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Ma D, Lai Z, Ding Q, Zhang K, Chang K, Li S, Zhao Z, Zhong F. Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:872137. [PMID: 35599909 PMCID: PMC9114813 DOI: 10.3389/fpls.2022.872137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.
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Affiliation(s)
- Dongna Ma
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Zhengfeng Lai
- Subtropical Agricultural Research Institute, Fujian Academy of Agriculture Sciences, Fujian, China
| | - Qiansu Ding
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Kun Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Kaizhen Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Zhizhu Zhao
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
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Ma D, Ding Q, Guo Z, Zhao Z, Wei L, Li Y, Song S, Zheng HL. Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum. Mol Genet Genomics 2021; 296:1235-1247. [PMID: 34363105 DOI: 10.1007/s00438-021-01810-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/22/2021] [Indexed: 11/25/2022]
Abstract
Lineage-specific genes (LSGs) are the genes that have no recognizable homology to any sequences in other species, which are important drivers for the generation of new functions, phenotypic changes, and facilitating species adaptation to environment. Aegiceras corniculatum is one of major mangrove plant species adapted to waterlogging and saline conditions, and the exploration of aegiceras-specific genes (ASGs) is important to reveal its adaptation to the harsh environment. Here, we performed a systematic analysis on ASGs, focusing on their sequence characterization, origination and expression patterns. Our results reveal that there are 4823 ASGs in the genome, approximately 11.84% of all protein-coding genes. High proportion (45.78%) of ASGs originate from gene duplication, and the time of gene duplication of ASGs is consistent with the timing of two genome-wide replication (WGD) events that occurred in A. corniculatum, and also coincides with a short period of global warming during the Paleocene-Eocene Maximum (PETM, 55.5 million years ago). Gene structure analysis showed that ASGs have shorter protein lengths, fewer exons, and higher isoelectric point. Expression patterns analysis showed that ASGs had low levels of expression and more tissue-specific expression. Weighted gene co-expression network analysis (WGCNA) revealed that 86 ASGs co-expressed gene modules were primarily involved in pathways related to adversity stress, including plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, peroxisome and pentose phosphate pathway. This study provides a comprehensive analysis of the characteristics and potential functions of ASGs and identifies key candidate genes, which will contribute to the subsequent further investigation of the adaptation of A. corniculatum to intertidal coastal wetland habitats.
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Affiliation(s)
- Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Qiansu Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Zejun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Zhizhu Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Liufeng Wei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Yiying Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shiwei Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China.
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Thümecke S, Schröder R. The odd-skipped related gene drumstick is required for leg development in the beetle Tribolium castaneum. Dev Dyn 2021; 251:1456-1471. [PMID: 33871128 DOI: 10.1002/dvdy.347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The evolutionarily conserved odd-skipped related genes odd-skipped (odd), drumstick (drm), sister of odd and bowel (sob), and brother-of-odd-with-entrails-limited (bwl) act downstream of the Notch pathway in various insect tissues including the appendages and the gut. While the function of some of these genes have been analyzed in the adult Tribolium beetle, the expression during and their requirement for embryonic development is not known. RESULTS We describe here the embryonic expression patterns of drm, sob, and bwl and analyze the RNAi knockdown phenotypes with emphasize on the appendages and the hindgut. We show that in Tribolium, drm acts independently of other odd-family members in the formation of legs, hindgut, and the dorsal epidermis. Moreover, we establish drm and sob as further markers for segment borders in the appendages that include the gnathobasic mandibles. CONCLUSIONS We conclude that the regulatory interrelationship among the odd genes differs between Tribolium and Drosophila, where odd and drm seem to act redundantly. In Tribolium, the genes drm and sob uncover the relict of a precoxal joint incorporated in the lateral body wall.
