Ubicación de genes relacionados con la meiosis en Brachiaria decumbens Stapf., una especie de reproducción apomíctica

La apomixis es un fenómeno de importancia evolutiva y económica que se define como reproducción asexual por semillas. Varias accesiones poliploides de especies del género Brachiaria son pastos forrajeros valiosos en Suramérica, que se reproducen a través de apomixis apospórica facultativa. En este trabajo se pretendió ubicar genes relacionados con la meiosis en el mapa existente de Brachiaria decumbens, realizando una aproximación hacia la constitución genómica de la especie. Se mapearon en total 117 fragmentos en dosis sencilla distribuidos en 20 grupos de ligamiento con un LOD de 8, cubriendo un total de 688.7 cM, con un promedio de 5,9 marcadores por grupo, y una distancia promedio entre marcadores de 5,8 cM. Para B. decumbens, se obtuvieron 256 bandas amplificadas, siendo 173 AFLPs, 45 microsatélites y 21 ESTs relacionados con características agronómicas de interés. Se aportaron al mapa 35 loci: 28 STS, 6 SNPs y una deleción de una base. Los rangos más representados de segregación de los marcadores estuvieron entre 0,75 y 1,75, correspondiendo con lo esperado para marcadores que segregan en una sola dosis, con un promedio de 1,57 para B. decumbens y 1,86 para B. ruziziensis1. MARCO TEÓRICO 18 1.1 CARACTERÍSTICAS DEL GÉNERO Brachiaria 18 1.2 CULTIVARES COMERCIALES DE Brachiaria 19 1.3 CITOGENÉTICA DE Brachiaria 20 1.4 APOMIXIS 21 1.5 CONTROL GENÉTICO Y HERENCIA DE LA APOMIXIS 24 1.6 MEIOSIS EN PLANTAS SEXUALES Y APOMÍCTICAS 25 1.7 MARCADORES MOLECULARES 26 1.8 MAPEO GENÉTICO 31 1.9 ANTECEDENTES TEÓRICOS 37 2. OBJETIVOS 40 2.1 OBJETIVO GENERAL 40 2.2 OBJETIVOS ESPECÍFICOS 40 3. MATERIALES Y MÉTODOS 41 3.1 MATERIAL VEGETAL 41 3.2 METODOLOGÍA 41 4. RESULTADOS 59 4.1 AMPLIFICACIÓN Y SELECCIÓN DE LAS SECUENCIAS RELACIONADAS CON LA MEIOSIS (SRM) 59 4.2 ANÁLISIS DE SEGREGACIÓN 68 4.3 MAPEO GENÉTICO DE LAS SRM EN B. decumbens y B. ruziziensis 71 4.4 COMPORTAMIENTO DE APAREAMIENTO CROMOSÓMICO 78 5. DISCUSIÓN 80 5.1 AMPLIFICACIÓN Y SELECCIÓN DE LAS SECUENCIAS RELACIONADAS CON LA MEIOSIS (SRM) 80 5.2 ANÁLISIS DE SEGREGACIÓN 83 5.3 MAPEO GENÉTICO DE LAS SRM EN B. decumbens y B. ruziziensis 86 5.4 COMPORTAMIENTO DE APAREAMIENTO CROMOSÓMICO 91PregradoBiólog

Temporal expression dynamics of plant biomass-degrading enzymes by a synthetic bacterial consortium growing on sugarcane bagasse

Plant biomass (PB) is an important source of sugars useful for biofuel production, whose degradation efficiency depends on synergistic and dynamic interactions of different enzymes. Here, using a metatranscriptomics-based approach, we explored the expression of PB-degrading enzymes in a five-species synthetic bacterial consortium during cultivation on sugarcane bagasse as a unique carbon source. By analyzing the temporal expression dynamics of a selection of enzymes we revealed the functional role of each consortium member and disentangled the potential interactions between them. Based on normalized expression values and the taxonomic affiliation of all the transcripts within thirty carbohydrate-active enzyme (CAZy) families, we observed a successional profile. For instance, endo-glucanases/-xylanases (e.g., GH8, GH10, and GH16) were significantly expressed at 12 h, whereas exo-glucanases (e.g., GH6 and GH48) and alpha-arabinosidases/beta-xylosidases (e.g., GH43) were highly expressed at 48 h. Indeed, a significant peak of extracellular beta-xylosidase activity was observed at this stage. Moreover, we observed a higher expression of several CAZy families at 12-48 h, suggesting easy access to the main plant polysaccharides. Based on this evidence, we predicted that the highest level of collaboration between strains takes place at the initial stages of growth. Here, Paenibacillus, Brevundimonas, and Chryseobacterium were the most important contributors, whereas Stenotrophomonas was highly active at the end of the culture (96-192 h) without contributing to a large extent to the expression of lignocellulolytic enzymes. Our results contribute to the understanding of enzymatic and ecological mechanisms within PB-degrading microbial consortia, yielding new perspectives to improve the PB saccharification processes

Functional and phylogenetic characterization of bacteria in bovine rumen using fractionation of ruminal fluid

Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem

Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus <i>Amanita</i>

Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size, or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations

Draft genome sequences of three fungal-interactive <i>Paraburkholderia terrae</i> strains, BS007, BS110 and BS437

Here, we report the draft genome sequences of three fungal-interactive Paraburkholderia terrae strains, denoted BS110, BS007 and BS437. Phylogenetic analyses showed that the three strains belong to clade II of the genus Burkholderia , which was recently renamed Paraburkholderia . This novel genus primarily contains environmental species, encompassing non-pathogenic plant- as well as fungal-interactive species. The genome of strain BS007 consists of 11,025,273 bp, whereas those of strains BS110 and BS437 have 11,178,081 and 11,303,071 bp, respectively. Analyses of the three annotated genomes revealed the presence of (1) a large suite of substrate capture systems, and (2) a suite of genetic systems required for adaptation to microenvironments in soil and the mycosphere. Thus, genes encoding traits that potentially confer fungal interactivity were found, such as type 4 pili, type 1, 2, 3, 4 and 6 secretion systems, and biofilm formation (PGA, alginate and pel) and glycerol uptake systems. Furthermore, the three genomes also revealed the presence of a highly conserved five-gene cluster that had previously been shown to be upregulated upon contact with fungal hyphae. Moreover, a considerable number of prophage-like and CRISPR spacer sequences was found, next to genetic systems responsible for secondary metabolite production. Overall, the three P. terrae strains possess the genetic repertoire necessary for adaptation to diverse soil niches, including those influenced by soil fungi