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Wang H, Umer MJ, Liu F, Cai X, Zheng J, Xu Y, Hou Y, Zhou Z. Genome-Wide Identification and Characterization of CPR5 Genes in Gossypium Reveals Their Potential Role in Trichome Development. Front Genet 2022; 13:921096. [PMID: 35754813 PMCID: PMC9213653 DOI: 10.3389/fgene.2022.921096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.
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Affiliation(s)
- Heng Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Jie Zheng
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China.,Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
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Zheng H, Wang S, Wu Y, Zou S, Dietemann V, Neumann P, Chen Y, Li-Byarlay H, Pirk C, Evans J, Hu F, Feng Y. Genomic signatures underlying the oogenesis of the ectoparasitic mite Varroa destructor on its new host Apis mellifera. J Adv Res 2022; 44:1-11. [PMID: 36725182 PMCID: PMC9936524 DOI: 10.1016/j.jare.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Host shift of parasites may have devastating effects on the novel hosts. One remarkable example is that of the ectoparasitic mite Varroa destructor, which has shifted its host from Eastern honey bees (Apis cerana) to Western honey bees (Apis mellifera) and posed a global threat to apiculture. OBJECTIVES To identify the genetic factors underlying the reproduction of host-shifted V. destructor on the new host. METHODS Genome sequencing was conducted to construct the phylogeny of the host-shifted and non-shifted mites and to screen for genomic signatures that differentiated them. Artificial infestation experiment was conducted to compare the reproductive difference between the mites, and transcriptome sequencing was conducted to find differentially expressed genes (DEGs) during the reproduction process. RESULTS The host-shifted and non-shifted V. destructor mites constituted two genetically distinct lineages, with 15,362 high-FST SNPs identified between them. Oogenesis was upregulated in host-shifted mites on the new host A. mellifera relative to non-shifted mites. The transcriptomes of the host-shifted and non-shifted mites differed significantly as early as 1h post-infestation. The DEGs were associated with nine genes carrying nonsynonymous high-FST SNPs, including mGluR2-like, Lamb2-like and Vitellogenin 6-like, which were also differentially expressed, and eIF4G, CG5800, Dap160 and Sas10, which were located in the center of the networks regulating the DEGs based on protein-protein interaction analysis. CONCLUSIONS The annotated functions of these genes were all associated with oogenesis. These genes appear to be the key genetic determinants of the oogenesis of host-shifted mites on the new host. Further study of these candidate genes will help elucidate the key mechanism underlying the success of host shifts of V. destructor.
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Affiliation(s)
- Huoqing Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Shuai Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yuqi Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Shengmei Zou
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Vincent Dietemann
- Swiss Bee Research Center, Agroscope, Bern, Switzerland; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Peter Neumann
- Swiss Bee Research Center, Agroscope, Bern, Switzerland; Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Yanping Chen
- USDA-ARS Bee Research Laboratory, Beltsville, MD, USA
| | - Hongmei Li-Byarlay
- Agricultural Research and Development Program, Central State University, Wilberforce, OH 45384, USA; Department of Agricultural and Life Science, Central State University, Wilberforce, OH 45384, USA
| | - Christian Pirk
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Jay Evans
- USDA-ARS Bee Research Laboratory, Beltsville, MD, USA
| | - Fuliang Hu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
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Kaseb MO, Umer MJ, Anees M, Zhu H, Zhao S, Lu X, He N, El-Remaly E, El-Eslamboly A, Yousef AF, Salama EAA, Alrefaei AF, Kalaji HM, Liu W. Transcriptome Profiling to Dissect the Role of Genome Duplication on Graft Compatibility Mechanisms in Watermelon. BIOLOGY 2022; 11:575. [PMID: 35453774 PMCID: PMC9029962 DOI: 10.3390/biology11040575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Watermelon (Citrullus lanatus) is a popular crop worldwide. Compared to diploid seeded watermelon, triploid seedless watermelon cultivars are in great demand. Grafting in triploid and tetraploid watermelon produces few seedlings. To learn more about how genome duplication affects graft compatibility, we compared the transcriptomes of tetraploid and diploid watermelons grafted on squash rootstock using a splicing technique. WGCNA was used to compare the expression of differentially expressed genes (DEGs) between diploid and tetraploid watermelon grafted seedlings at 0, 3, and 15 days after grafting (DAG). Only four gene networks/modules correlated significantly with phenotypic characteristics. We found 11 genes implicated in hormone, AOX, and starch metabolism in these modules based on intramodular significance and RT-qPCR. Among these genes, two were linked with IAA (r2 = 0.81), one with ZR (r2 = 0.85) and one with POD (r2 = 0.74). In the MElightsteelblue1 module, Cla97C11G224830 gene was linked with CAT (r2 = 0.81). Two genes from the MEivory module, Cla97C07G139710 and Cla97C04G077300, were highly linked with SOD (r2 = 0.72). Cla97C01G023850 and Cla97C01G006680 from the MEdarkolivegreen module were associated with sugars and starch (r2 = 0.87). Tetraploid grafted seedlings had higher survival rates and hormone, AOX, sugar, and starch levels than diploids. We believe that compatibility is a complicated issue that requires further molecular research. We found that genome duplication dramatically altered gene expression in the grafted plants' IAA and ZR signal transduction pathways and AOX biosynthesis pathways, regulating hormone levels and improving plant survival.
