Integrated miRNA and transcriptome profiling to explore the molecular determinism of convergent adaptation to corn in two lepidopteran pests of agriculture

Abstract Background The degree to which adaptation to same environment is determined by similar molecular mechanisms, is a topic of broad interest in evolutionary biology, as an indicator of evolutionary predictability. We wished to address if adaptation to the same host plant in phytophagous insects involved related gene expression patterns. We compared sRNA-Seq and RNA-Seq data between two pairs of taxa of Ostrinia and Spodoptera frugiperda sharing maize as host-plant. For the latter, we had previously carried out a reciprocal transplant experiment by feeding of the larvae of the Corn strain (Sf-C) and the Rice strain (Sf-R) on corn versus rice and characterized the mRNA and miRNA responses. Results First, we predicted the genes encoding miRNA in Ostrinia nubilalis (On) and O. scapulalis (Os). Respectively 67 and 65 known miRNA genes, as well as 196 and 190 novel ones were predicted with Os genome using sncRNAs extracted from whole larvae feeding on corn or mugwort. In On, a read counts analysis showed that 37 (55.22%) known miRNAs and 19 (9.84%) novel miRNAs were differentially expressed (DE) on mugwort compared to corn (in Os, 25 known miRs (38.46%) and 8 novel ones (4.34%)). Between species on corn, 8 (12.5%) known miRNAs and 8 (6.83%) novel ones were DE while only one novel miRNA showed expression variation between species on mugwort. Gene target prediction led to the identification of 2953 unique target genes in On and 2719 in Os, among which 11.6% (344) were DE when comparing species on corn. 1.8% (54) of On miR targets showed expression variation upon a change of host-plant. We found molecular changes matching convergent phenotype, i.e., a set of nine miRNAs that are regulated either according to the host-plant both in On and Sf-C or between them on the same plant, corn. Among DE miR target genes between taxa, 13.7% shared exactly the same annotation between the two pairs of taxa and had function related to insect host-plant interaction. Conclusion There is some similarity in underlying genetic mechanisms of convergent evolution of two distant Lepidopteran species having adopted corn in their host range, highlighting possible adaptation genes.

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Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

BioMed Research International ◽

10.1155/2016/3702789 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Liangbin Zeng ◽

Airong Shen ◽

Jia Chen ◽

Zhun Yan ◽

Touming Liu ◽

...

Keyword(s):

Protein Function ◽

Molecular Mechanisms ◽

Defense Mechanism ◽

Natural Fiber ◽

De Novo ◽

Average Length ◽

Expression Patterns ◽

Transcriptome Profiling ◽

Cdna Libraries ◽

Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

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Identification of the Q Gene Playing a Role in Spike Morphology Variation in Wheat Mutants and Its Regulatory Network

Frontiers in Plant Science ◽

10.3389/fpls.2021.807731 ◽

2022 ◽

Vol 12 ◽

Author(s):

Jiazi Zhang ◽

Hongchun Xiong ◽

Huijun Guo ◽

Yuting Li ◽

Xiaomei Xie ◽

...

Keyword(s):

Regulatory Network ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Patterns ◽

Spike Morphology ◽

Regulatory Pathways ◽

Dynamic Expression ◽

Spike Development ◽

Family Gene ◽

Q Gene

The wheat AP2 family gene Q controls domestication traits, including spike morphology and threshability, which are critical for the widespread cultivation and yield improvement of wheat. Although many studies have investigated the molecular mechanisms of the Q gene, its direct target genes, especially those controlling spike morphology, are not clear, and its regulatory pathways are not well established. In this study, we conducted gene mapping of a wheat speltoid spike mutant and found that a new allele of the Q gene with protein truncation played a role in spike morphology variation in the mutant. Dynamic expression levels of the Q gene throughout the spike development process suggested that the transcript abundances of the mutant were decreased at the W6 and W7 scales compared to those of the WT. We identified several mutation sites on the Q gene and showed that mutations in different domains resulted in distinct phenotypes. In addition, we found that the Q gene produced three transcripts via alternative splicing and that they exhibited differential expression patterns in nodes, internodes, flag leaves, and spikes. Finally, we identified several target genes directly downstream of Q, including TaGRF1-2D and TaMGD-6B, and proposed a possible regulatory network. This study uncovered the target genes of Q, and the results can help to clarify the mechanism of wheat spike morphology and thereby improve wheat grain yield.

