TY  - JOUR
A1  - Casas-Marce, Mireia
A1  - Marmesat, Elena
A1  - Soriano, Laura
A1  - Martinez-Cruz, Begona
A1  - Lucena-Perez, Maria
A1  - Nocete, Francisco
A1  - Rodriguez-Hidalgo, Antonio
A1  - Canals, Antoni
A1  - Nadal, Jordi
A1  - Detry, Cleia
A1  - Bernaldez-Sanchez, Eloisa
A1  - Fernandez-Rodriguez, Carlos
A1  - Perez-Ripoll, Manuel
A1  - Stiller, Mathias
A1  - Hofreiter, Michael
A1  - Rodriguez, Alejandro
A1  - Revilla, Eloy
A1  - Delibes, Miguel
A1  - Godoy, Jose A.
T1  - Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA
JF  - Molecular biology and evolution
N2  - There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions.
KW  - Iberian lynx
KW  - ancient DNA
KW  - paleogenetics
KW  - genetic erosion
KW  - endangered species
Y1  - 2017
U6  - https://doi.org/10.1093/molbev/msx222
SN  - 0737-4038
SN  - 1537-1719
VL  - 34
SP  - 2893
EP  - 2907
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Botero, David
A1  - Monk, Jonathan
A1  - Rodriguez Cubillos, Maria Juliana
A1  - Rodriguez Cubillos, Andres Eduardo
A1  - Restrepo, Mariana
A1  - Bernal-Galeano, Vivian
A1  - Reyes, Alejandro
A1  - Gonzalez Barrios, Andres
A1  - Palsson, Bernhard O.
A1  - Restrepo, Silvia
A1  - Bernal, Adriana
T1  - Genome-scale metabolic model of Xanthomonas phaseoli pv. manihotis
BT  - an approach to elucidate pathogenicity at the metabolic level
JF  - Frontiers in genetics
N2  - Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)(+) balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species.
KW  - Xanthomonas
KW  - Xpm
KW  - cassava bacterial blight
KW  - genome-scale metabolic
KW  - model
KW  - quorum sensing
Y1  - 2020
U6  - https://doi.org/10.3389/fgene.2020.00837
SN  - 1664-8021
VL  - 11
PB  - Frontiers Media
CY  - Lausanne
ER  -