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Affiliation(s)
- Mohamed Omar Kaseb
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
- Cross Pollenated Plants Department, Horticulture Research Institute, Agriculture Research Center, Giza 12119, Egypt; (E.E.-R.); (A.E.-E.)
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Muhammad Anees
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Eman El-Remaly
- Cross Pollenated Plants Department, Horticulture Research Institute, Agriculture Research Center, Giza 12119, Egypt; (E.E.-R.); (A.E.-E.)
| | - Ahmed El-Eslamboly
- Cross Pollenated Plants Department, Horticulture Research Institute, Agriculture Research Center, Giza 12119, Egypt; (E.E.-R.); (A.E.-E.)
| | - Ahmed F. Yousef
- Department of Horticulture, College of Agriculture, Al-Azhar University (Branch Assiut), Assiut 71524, Egypt;
| | - Ehab A. A. Salama
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt;
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 1145, Saudi Arabia;
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, 02-787 Warsaw, Poland;
- Institute of Technology and Life Sciences–National Research Institute (ITP), 05-090 Raszyn, Poland
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
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Liu L, Zheng Y, Feng S, Yu L, Li Y, Zong Y, Chen W, Liao F, Yang L, Guo W. Transcriptomic and Physiological Analysis Reveals the Responses to Auxin and Abscisic Acid Accumulation During Vaccinium corymbosum Flower Bud and Fruit Development. FRONTIERS IN PLANT SCIENCE 2022; 13:818233. [PMID: 35242154 PMCID: PMC8886112 DOI: 10.3389/fpls.2022.818233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Blueberry (Vaccinium corymbosum) is reputed as a rich source of health-promoting phytonutrients, which contributes to its burgeoning consumer demand and production. However, blueberries are much smaller and have lower yields than most domesticated berries, and the inherent regulatory mechanisms remain elusive. In this study, the cytological and physiological changes, as well as comparative transcriptomic analysis throughout flower and fruit development in the southern highbush blueberry cultivar 'O'Neal' were performed. 'O'Neal' hypanthium and fruit exhibited a distinctive cell proliferation pattern, and auxin accumulation was unusual throughout development, while abscisic acid (ABA) levels rapidly increased in association with anthocyanin accumulation, total phenolic reduction and fruit maturation. Transcriptomic data showed that many differentially expressed genes (DEGs) were specifically expressed at each flower bud and fruit developmental stage. Further weighted gene co-expression network analysis (WGCNA) revealed numerous DEGs that correlated with the cell numbers of outer mesocarp and columella, showed two distinctive expression patterns. Most of the DEGs involved in auxin biosynthesis, transportation and signal transduction were upregulated, and this upregulation was accompanied by cell expansion, and flower bud and fruit development. However, individual members of VcSAUR50 and VcIAA9 families might be insensitive to auxin, suggesting that these genes play a distinctive role in the growth and development of blueberry fruits. These results will support future research to better understand the flower and fruit development of southern highbush blueberry.