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An experimental approach to understanding elevation limits in a montane terrestrial salamander, plethodon montanus

10.1101/131573 ◽

2017 ◽

Cited By ~ 1

Author(s):

Nicholas M. Caruso ◽

Jeremy F. Jacobs ◽

Leslie J. Rissler

Keyword(s):

Evolutionary Biology ◽

Abiotic Factors ◽

Transplant Experiment ◽

Biotic Factors ◽

Reciprocal Transplant Experiment ◽

Abiotic Environment ◽

Environmental Suitability ◽

Lower Elevation ◽

Survival And Growth ◽

Growth And Reproduction

AbstractUnderstanding the abiotic and biotic factors that determine the limits to species’ range is an essential goal in ecology, biogeography, evolutionary biology, and conservation biology. Moreover, predictions of shifts in species’ distributions under future changes in climate can be improved through understanding the spatial variation in survival, growth, and reproduction. A long-standing hypothesis postulates that, for Northern Hemisphere species, abiotic factors like temperature limit northern and/or higher elevation extents, while biotic factors like competition limit the southern and/or lower elevation range edges; though amphibians may not follow this general trend. Therefore, we combined environmental suitability models and a reciprocal transplant experiment across an elevational gradient to explore the role of the abiotic environment on the range limits of a montane salamander (Plethodon montanus). We first determined suitability of the abiotic environment for P. montanus, under current (1960 – 2000) and future (2050) climate scenarios. Second, we collected juveniles from each of three elevations and transplanted them within mesocosms such that each origin population was represented within each transplant location and vice-versa. We found that environmental suitability in 2050 decreased throughout the range compared to current predictions, especially at lower elevations. Additionally, we found that individuals’ starting body condition and transplant location were important predictors of survival, growth, and reproduction condition; importantly, individuals transplanted to low elevation had lower survival and growth rates compared to those moved to mid or high elevations. Our study provides experimental support that the abiotic environment limits the lower elevation distribution of P. montanus and, unfortunately, our results also paint a possible bleak future for this species and likely other montane terrestrial plethodontids. The abiotic environment, which will become increasingly limited under future changes in climate, was found to have more influence on survival and growth than population identity.

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Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe)

BMC Genomics ◽

10.1186/s12864-021-08273-y ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Haitao Xing ◽

Yuan Li ◽

Yun Ren ◽

Ying Zhao ◽

Xiaoli Wu ◽

...

Keyword(s):

Mirna Target ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Qrt Pcr ◽

Putative Target ◽

Genome Wide ◽

Ginger Rhizome ◽

Rhizome Development

Abstract Background MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. Results In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. Conclusion This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.

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Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during MT-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)

10.21203/rs.2.11289/v2 ◽

2019 ◽

Author(s):

Xiaochun Liu ◽

Xi Wu ◽

Yang Yang ◽

Chaoyue Zhong ◽

Yin Guo ◽

...

Keyword(s):

Germ Cells ◽

Cellular Localization ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Functional Characterization ◽

