Gene organization of the mating type regions in the ectomycorrhizal fungus Laccaria bicolor reveals distinct evolution between the two mating type loci

Seleccionado por: Chris

Niculita-Hirzel H, Labbé J, Kohler A et al. (2008) Gene organization of the mating type regions in the ectomycorrhizal fungus Laccaria bicolor reveals distinct evolution between the two mating type loci. New Phytologist, 180, 329–342.

Abstract
In natural conditions, basidiomycete ectomycorrhizal fungi such as Laccaria bicolor are typically in the dikaryotic state when forming symbioses with trees, meaning that two genetically different individuals have to fuse or 'mate'. Nevertheless, nothing is known about the molecular mechanisms of mating in these ecologically important fungi. Here, advantage was taken of the first sequenced genome of the ectomycorrhizal fungus, Laccaria bicolor, to determine the genes that govern the establishment of cell-type identity and orchestrate mating. The L. bicolor mating type loci were identified through genomic screening. The evolutionary history of the genomic regions that contained them was determined by genome-wide comparison of L. bicolor sequences with those of known tetrapolar and bipolar basidiomycete species, and by phylogenetic reconstruction of gene family history. It is shown that the genes of the two mating type loci, A and B, are conserved across the Agaricales, but they are contained in regions of the genome with different evolutionary histories. The A locus is in a region where the gene order is under strong selection across the Agaricales. By contrast, the B locus is in a region where the gene order is likely under a low selection pressure but where gene duplication, translocation and transposon insertion are frequent.

Los hongos agaricales son sumamente específicos en el momento del apareamiento. Esto ocurre en los suelos con hifas primarias, ósea, monocarióticas. Para poder formar el micelio secundario, dicariótico, es necesario la unión de dos hifas primarias, y para que suceda el mating entre las hifas hay un show genetico tras esto. El articulo trata de los loci encargados del "mating" en Laccaria bicolor. Los autores intentan demostrar la ubicación de dichos loci, haciendo comparaciones con otros genomas de agaricales, expresión de genes y filogenia molecular.

Distribution and Differentiation of Wild, Feral, and Cultivated Populations of Perennial Upland Cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean

Seleccionado por: Ana

Coppens d’Eeckenbrugge G, Lacape J-M (2014) Distribution and Differentiation of Wild, Feral, and Cultivated Populations of Perennial Upland Cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean. PLoS ONE, 9, e107458.

 

Abstract

Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race ‘yucatanense’ from northern Yucatán. ‘Marie-Galante’, the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats), wild/feral (protected habitats), and truly wild cotton (TWC) populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida), as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating ‘Marie-Galante’ from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively low genetic divergence between the Mesoamerican and Caribbean domesticated pools supports the hypothesis of domestication of G. hirsutum in northern Yucatán. 

Rare and common variants: twenty arguments

Seleccionado por: Daniel

 

Gibson, G. 2012. Rare and common variants: twenty arguments. Nature Reviews Genetics 13:135–145.

 

Absract

Genome-wide association studies have greatly improved our understanding of the genetic basis of disease risk. The fact that they tend not to identify more than a fraction of the specific causal loci has led to divergence of opinion over whether most of the variance is hidden as numerous rare variants of large effect or as common variants of very small effect. Here I review 20 arguments for and against each of these models of the genetic basis of complex traits and conclude that both classes of effect can be readily reconciled.

 

 

Para estimar la heredabilidad (h2) se han usado tradicionalmente dos métodos y mas recientemente uno con un enfoque genómico. El primero de ellos se basa en la correlación entre parientes donde los parámetros de la regression se pueden usar para estimar la heredabilidad. El segundo está basado en los resultados de experimentos de selección artificial donde la respuesta a la selección es product del diferencial de selección y la heredabilidad. Finalmente el tercero se basa en estudios de GWAS (Genome Wide Association Studies) donde se han identificado por ejemplo hasta 90,000 SNPs que explican solo el 10% de la varianza fenotípica asociada con la altura en poblaciones humanas mientras que con el enfoque de correlación entre parientes se ha estimado en un 80%. A esta enorme diferencia se le ha bautizado como el problema de la heredabilidad perdida (missing heritability problem) y se han propuesto varias causas posibles para explicarla como la interacción entre loci o la variación epigenética, entre otras.
En este artículo Gibson presenta cuatro modelos de la arquitectura genetica que han sido propuestos para explicar el problema de la heredabilidad perdida sobre todo en enfermedades de poblaciones humanas que en mi opinion puede extrapolarse a cualquier fenotipo de cualquier especie de interés.