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Affiliation(s)
- Liangmiao Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
| | - Yiqi Zheng
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
| | - Shiji Feng
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
| | - Lei Yu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
| | - Yongqiang Li
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Yu Zong
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Wenrong Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Fanglei Liao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Li Yang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
| | - Weidong Guo
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Zhejiang, China
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5
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Anees M, Gao L, Umer MJ, Yuan P, Zhu H, Lu X, He N, Gong C, Kaseb MO, Zhao S, Liu W. Identification of Key Gene Networks Associated With Cell Wall Components Leading to Flesh Firmness in Watermelon. FRONTIERS IN PLANT SCIENCE 2021; 12:630243. [PMID: 34239519 PMCID: PMC8259604 DOI: 10.3389/fpls.2021.630243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/20/2021] [Indexed: 05/15/2023]
Abstract
Flesh firmness of watermelon is an important quality trait for commercial fruit values, including fruit storability, transportability, and shelf life. To date, knowledge of the gene networks underlying this trait is still limited. Herein, we used weighted genes co-expression network analysis (WGCNA) based on correlation and the association of phenotypic data (cell wall contents) with significantly differentially expressed genes between two materials, a near isogeneic line "HWF" (with high average flesh firmness) and inbred line "203Z" (with low average flesh firmness), to identify the gene networks responsible for changes in fruit flesh firmness. We identified three gene modules harboring 354 genes; these gene modules demonstrated significant correlation with water-soluble pectin, cellulose, hemicellulose, and protopectin. Based on intramodular significance, eight genes involved in cell wall biosynthesis and ethylene pathway are identified as hub genes within these modules. Among these genes, two genes, Cla012351 (Cellulose synthase) and Cla004251 (Pectinesterase), were significantly correlated with cellulose (r 2 = 0.83) and protopectin (r 2 = 0.81); three genes, Cla004120 (ERF1), Cla009966 (Cellulose synthase), and Cla006648 (Galactosyltransferase), had a significant correlation with water-soluble pectin (r 2 = 0.91), cellulose (r 2 = 0.9), and protopectin (r 2 = 0.92); and three genes, Cla007092 (ERF2a), Cla004119 (probable glycosyltransferase), and Cla018816 (Xyloglucan endotransglucosylase/hydrolase), were correlated with hemicellulose (r 2 = 0.85), cellulose (r 2 = 0.8), and protopectin (r 2 = 0.8). This study generated important insights of biosynthesis of a cell wall structure and ethylene signaling transduction pathway, the mechanism controlling the flesh firmness changes in watermelon, which provide a significant source to accelerate future functional analysis in watermelon to facilitate crop improvement.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shengjie Zhao
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenge Liu
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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6
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Umer MJ, Bin Safdar L, Gebremeskel H, Zhao S, Yuan P, Zhu H, Kaseb MO, Anees M, Lu X, He N, Gong C, Liu W. Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles. HORTICULTURE RESEARCH 2020; 7:193. [PMID: 33328462 PMCID: PMC7705761 DOI: 10.1038/s41438-020-00416-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/14/2020] [Accepted: 09/10/2020] [Indexed: 05/03/2023]
Abstract
The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents, which undergo considerable variations during development and maturation. The molecular mechanisms underlying these variations remain unclear. In this study, we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism. We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids. Within these modules, based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction (RT-qPCR), we identified 7 genes involved in the metabolism of sugars and organic acids. Among these genes, Cla97C01G000640, Cla97C05G087120 and Cla97C01G018840 (r2 = 0.83 with glucose content) were identified as sugar transporters (SWEET, EDR6 and STP) and Cla97C03G064990 (r2 = 0.92 with sucrose content) was identified as a sucrose synthase from information available for other crops. Similarly, Cla97C07G128420, Cla97C03G068240 and Cla97C01G008870, having strong correlations with malic (r2 = 0.75) and citric acid (r2 = 0.85), were annotated as malate and citrate transporters (ALMT7, CS, and ICDH). The expression profiles of these 7 genes in diverse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon. These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.
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Affiliation(s)
- Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Luqman Bin Safdar
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Haileslassie Gebremeskel
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Pingli Yuan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - M O Kaseb
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Muhammad Anees
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Chengsheng Gong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China.