Transcriptome Profiling ◽

Sex Reversal ◽

Epinephelus Coioides ◽

Isolated Cells ◽

Male Germ Cells

Abstract Background: Spermatogenesis is an intricate process regulated by a finely organized network. The orange-spotted grouper (Epinephelus coioides) is a protogynous hermaphroditic fish, but the process of its spermatogenesis is not well-understood. In the present study, transcriptome sequencing of the male germ cells from orange-spotted grouper was performed to explore the molecular mechanisms underlying spermatogenesis. Results: In this study, the orange-spotted grouper was induced to change sex from female to male by 17alpha-methyltestosterone implantation. During the artificial spermatogenesis, different cell types from cysts containing spermatogonia, spermatocytes, spermatids, and spermatozoa were isolated by laser capture microdissection. Subsequently, transcriptomic analysis for the isolated cells were performed. A series of genes was used to verify and investigate the expression patterns in spermatogenesis. Furthermore, we also analyzed the expression of the same set of genes involved with steroid metabolism and sex throughout spermatogenesis (early-mid, late, and maturing stages) in the orange-spotted grouper. Several generally female-related genes took significantly changes in sex reversal hinted that the female-related genes in previously recognized may also play vital roles in spermatogenesis and sex reversal. In the transcriptomic data, we focused on zbtb family genes, which may be related to the process of spermatogenesis. Their expression patterns and cellular localization were examined, and the location of Eczbtb40 in different gonadal stages was investigated. We found that Eczbtb40 was expressed throughout spermatogenesis. These preliminary findings suggest that Eczbtb40 is highly conserved during vertebrate evolution and plays roles in spermatogenesis. Besides, the expression of Eczbtb40 and Eccyp17a1a overlapped in male germ cells, especially spermatogonium and spermatocyte, which suggested that Eczbtb40 might interact with Eccyp17a1a participant in spermatogenesis and sex reversal. Conclusions: The present study first depicted RNA sequencing of the male germ cells from orange-spotted grouper, and identified many important functional genes and pathways involved in spermatogenesis. The Eczbtb40 gene was subjected to molecular characterization and expression pattern analysis. These results will contribute to future studies of the molecular mechanism of spermatogenesis and sex reversal.

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Characterization of the microRNA Expression Profiles in the Goat Kid Liver

Frontiers in Genetics ◽

10.3389/fgene.2021.794157 ◽

2022 ◽

Vol 12 ◽

Author(s):

Xiaodong Zhao ◽

Zhibin Ji ◽

Rong Xuan ◽

Aili Wang ◽

Qing Li ◽

...

Keyword(s):

Differential Expression ◽

Fatty Acid Synthase ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Metabolic Process ◽

Liver Development ◽

Hormone Synthesis ◽

Liver Tissues

The liver is the largest digestive gland in goats with an important role in early metabolic function development. MicroRNAs (miRNA) are crucial for regulating the development and metabolism in the goat liver. In the study, we sequenced the miRNAs in the liver tissues of the goat kid to further research their regulation roles in early liver development. The liver tissues were procured at 5-time points from the Laiwu black goats of 1 day (D1), 2 weeks (W2), 4 weeks (W4), 8 weeks (W8), and 12 weeks (W12) after birth, respectively with five goats per time point, for a total of 25 goats. Our study identified 214 differential expression miRNAs, and the expression patterns of 15 randomly selected miRNAs were examined among all five age groups. The Gene ontology annotation results showed that differential expression miRNA (DE miRNA) target genes were significantly enriched in the fatty acid synthase activity, toxin metabolic process, cell surface, and antibiotic metabolic process. The KEGG analysis result was significantly enriched in steroid hormone synthesis and retinol metabolism pathways. Further miRNA-mRNA regulation network analysis reveals 9 differently expressed miRNA with important regulation roles. Overall, the DE miRNAs were mainly involved in liver development, lipid metabolism, toxin related metabolism-related biological process, and pathways. Our results provide new information about the molecular mechanisms and pathways in the goat kid liver development.

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Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs

Frontiers in Plant Science ◽

10.3389/fpls.2021.643137 ◽

2021 ◽

Vol 12 ◽

Author(s):

Anna V. Shchennikova ◽

Alexey V. Beletsky ◽

Mikhail A. Filyushin ◽

Maria A. Slugina ◽

Eugeny V. Gruzdev ◽

...

Keyword(s):

Evolutionary Biology ◽

Molecular Mechanisms ◽

Developmental Stages ◽

De Novo ◽

Transcriptome Profiling ◽

Mads Box ◽

Mads Box Genes ◽

Evolutionary Origins ◽

Novel Structure ◽

Genes Encoding

The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant Nepenthes ventricosa × Nepenthes alata. Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled de novo. In comparison with leaves, pitchers at all developmental stages were found to be highly enriched with upregulated genes involved in stress response, specification of shoot apical meristem, biosynthesis of sucrose, wax/cutin, anthocyanins, and alkaloids, genes encoding digestive enzymes (proteases and oligosaccharide hydrolases), and flowering-related MADS-box genes. At the same time, photosynthesis-related genes in pitchers were transcriptionally downregulated. As the MADS-box genes are thought to be associated with the origin of flower organs from leaves, we suggest that Nepenthes species could have employed a similar pathway involving highly conserved MADS-domain transcription factors to develop a novel structure, pitcher-like trap, for capture and digestion of animal prey during the evolutionary transition to carnivory. The data obtained should clarify the molecular mechanisms of trap initiation and development and may contribute to solving the problem of its emergence in plants.