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Affiliation(s)
- Susanne Thümecke
- Institut für Insektenbiotechnologie, Universität Gießen, Gießen, Germany.,Institut für Biowissenschaften, Universität Rostock, Rostock, Germany
| | - Reinhard Schröder
- Institut für Biowissenschaften, Universität Rostock, Rostock, Germany
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Alshukri B, Astarita F, Al‐Esawy M, El Halim HMESA, Pennacchio F, Gatehouse AMR, Edwards MG. Targeting the potassium ion channel genes SK and SH as a novel approach for control of insect pests: efficacy and biosafety. PEST MANAGEMENT SCIENCE 2019; 75:2505-2516. [PMID: 31207012 PMCID: PMC6771844 DOI: 10.1002/ps.5516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Potassium ion channels play a critical role in the generation of electrical signals and thus provide potential targets for control of insect pests by RNA interference. RESULTS Genes encoding the small conductance calcium-activated potassium channel (SK) and the voltage-gated potassium channel (SH) were knocked down in Tribolium castaneum by injection and oral delivery of dsRNA (dsTcSK and dsTcSH, respectively). Irrespective of the delivery mechanism a dose-dependent effect was observed for knockdown (KD) of gene expression and insect mortality for both genes. Larvae fed a 400 ng dsRNA mg-1 diet showed significant gene (P < 0.05) knockdown (98% and 83%) for SK and SH, respectively, with corresponding mortalities of 100% and 98% after 7 days. When injected (248.4 ng larva-1 ), gene KD was 99% and 98% for SK and SH, causing 100% and 73.4% mortality, respectively. All developmental stages tested (larvae, early- and late-stage pupae and adults) showed an RNAi-sensitive response for both genes. LC50 values were lower for SK than SH, irrespective of delivery method, demonstrating that the knockdown of SK had a greater effect on larval mortality. Biosafety studies using adult honeybee Apis mellifera showed that there were no significant differences either in expression levels or mortality of honeybees orally dosed with dsTcSK and dsTcSH compared to control-fed bees. Similarly, there was no significant difference in the titre of deformed wing virus, used as a measure of immune suppression, between experimental and control bees. CONCLUSION This study demonstrates the potential of using RNAi targeting neural receptors as a technology for the control of T. castaneum. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Baida Alshukri
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Federica Astarita
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle‐upon‐TyneUK
- Department of Agricultural Sciences, Laboratory of Entomology “E. Tremblay”University of Napoli “Federico II”PorticiItaly
| | - Mushtaq Al‐Esawy
- Institute of Neuroscience, Newcastle UniversityNewcastle‐upon‐TyneUK
- Department of Plant ProtectionUniversity of KufaIraq
| | - Hesham Mohamed El Sayed Abd El Halim
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle‐upon‐TyneUK
- Entomology Department, Faculty of ScienceBenha UniversityBenhaEgypt
| | - Francesco Pennacchio
- Department of Agricultural Sciences, Laboratory of Entomology “E. Tremblay”University of Napoli “Federico II”PorticiItaly
| | | | - Martin Gethin Edwards
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle‐upon‐TyneUK
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UTR-specific knockdown of Distal-less and Sp8 leads to new phenotypic variants in the flour beetle Tribolium. Dev Genes Evol 2018; 228:163-170. [PMID: 29855703 DOI: 10.1007/s00427-018-0614-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/08/2018] [Indexed: 10/14/2022]
Abstract
RNA interference (RNAi)-mediated knockdown serves as an effective technique for the functional analysis of developmental genes that is well established in many organisms. In the beetle Tribolium castaneum, double-stranded RNA is applied by simple injection and distributes systemically within the tissue. Thus, systematic testing for RNAi specificity and efficiency is easily possible in this organism. Generally, the use of non-overlapping dsRNA fragments yielding qualitatively identical phenotypes is the method of choice to verify target-specific knockdown effects. Here, we show that UTR-specific RNAi results in different effects regarding quality, severity and penetrance when compared to RNAi fragments directed at the coding region. Furthermore, when using 3'UTR-specific dsRNA, we first describe the Distal-lessRNAi antenna-to-leg transformation phenotype in the Tribolium larva, which has only been observed in the adult beetle and Drosophila so far. In addition, we unexpectedly observed sterility effects caused by 3'UTR-specific knockdown of the Tribolium-Sp8 orthologue that is not seen when dsRNA targeted a sequence within the coding-region or the 5'UTR that itself led to early embryonic lethality. We conclude that targeting UTR sequences by region-specific RNAi can reveal unexpected new aspects of gene function applicable in basic research and crop protection.
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