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Bendena, W.

Publications and source records attributed to Bendena, W..

3 recordsLinked to original sources

Chromosomal-level reference genome and microRNAs of the ricefield flatsedge Cyperus iria

BackgroundGrass-like plants in the Cyperaceae family, commonly known as sedges, have a global distribution and include many economically problematic weeds. The ricefield flatsedge, Cyperus iria, is an aggressive weed in rice crops in Asia. ResultHere, we present a chromosomal-level genome assembly for C. iria (461.2 Mb, scaffold N50 = 7.3 Mbp, 99.6% BUSCO score) providing potential targets for the control of this devastating weed. Based on the genome assembly and transcriptomes of vegetative tissues, 52,574 protein-coding genes were predicted to be encoded. A total of 26 conserved and 75 novel microRNAs, including 9 microRNA clusters, were also annotated. Synteny and microRNA cluster analyses further showed that C. iria had undergone at least one round of whole genome duplication. ConclusionThe genomic resource established in this study sets up a foundation to further address basic and applied questions in the Cyperaceae.

genomics↗

Insect metamorphosis is regulated differently between sexes by members of a microRNA cluster

Insects comprise the majority of all described animal species and dominate the terrestrial habitats. The evolution of insect metamorphosis played a profound role in their successful adaptation and radiation. Insect metamorphosis is dependent on hormones ecdysteroids and sesquiterpenoids such as juvenile hormone. Despite the fact there are genuine differences between sexes during insect metamorphosis which facilitate their successful mating, how such sexual dimorphism in metamorphosis is being controlled is poorly known. We first generated transcriptomic profiles of male and female flies in late larvae and early pupae stages. Using a combination of genome-wide prediction and in vitro dual-luciferase validations, members of a microRNA cluster miR-277/34 were found to potentially regulate the neuropeptide receptor (AstC-R1) that when activated inhibits the sesquiterpenoid pathway and a juvenile hormone-dependent transcription factor (Kr-h1) in fly Drosophila melanogaster. Loss-of-function mutants were created deleting either miR-277 or miR-34, and expression levels of both AstC-R1 and Kr-h1 as well as ecdysteroid and sesquiterpenoid hormone titres were altered. Further comparison of transcriptomes of the late larvae and early pupae of both sexes revealed differential gene pathways being regulated by members of miR-277/34 between sexes during metamorphosis. This study highlights how members of a microRNA cluster control hormonal and developmental gene pathways in different sexes of insects during metamorphosis.

evolutionary biology↗

A functional study of all 40 C. elegans insulin-like peptides

The human genome encodes ten insulin-like genes, whereas the C. elegans genome remarkably encodes forty insulin-like genes. The roles of insulin/insulin-like peptide ligands (INS) in C. elegans are not well understood. The functional redundancy of the forty INS genes makes it challenging to address their functions by using knock out strategies. Here, we individually overexpressed each of the forty ins genes pan-neuronally, and monitored multiple phenotypes including: L1 arrest life span, neuroblast divisions under L1 arrest, dauer formation and fat accumulation, as readouts to characterize the functions of each INS in vivo. Of the 40 INS peptides, we found functions for 35 INS peptides and functionally categorized each as agonists, antagonists or of pleiotropic function. In particular, we found that 9 of 16 agonistic INS peptides shortened L1 arrest life span and promoted neuroblast divisions during L1 arrest. Our study revealed that a subset of {beta}-class INS peptides that contain a distinct F peptide sequence are agonists. Our work is the first to categorize the structures of INS peptides and relate these structures to the functions of all forty INS peptides in vivo. Our findings will promote the study of insulin function on development, metabolism, and aging-related diseases.\n\nAuthor SummaryInsulin and insulin-like growth factors are found in all animals and regulate many physiological and developmental processes. The human genome has 10 insulin-like peptides including the well characterized insulin hormone. The nematode C. elegans has 40 insulin-like (INS) peptide genes. All 40 INS peptides have been knocked out but no single INS gene knock out resembles the loss of the C. elegans insulin receptor suggesting that the other INS peptides can compensate when one INS is lost. We have used a genetic approach to overexpress each of the 40 INS peptides in C. elegans and have identified in vivo function for 35 of the 40 INS peptides. Like the human insulin and IGF-1, C. elegans INS peptides are derived from a precursor protein and we have shown that INS peptides with an associated peptide called the F peptide are strong activators of the C. elegans insulin-like receptor. We also identified several INS peptides that inhibit the insulin-like receptor and these inhibitory INS peptides may have therapeutic potential.

genetics↗