Exploring the GRAS gene family in common bean (Phaseolus vulgaris L.): characterization, evolutionary relationships, and expression analyses in response to abiotic stresses.

MAIN CONCLUSION: Genome-wide identification reveals 55 PvuGRAS genes belonging to 16 subfamilies and their gene structures and evolutionary relationships were characterized. Expression analyses highlight their prominence in plant growth, development and abiotic stress responses. GRAS proteins comprise a plant-specific transcription factor family involved in multiple growth regulatory pathways and environmental cues including abiotic/biotic stresses. Despite its crucial importance, characterization of this gene family is still elusive in common bean. A systematic genome-wide scan identified 55 PvuGRAS genes unevenly anchored to the 11 common bean chromosomes. Segmental duplication appeared to be the key driving force behind expansion of this gene family that underwent purifying selection during evolution. Computational investigation unraveled their intronless organization and identified similar motif composition within the same subfamily. Phylogenetic analyses clustered the PvuGRAS proteins into 16 phylogenetic clades and established extensive orthologous relationships with Arabidopsis and rice. Analysis of the upstream promoter region uncovered cis-elements responsive to growth, development, and abiotic stresses that may account for their differential expression. The identified SSRs could serve as putative molecular markers facilitating future breeding programs. 37 PvuGRAS transcripts were post-transcriptionally regulated by different miRNA families, miR171 being the major player preferentially targeting members of the HAM subfamily. Global expression profile based on RNA-seq data indicates a clade specific expression pattern in various tissues and developmental stages. Additionally, nine PvuGRAS genes were chosen for further qPCR analyses under drought, salt, and cold stress suggesting their involvement in acclimation to environmental stimuli. Combined, the present results significantly contribute to the current understanding of the complexity and biological function of the PvuGRAS gene family. The resources generated will provide a solid foundation in future endeavors for genetic improvement in common bean.

Patterns of morphological traits shaping the feeding guilds in the intertidal mudflat fishes of the Indian Sundarbans.

Broad-scale patterns of resource utilization and the corresponding morphological evolution is a result of an integral relationship among form and function. In addition, there is also an inherent role of the latter in determining species co-interaction and assemblage pattern that forms an integral aspect of ecological research. The present study aimed to evaluate the ecomorphological relationship among 37 fish species inhabiting the intertidal mudflats of the Indian Sundarbans by outlining the following objectives: (i) identifying and characterizing feeding guilds/groups and (ii) understanding the inter-relationship between morphometry with (a) the established feeding guild classifications and (b) observed prey taxa (that characterizes these feeding groups) for determining the role of morphometry in prey acquisition followed by (iii) the evaluation of their potential phylogenetic convergence among the species. For the first objective, two approaches for feeding guild classification were made (3-Guild and 8-Guild) for assessing the prediction accuracy of morphological characters in identifying the different guilds. While the former was based on troph values, the latter classification mode relied on the similarities in diet composition among the different fish species. For addressing the second objective, we employed two different models namely, linear discriminant (LDA) and redundancy analysis (RDA). While the LDA model tested the prediction accuracy of morphological traits in classifying the different feeding guilds, RDA was applied to model the correlation between the morphological traits and the prey categories. In the LDA model, morphological characters showed higher accuracy (78.4%) in classifying three feeding groups rather than eight feeding groups (73%). Following this, the RDA model (explaining 79.78% of constrained variance) showed gill raker intensity, protrusion length, head depth, caudal peduncle, eye diameter and inter-orbital distance to be highly associated with selection of specific prey types by species, thereby characterizing a particular feeding guild. However, generalized linear models testing for correlation between troph value and feeding groups showed substantial variation (90.35%) in the dietary index being explained by the 8-Guild classification. Hence, our study maintains the assumption that broad morphological differentiation acts as one of the underlying processes resulting in dietary variations that results in the varying modes of resource utilization by the coexisting species, thereby determining the structure of a trophic guild. Furthermore, it also suggests that in terms of prey abundance or selectivity, the 8-Guild model is much more conducive in representing the feeding habits of the species while the morphological traits reflected a relatively broader scheme of classification, (i.e., 3-Guild model) with certain traits being phylogenetically conserved within these groups.