 

 

 

 

Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives

Selecionado por: Laura

Baute, G. J., N. C. Kane, C. J. Grassa, Z. Lai, and L. H. Rieseberg. 2015. Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives. New Phytologist 206:830–838.

 

Abstract

 

The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study, we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower (Helianthus annuus), a globally important oilseed.

To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of H. annuus, as well as two cross-compatible wild relatives, Helianthus argophyllus and Helianthus petiolaris.

Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped quantitative trait loci (QTLs), such as branching. Admixture analyses revealed that all the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line.

Cumulatively, introgressions cover c. 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes, probably because of the reintroduction of branching.

 

 Lo escogí por los énfasis en los cambios en los patrones de expresión, y la detección de selección en distintos eventos, e hibridización.

 

 

Epigenetic Variability in the Genetically Uniform Forest Tree Species Pinus pinea L

Seleccionado por: Myriam

Sáez-Laguna, Enrique, María-Ángeles Guevara, Luis-Manuel Díaz, David Sánchez-Gómez, Carmen Collada, Ismael Aranda, y María-Teresa Cervera. «Epigenetic Variability in the Genetically Uniform Forest Tree Species Pinus Pinea L». Editado por Khalil Kashkush. PLoS ONE 9, n.^o 8 (1 de agosto de 2014): e103145. doi:10.1371/journal.pone.0103145.

Abstract
There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

Como ya saben el campo de la epigenética ha tomado auge en los últimos años desarrollándose más en el campo clínico, sin embargo actualmente van en aumento los trabajos que se enfocan a la ecología, evolución y procesos de plasticidad fenotípica y adaptación de los organismos.

La manera en que se regula el nivel de expresión y el momento en el que se expresan los genes, hasta hace no mucho era desconocido, ahora sabemos que la metilación en ciertas regiones puede regular estos procesos clave para que los organismos lleguen a adaptarse  a ciertas condiciones ambientales, y como es que estos procesos pueden ser plásticos y modificarse de acuerdo a cambios ambientales. Escogí este artículo porque considero que será interesante para muchos de nosotros, más para aquellos que trabajan con grupos con poca variación genética y resultan ser altamente exitosas en diferentes condiciones ambientales, además de que trata de explicar procesos que ocurren a nivel poblacional mediante mecanismos moleculares y esto nos da un panorama más completo de los procesos poblacionales.

 

Adaptations to Climate-Mediated Selective Pressures in Sheep

Seleccionado por: Vero

Feng-Hua, Lv, S. Agha, J. Kantanen, L. Colli, S. Stucki, J. W. Kijas, S. Joost, M.-H. Li, y P. Ajmone Marsan. «Adaptations to Climate-Mediated Selective Pressures in Sheep». Molecular Biology and Evolution 31, n.^o 12 (1 de diciembre de 2014): 3324-43. doi:10.1093/molbev/msu264.

