Biology subjects

Tobe, S. S.

Publications and source records attributed to Tobe, S. S..

6 recordsLinked to original sources

bioRxiv2024

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↗

bioRxiv2024

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↗

bioRxiv2024

Response of protein coding genes and microRNAs to temperature changes in four insect species

Insects are the most abundant described living creatures in the world, and they play important roles in our global ecosystem. Climate change affects global biodiversity, and researchers in many fields are striving to better understand the impact of the climate crisis. One such endeavour is the study of temperature-dependent effects on insects. At present, we know little of how climate affects gene expression in insects of different sexes. Here, we took four species of fruit flies of the genus Drosophila (D. melanogaster, D. virilis, D. pseudoobscura, and D. erecta), and subjected the male and female flies of each species to three different temperatures to test their sex-specific gene expression responses. A total of 144 transcriptomic profiles of protein-coding genes and microRNAs were generated. We found that, at the same temperature, there were more male-biased than female-biased protein-coding genes and microRNAs in all four investigated drosophilid species. Interestingly, upon temperature changes, there were more differentially expressed protein-coding genes in females than in males in all four investigated species, while the microRNAs were highly species- and sex-specific. This study provides the first evidence that sex-biased protein-coding gene and microRNA expression responses to temperature change differ between insect species within the same genus, and demonstrates the complexity of sex-specific responses of insects to climate change. HighlightsO_LIAt the same temperature, protein coding gene and microRNA expression showed a greater bias towards males than towards females in all four tested insect species. C_LIO_LIIn response to increasing temperature, females of all 4 tested species exhibited more differentially expressed genes than did males, and enrichment analyses showed that they are species-specific. C_LIO_LIDifferentially expressed microRNAs did not show a conserved trend between insects upon temperature changes. C_LIO_LISex-specific gene and microRNA expression of insects in response to climate change evidently involves a complex adaptation mechanism. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/591511v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1037b18org.highwire.dtl.DTLVardef@18683f3org.highwire.dtl.DTLVardef@40dee5org.highwire.dtl.DTLVardef@e9a108_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond

Insects provide an unparalleled opportunity to link genomic changes with the rise of novel phenotypes, given tremendous variation in the numerous and complex adaptations displayed across the group. Among these numerous and complex adaptations, live-birth has arisen repeatedly and independently in insects and across the tree of life, suggesting this is one of the most common types of convergent evolution among animals. We sequenced the genome and transcriptome of the Pacific beetle-mimic cockroach, the only truly viviparous cockroach, and performed comparative analyses including two other viviparous insect lineages, the tsetse and aphids, to unravel the genomic basis underlying the transition to viviparity in insects. We identified pathways experiencing adaptive evolution, common in all viviparous insects surveyed, involved in uro-genital remodeling, maternal control of embryo development, tracheal system, and heart development. Our findings suggest the essential role of those pathways for the development of placenta-like structure enabling embryo development and nutrition. Viviparous transition seems also to be accompanied by the duplication of genes involved in eggshell formation. Our findings from the viviparous cockroach and tsetse reveal that genes involved in uterine remodeling are up-regulated and immune genes are down-regulated during the course of pregnancy. These changes may facilitate structural changes to accommodate developing young and protect them from the mothers immune system. Our results denote a convergent evolution of live-bearing in insects and suggest similar adaptive mechanisms occurred in vertebrates, targeting pathways involved in eggshell formation, uro-genital remodeling, enhanced tracheal and heart development, and reduced immunity.

genomics↗

bioRxiv2020

Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication

Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7Gb, N50 = 90.2Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7Gb, N50 = 109.7Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD, and that these WGD events are shared with spiders. Comparison of the genomes of C. rotundicauda and T. tridentatus populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for a better understanding of the consequences of invertebrate WGD events on evolutionary fates of genes and microRNAs at individual and population levels, and highlights the genetic diversity with practical values for breeding programs and conservation of horseshoe crabs.

evolutionary biology↗

bioRxiv2019

Varying constraints impact the miR-6/5/4/286/3/309 microRNA cluster in Drosophila leg development

A striking feature of microRNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a microRNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this microRNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of microRNA cluster members were also constructed. Expression of individual microRNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient microRNAs together (miR-5/4/286/3/309) or more recently evolved clustered microRNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed down-regulation of leg patterning gene cassettes in generation of the leg-shortening phenotype. Furthermore, cell transfection with different combinations of microRNA cluster members revealed a suite of downstream genes targeted by all cluster members, as well as complements of targets that are unique for distinct microRNAs. Considering together the microRNA targets and the evolutionary ages of each microRNA in the cluster demonstrates the importance of microRNA clustering, where new members can reinforce and modify the selection forces on both the cluster regulation and the gene regulatory network of existing microRNAs.

evolutionary biology↗