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Inversion frequencies and phenotypic effects are modulated by the environment

10.1101/295568 ◽

2018 ◽

Cited By ~ 1

Author(s):

Emma Berdan ◽

Hanna Rosenquist ◽

Keith Larson ◽

Maren Wellenreuther

Keyword(s):

Body Size ◽

Evolutionary Biology ◽

Development Time ◽

Transplant Experiment ◽

Heterogeneous Environments ◽

Reciprocal Transplant Experiment ◽

Environment Effects ◽

Different Populations ◽

Natural Breeding ◽

Coelopa Frigida

AbstractUnderstanding how environmental variation drives phenotypic diversification within species is a major objective in evolutionary biology. The seaweed fly Coelopa frigida provides an excellent model for the study of genetically driven phenotypes because it carries an α/β inversion polymorphism that affects body size. Coelopa frigida inhabits highly variable beds of decomposing seaweed on the coast in Scandinavia thus providing a suitable test ground to investigate the genetic effects of substrate on both the frequency of the inversion (directional selection) and on the phenotype (genotype x environment effects). Here we use a reciprocal transplant experiment to test the effect of the α/β inversion on body size traits and development time across four suitable natural breeding substrates from the clinal distribution. We show that while development time is unaffected by GxE effects, both the frequency of the inversion and the relative phenotypic effects of the inversion on body size differ between population x substrate combinations. This indicates that the environment modulates the fitness as well as the phenotypic effects of the inversion karyotypes. It further suggests that the inversion may have accumulated qualitatively different mutations in different populations that interact with the environment. Together our results are consistent with the idea that the inversion in C. frigida likely evolves via a combination of local mutation, GxE effects, and differential fitness of inversion karyotypes in heterogeneous environments.

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Molecular and cytological analysis of widely-used Gal4 driver lines for Drosophila neurobiology

BMC Genetics ◽

10.1186/s12863-020-00895-7 ◽

2020 ◽

Vol 21 (S1) ◽

Author(s):

Anna A. Ogienko ◽

Evgeniya N. Andreyeva ◽

Evgeniya S. Omelina ◽

Anastasiya L. Oshchepkova ◽

Alexey V. Pindyurin

Keyword(s):

Molecular Mechanisms ◽

Target Genes ◽

Expression Patterns ◽

Cell Types ◽

Specific Cell ◽

Gal4 Driver ◽

Genomic Location ◽

Insertion Sites ◽

Convenient Model ◽

Gal4 Line

Abstract Background The Drosophila central nervous system (CNS) is a convenient model system for the study of the molecular mechanisms of conserved neurobiological processes. The manipulation of gene activity in specific cell types and subtypes of the Drosophila CNS is frequently achieved by employing the binary Gal4/UAS system. However, many Gal4 driver lines available from the Bloomington Drosophila Stock Center (BDSC) and commonly used in Drosophila neurobiology are still not well characterized. Among these are three lines with Gal4 driven by the elav promoter (BDSC #8760, #8765, and #458), one line with Gal4 driven by the repo promoter (BDSC #7415), and the 69B-Gal4 line (BDSC #1774). For most of these lines, the exact insertion sites of the transgenes and the detailed expression patterns of Gal4 are not known. This study is aimed at filling these gaps. Results We have mapped the genomic location of the Gal4-bearing P-elements carried by the BDSC lines #8760, #8765, #458, #7415, and #1774. In addition, for each of these lines, we have analyzed the Gal4-driven GFP expression pattern in the third instar larval CNS and eye-antennal imaginal discs. Localizations of the endogenous Elav and Repo proteins were used as markers of neuronal and glial cells, respectively. Conclusions We provide a mini-atlas of the spatial activity of Gal4 drivers that are widely used for the expression of UAS–target genes in the Drosophila CNS. The data will be helpful for planning experiments with these drivers and for the correct interpretation of the results.

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