Abstract:
Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and has left genetic “footprints” in the genome of breeds raised in different agroecological zones. Unlike numerous studies that have searched for evidence of selection using only population genetics data, here, we conducted an integrated coanalysis of environmental data with single nucleotide polymorphism (SNP) variation. By examining 49,034 SNPs from 32 old, autochthonous sheep breeds that are adapted to a spectrum of different regional climates, we identified 230 SNPs with evidence for selection that is likely due to climate-mediated pressure. Among them, 189 (82%) showed significant correlation (P ≤ 0.05) between allele frequency and climatic variables in a larger set of native populations from a worldwide range of geographic areas and climates. Gene ontology analysis of genes colocated with significant SNPs identified 17 candidates related to GTPase regulator and peptide receptor activities in the biological processes of energy metabolism and endocrine and autoimmune regulation. We also observed high linkage disequilibrium and significant extended haplotype homozygosity for the core haplotype TBC1D12-CH1 of TBC1D12. The global frequency distribution of the core haplotype and allele OAR22_18929579-A showed an apparent geographic pattern and significant (P ≤ 0.05) correlations with climatic variation. Our results imply that adaptations to local climates have shaped the spatial distribution of some variants that are candidates to underpin adaptive variation in sheep.


Este me pareció adecuado ya que aborda la adaptación a presiones selectivas que llaman "footprints" dejadas en el genoma, tales como las del clima, en un modelo que ha tenido un amplia adaptación a diversos ambientes y sistemas de producción: las ovejas. Feng Hua Lv y su equipo trabajan cuestiones asociadas al genoma en la domesticación de la oveja y en este artículo  proponen un coanálisis de datos ambientales y de variaciones en los SNP en lugar de solo usar elementos de genética de poblaciones para buscar evidencias de selección, para ello usaron poblaciones nativas de ovejas de amplias áreas geográficas y climas del mundo. Logrando obtener resultados que indican que ciertas regiones genomicas y genes candidatos bajo adaptación local a climas han conformado la distribución espacial de algunas variantes que son candidatas a consolidar la variación adaptativa en las ovejas, siendo su estudio un punto de partida para la investigación de los procesos biológicos y posibles mecanismos fundamentales en la adaptación ambiental genética. Por lo cual ellos proponen continuar con más estudios que confirmen sus resultados ayudándose ahora de datos genómicos y una mayor gama de variables ambientales, ya que muchas están relacionadas con factores climáticos. Esto lo plantean porque en su investigación notan las dificultades  de distinguir la presión selectiva causal de otras presiones además de que las variables ambientales en las que se encontraba cada raza podrían variar con el hábitat de la región.  

Comparative genomics reveals insights into avian genome evolution and adaptation

Seleccionado por: Azalea

Zhang, Guojie, Cai Li, Qiye Li, Bo Li, Denis M. Larkin, Chul Lee, Jay F. Storz, et al. «Comparative Genomics Reveals Insights into Avian Genome Evolution and Adaptation». Science 346, n.^o 6215 (12 de diciembre de 2014): 1311-20. doi:10.1126/science.1251385.

Abstract:
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.



Cómo evolucionan, se adaptan y diversifican las especies ha sido un cuestionamiento central en la biología. Sin embargo, pese al desarrollo teórico en el tema, los datos empíricos frecuentemente no muestran señales o pistas tan claras de cómo han actuado e interactuado las fuerzas evolutivas. Aunado a lo anterior, los trabajos que tratan de vincular los procesos moleculares con fenotipos adaptados no son tan comunes (aunque ya hemos revisado un par de artículos en el seminario), en gran parte debido a la complejidad, pero quizá también a la falta de una visión integrativa.

La secuenciación de siguiente generación nos permite estudiar cómo se han plasmado las respuestas a las presiones selectivas, los procesos de diversificación y especiación en los genomas. Así, la genómica comparada es una herramienta con la que podemos retomar las clásicas preguntas evolutivas. En el artículo que propongo, titulado“Comparative genomics reveals insights into avian genome evolution and adaptation”, estudian los patrones macroevolutivos usando 48 genomas de aves, que tienen la ventaja de ser un grupo ampliamente estudiado y cuya filogenia está prácticamente resuelta. No sólo detectan señales de selección en diversas zonas del genoma (algunas asociadas a atributos importantes de las aves), sino que además comparar esa cantidad de genomas les permitió hacer interpretaciones funcionales a niveles supraespecíficos. Me parece que este trabajo retoma y trata de conciliar los procesos microevolutivos con los fenotipos y los patrones macroevolutivos, temas que hemos revisado en el seminario pero por separado.