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7
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Amiri E, Herman JJ, Strand MK, Tarpy DR, Rueppell O. Egg transcriptome profile responds to maternal virus infection in honey bees, Apis mellifera. INFECTION GENETICS AND EVOLUTION 2020; 85:104558. [PMID: 32947033 DOI: 10.1016/j.meegid.2020.104558] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Trans-generational disease effects include vertical pathogen transmission but also immune priming to enhance offspring immunity. Accordingly, the survival consequences of maternal virus infection can vary and its molecular consequences during early development are poorly understood. The honey bee queen is long-lived and represents the central hub for vertical virus transmission as the sole reproductive individual in her colony. Even though virus symptoms in queens are mild, viral infection may have severe consequences for the offspring. Thus, transcriptome patterns during early developmental are predicted to respond to maternal virus infection. To test this hypothesis, gene expression patterns were compared among pooled honey bee eggs laid by queens that were either infected with Deformed wing virus (DWV1), Sacbrood virus (SBV2), both viruses (DWV and SBV), or no virus. Whole transcriptome analyses revealed significant expression differences of a few genes, some of which have hitherto no known function. Despite the paucity of single gene effects, functional enrichment analyses revealed numerous biological processes in the embryos to be affected by virus infection. Effects on several regulatory pathways were consistent with maternal responses to virus infection and correlated with responses to DWV and SBV in honey bee larvae and pupae. Overall, effects on egg transcriptome patterns were specific to each virus and the results of dual-infection samples suggested synergistic effects of DWV and SBV. We interpret our results as consequences of maternal infections. Thus, this first study to document and characterize virus-associated changes in the transcriptome of honey bee eggs represents an important contribution to understanding trans-generational virus effects, although more in-depth studies are needed to understand the detailed mechanisms of how viruses affect honey bee embryos.
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Affiliation(s)
- Esmaeil Amiri
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402, USA; Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
| | - Jacob J Herman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Micheline K Strand
- Life Sciences Division, U.S. Army Research Office, CCDC-ARL, Research Triangle Park, Durham, NC 27709, USA
| | - David R Tarpy
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402, USA; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Li H, Li Y, Yu J, Wu T, Zhang J, Tian J, Yao Y. MdMYB8 is associated with flavonol biosynthesis via the activation of the MdFLS promoter in the fruits of Malus crabapple. HORTICULTURE RESEARCH 2020; 7:19. [PMID: 32025322 PMCID: PMC6994661 DOI: 10.1038/s41438-020-0238-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/10/2019] [Indexed: 05/20/2023]
Abstract
Flavonols are polyphenolic compounds that play important roles in plant stress resistance and development. They are also valuable components of the human diet. The Malus crabapple cultivar 'Flame' provides an excellent model for studying flavonol biosynthesis due to the high flavonol content of its fruit peel. To obtain a more detailed understanding of the flavonol regulatory network involved in fruit development, the transcriptomes of the fruit of the Malus cv. 'Flame' from five continuous developmental stages were analyzed using RNA sequencing. A flavonol-related gene module was identified through weighted gene coexpression network analysis (WGCNA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that phytohormones are involved in regulating flavonol biosynthesis during fruit development. A putative transcription factor, MdMYB8, was selected for further study through hub gene correlation network analysis and yeast one-hybrid assays. Stable overexpression or RNAi knockdown of MdMYB8 in transgenic 'Orin' apple calli resulted in a higher or lower flavonol content, respectively, suggesting that MdMYB8 is a regulator of flavonol biosynthesis. This transcriptome analysis provides valuable data for future studies of flavonol synthesis and regulation.
