Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots

Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species

GreenPhylDB v2.0: An improved database for plant functional genomics

Poster presented at 2009 Annual Research Meeting of the Generation Challenge Programme. Bamako (Mali), 20-23 September 200

CHANGE OF SPEED IN SIMULATED CROSS-COUNTRY SKI RACING: A KINEMATIC ANALYSIS

The purpose of the study was to identify the kinematic changes of the diagonal stride technique (DST) associated to a decrease of speed during a simulated cross-country ski race. Eight male cross-country skiers skied a 15 km course composed of 6 laps of 2.5 km. Full DST cycles were recorded using a digital camera for each lap. The fastest and slowest laps for each skier were selected, from which the following variables were studied: (i) cycle length and cycle frequency, (ii) propulsion length and duration, (iii) swing length and duration and (iv) trunk and knee angles. The skiing speed was significantly decreased between the first and the second part of the simulated race. The speed change was associated only with modification of the spatial components of the DST cycle (cycle and phase lengths, trunk and knee angles). The cycle durations remained constant. It was concluded that the decrease of speed resulted from a deterioration of the technique reducing the application of propulsion forces

Using genotyping-by-sequencing to understand Musa diversity

Poster presented at Plant and Animal Genome, PAG XXII. San Diego (USA), 11-15 Jan 201

Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and preflowering growth stages

Open Access Journal; Published online: 15 March 2019Bananas (Musa spp.) are consumed worldwide as dessert and cooking types. Edible banana varieties are for the most part seedless and sterile and therefore vegetatively propagated. This confers difficulties for breeding approaches against pressing biotic and abiotic threats and for the nutritional enhancement of banana pulp. A panel of banana accessions, representative of the diversity of wild and cultivated bananas, was analysed to assess the range of chemotypes available globally. The focus of this assessment was banana leaves at two growth stages (juvenile and pre-flowering), to see when during the plant growth metabolic differences can be established. The metabolic data corresponded to genomic trends reported in previous studies and demonstrated a link between metabolites/pathways and the genomes of M. acuminata and M. balbisiana. Furthermore, the vigour and resistance traits of M. balbisiana was connected to the phenolic composition and showed differences with the number of B genes in the hybrid accessions. Differences in the juvenile and pre-flowering data led to low correlation between the growth stages for prediction purposes

The gliding phase in swimming: the effect of water depth

Aiming to achieve higher performances, swimmers should maximize each component of swimming races. During starts and turns, the gliding phase represents a determinant part of these race components. Thus, the depth position allowing minimizing the hydrodynamic drag force represents an important concern in swimming research. The aim of this study was to analyse the effect of depth on drag during the underwater gliding, using computational fluid dynamic

How do roots respond to osmotic stress? A transcriptomic approach to address this question in a non-model crop

Drought is a complex phenomenon that is relevant for many crops. Performing high-throughput transcriptomics in non-model crops is challenging. The non-model crop where our workflow has been tested on is banana (Musa spp.), which ranks among the top ten staple foods (total production over 145 million tons in 2013 (FAOstat)[1]). Bananas need vast amounts of water and even mild-drought conditions are responsible for considerable yield losses[2]. To characterize drought in the roots of different banana genotypes, we designed a lab model based on osmotic stress (5% PEG treatment for 3 days) and performed mRNA-seq analysis[3]. Using Illumina technology, 18 cDNA libraries were sequenced producing around 568 million high quality reads, of which 70-84% were mapped to the diploid reference genome[4]. We show that the applied stress leads to a drop in energy levels inducing a metabolic shift towards (i) higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. We also analyzed the expression patterns of paralogous genes belonging to the same gene families and detected possible cases of sub-functionalization

Diversity of tfdC genes: distribution and polymorphism among 2,4-dichlorophenoxyacetic acid degrading soil bacteria

The aim of the present work was to study the occurrence, distribution and diversity of 1,2-dichlorocatechol dioxygenase genes among 2,4-dichlorophenoxyacetic acid degrading bacteria. Phylogenetic relationships between the 31 strains or isolates were evaluated by amplified ribosomal DNA restriction analysis of the 16S rDNA gene. All the strains could be assigned to the beta or gamma subdivisions of the Proteobacteria. tfdC genes were detected by PCR amplification using degenerated primers. Two specific probes were produced from Ralstonia eutropha strain JMP134 and from a soil isolate strain PLAE6 which was grouped with Variovorax paradoxus. Sequence analysis of the probes revealed that they were homologous to the tfdC genes of JMP134 located on plasmid pJP4 and to the tfdC gene of Pseudomonas putida strain PaW85 located on plasmid pEST4011, The localization and the copy number of tfdC genes were determined by hybridization of plasmid profiles and genomic DNA restriction fragment length polymorphism profiles with the two probes. Most of the strains were found to bear tfdC genes on plasmids ranging from 78 to 532 kb; two strains without any plasmids were also found to hybridize with the probes, revealing a chromosomal localization of catabolic genes. Sequence analysis of the PCR products from different strains confirmed that four different classes of chlorocatechol 1,2-dioxygenase genes were present in the strains and isolates studied