs to be organized, analyzed and stored to understand phenomena associated with living organisms related to their evolution, behavior in different ecosystems, and the development of applications that can be derived from this analysis.
Frontiers in Marine Science, Jun 26, 2019
Microorganisms represent nearly 90% of ocean biomass and are fundamental for the functioning and ... more Microorganisms represent nearly 90% of ocean biomass and are fundamental for the functioning and health of marine ecosystems due to their integral contribution to biogeochemical cycles and biological processes. In marine environments, microorganisms exist as microbial communities in the water column, benthonic substrates, and macroorganisms, where they establish symbiotic interactions and fulfill their ecological roles. Such interactions can have a harmful or beneficial impact on the hosts depending on the emergent properties of the communities, their taxonomic structure, and functionality. To evaluate these features, culture independent approaches like metabarcoding have been developed and have hugely contributed to the characterization of marine microbial diversity. The present study was aimed to explore the structure and metabolic functionality of microbial communities associated to marine hosts at the Serrana Bank, a coral atoll part of the Seaflower Biosphere Reserve (Archipelago of San Andrés, Old Providence and Saint Catalina, Colombia). We found a highly diverse microbial assemblage associated with the corals Siderastrea siderea, Colpophyllia natans, and Orbicella annularis, the sponge Haliclona sp. and sediment from Isla de los Pájaros lagoon. However, the coral Porites astreoides had significantly lower bacterial diversity and a different community composition. Proteobacteria was the most abundant phylum within bacterial communities in the evaluated hosts, except in P. astreoides, where Cyanobacteria was the predominant group. Firmicutes, Actinobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and Gemmatimonadetes were also identified within all microbiomes, but their dominance varied between hosts. Additionally, the most abundant group among the fungi communities associated with O. annularis, S. siderea, and C. natans was Ascomycota, but significant differences between clasess and order were observed among hosts. Finally, functional profiles revealed that the principal microbial functions were focused on membrane transport, carbohydrates, amino acids and energy metabolism, replication, and translation processes. A significant higher metabolic functionality was found in the sponge microbiome in comparison to the coral microbial communities.
Agronomy, Jul 13, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Journal of Phytopathology, Sep 21, 2012
Since 2008, Colombia has been experiencing an epidemic of the coffee rust Hemileia vastatrix. The... more Since 2008, Colombia has been experiencing an epidemic of the coffee rust Hemileia vastatrix. The altitude range of the disease has expanded, and nursery and young plants that were usually not attacked by the disease are now significantly affected. To determine whether this new epidemic has been caused by a new pathogenic isolate, the molecular diversity of the pathogen causing the epidemic in different regions of the country was assessed, using AFLP molecular markers on isolates collected from coffee fields prior and after the year 2008. We also evaluated the aggressiveness of isolates collected from diverse coffee‐producing areas and from different coffee genotypes. Isolates collected before and during the present epidemic were quite similar both genetically and with regard to their aggressiveness. Out of a total of 349 fragments amplified from 6 AFLP primer combinations, 48 (13.2%) were polymorphic and only 18 were unique among H. vastatrix isolates representative of pre‐2008 and post‐2008 epidemic populations. We conclude that the epidemic was caused by the excessive rainfall that has occurred in Colombia since 2006 and that extended to 2011 and not by the arrival of a new isolate of the pathogen or a change in virulence of the species present in the country.
Nature Precedings, Mar 27, 2012
Genetics and Molecular Research, 2008
The aim of the present research was to test the transferability of simple sequence repeat (SSR) m... more The aim of the present research was to test the transferability of simple sequence repeat (SSR) markers developed in two Uredinales species to Hemileia vastatrix, coffee rust. The development of efficient techniques for the identification of H. vastatrix isolates is imperative, given the continuous development of new races. The transferability of 25 SSR markers developed in the related Uredinales species Puccinia coronata f. sp lolli and Melampsora linii to H. vastatrix was tested. A low level of transferability of SSRs was detected, and only 4 potential markers that can be used to fingerprint the coffee rust races were identified.
Euphytica, 2009
This study reports the implementation of three strategies for the development of genetic markers ... more This study reports the implementation of three strategies for the development of genetic markers and their evaluation in both progenitors of an F2 population used for the construction of a genetic map of Coffea arabica. The strategies were Cleaved Amplified Polymorphic Sequences (CAPS), Single Strand Conformational Polymorphism (SSCP), and sequence analysis predicted Single Nucleotide Polymorphism (SNP). The methodologies were developed from different sequence sources: For CAPS, we used 25 COS sequences derived from Hedyotis spp. and 29 COSII sequences derived from Solanaceae and Rubiaceae species; for SSCP, we used 111 coffee EST sequences, 50 COSII sequences, and 10 C. arabica BAC end sequences. A low polymorphism was identified with the CAPS and SSCP methodologies. A total of 61 SNPs were identified in silico from 5,371 ESTs of coffee and from amplified, cloned, and sequenced COSII markers. Sixteen of these SNPs were validated with Luminex technology and 2 of them were polymorphic in C. arabica genotypes. This study highlights the difficulties of finding polymorphism in the species C. arabica where SNP identification seems to be the best strategy to search for polymorphic markers for this low diversity plant.
… Conference on Coffee …, 2007
Latin America is one of the regions in which the COVID-19 pandemic has had a stronger impact, wit... more Latin America is one of the regions in which the COVID-19 pandemic has had a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic.To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America.A total of 1534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance o...
Agronomy
Coffee leaf rust is the most damaging disease for coffee cultivation around the world. It is caus... more Coffee leaf rust is the most damaging disease for coffee cultivation around the world. It is caused by a fungal pathogen, Hemileia vastatrix (Hva), belonging to the phylum Basidiomycota. Coffee leaf rust causes significant yield losses and increases costs related to its control, with evaluated losses of USD 1–2 billion annually. It attacks both the cultivated coffee species Coffea canephora (Robusta coffee) and Coffea arabica (Arabica coffee). New races, or pathotypes, are constantly emerging with increased virulence, suggesting a rapid evolution of the pathogen. Previous genetic and genomic studies have indicated a limited nucleotide diversity of Hva despite a high genetic diversity and large genome size estimated to be ~800 Mb, with a high content of repeated sequences (>74%). Despite several genomic resources and the release of a recent partial genome sequence, the diversity of these repeated sequences and how they may impact the evolution of the leaf rust genome have not been...
Genetic Resources and Crop Evolution, 2004
The genetic diversity of 50 wild and semi-wild accessions of the Coffea arabica L. germplasm coll... more The genetic diversity of 50 wild and semi-wild accessions of the Coffea arabica L. germplasm collection, gathered by the FAO and ORSTOM missions to Ethiopia, and maintained in Colombia by CENICAFE, was evaluated with RAPD markers. The evaluation was carried out in two phases: In phase one, the polymorphism of 8 Ethiopian accessions of different geographic origin, plus the cultivated variety 'Caturra' was assessed with the RAPD technique with forty-two 10-mer oligonucleotides. In phase two, 51 accessions were assessed with a set of 5 polymorphic primers that reproduced, with a correlation of 95%, the groups generated by the 24 polymorphic primers found in phase one. Principal Coordinate Analysis of molecular data revealed that a closely related group consisting of 86% of the Ethiopian C. arabica accessions evaluated are significantly different from the Caturra variety and could be used in a genetic breeding initiative to increase the variability of cultivated varieties. The results also indicate that a larger polymorphism is present in the Colombian replica of FAO Ethiopian coffee germplasm collection than previously reported.
PLOS Computational Biology
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Papers by Marco Cristancho