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Affiliation(s)
- Hua Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Jiaxuan Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
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Song T, Li K, Wu T, Wang Y, Zhang X, Xu X, Yao Y, Han Z. Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures. PLoS One 2019; 14:e0210672. [PMID: 30695036 PMCID: PMC6350969 DOI: 10.1371/journal.pone.0210672] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022] Open
Abstract
Anthocyanin pigments play many roles in plants, including providing protection against biotic and abiotic stresses. To identify new regulatory genes in apple (Malus domestica) that may be involved in regulating low temperature induced anthocyanin biosynthesis, we performed RNA-seq analysis of leaves from the ‘Gala’ apple cultivar following exposure to a low temperature (16 °C). A visible red color appeared on the upper leaves and the anthocyanin content increased significantly after the low temperature treatment. Genes from the flavonoid biosynthesis pathway were significantly enriched among the differentially expressed genes, and the expression of several transcription factors was shown by WGCNA (weighted gene co-expression network analysis) to correlate with anthocyanin accumulation, including members of the MYB, MADS, WRKY, WD40, Zinc Finger and HB-ZIP families. Three MYB transcription factors (MdMYB12, MdMYB22 and MdMYB114), which had several CBF/DREB response elements in their promoters, were significantly induced by low temperature exposure and their expression also correlated highly with anthocyanin accumulation. We hypothesize that they may act as regulators of anthocyanin biosynthesis and be regulated by CBF/DREB transcription factors in apple leaves under low temperature conditions. The analyses presented here provide insights into the molecular mechanisms underlying anthocyanin accumulation during low temperature exposure.
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Affiliation(s)
- Tingting Song
- College of Horticulture, China Agricultural University, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Keting Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
| | - Yuncong Yao
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
- * E-mail:
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Mondet F, Rau A, Klopp C, Rohmer M, Severac D, Le Conte Y, Alaux C. Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle. BMC Genomics 2018; 19:328. [PMID: 29728057 PMCID: PMC5936029 DOI: 10.1186/s12864-018-4668-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/12/2018] [Indexed: 12/16/2022] Open
Abstract
Background The parasite Varroa destructor represents a significant threat to honeybee colonies. Indeed, development of Varroa infestation within colonies, if left untreated, often leads to the death of the colony. Although its impact on bees has been extensively studied, less is known about its biology and the functional processes governing its adult life cycle and adaptation to its host. We therefore developed a full life cycle transcriptomic catalogue in adult Varroa females and included pairwise comparisons with males, artificially-reared and non-reproducing females (10 life cycle stages and conditions in total). Results Extensive remodeling of the Varroa transcriptome was observed, with an upregulation of energetic and chitin metabolic processes during the initial and final phases of the life cycle (e.g. phoretic and post-oviposition stages), whereas during reproductive stages in brood cells genes showing functions related to transcriptional regulation were overexpressed. Several neurotransmitter and neuropeptide receptors involved in behavioural regulation, as well as active compounds of salivary glands, were also expressed at a higher level outside the reproductive stages. No difference was detected between artificially-reared phoretic females and their counterparts in colonies, or between females who failed to reproduce and females who successfully reproduced, indicating that phoretic individuals can be reared outside host colonies without impacting their physiology and that mechanisms underlying reproductive failure occur before oogenesis. Conclusions We discuss how these new findings reveal the remarkable adaptation of Varroa to its host biology and notably to the switch from living on adults to reproducing in sealed brood cells. By spanning the entire adult life cycle, our work captures the dynamic changes in the parasite gene expression and serves as a unique resource for deciphering Varroa biology and identifying new targets for mite control. Electronic supplementary material The online version of this article (10.1186/s12864-018-4668-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fanny Mondet
- INRA, UR 406 Abeilles et Environnement, 84914, Avignon, France.
| | - Andrea Rau
- INRA, UMR 1313 GABI Génétique Animale et Biologie Intégrative, 78350, Jouy-en-Josas, France
| | - Christophe Klopp
- INRA, Genotoul Bioinfo, UR 875 MIAT Mathématiques et Informatique Appliquées de Toulouse, 31326, Castanet-Tolosan, France
| | - Marine Rohmer
- Institut de Génomique Fonctionnelle, UMR 5203 CNRS, U661 INSERM, Universités Montpellier 1 & 2, 34094, Montpellier, France
| | - Dany Severac
- Institut de Génomique Fonctionnelle, UMR 5203 CNRS, U661 INSERM, Universités Montpellier 1 & 2, 34094, Montpellier, France
| | - Yves Le Conte
- INRA, UR 406 Abeilles et Environnement, 84914, Avignon, France
| | - Cedric Alaux
- INRA, UR 406 Abeilles et Environnement, 84914, Avignon, France.
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McAfee A, Chan QWT, Evans J, Foster LJ. A Varroa destructor protein atlas reveals molecular underpinnings of developmental transitions and sexual differentiation. Mol Cell Proteomics 2017; 16:2125-2137. [PMID: 28867676 PMCID: PMC5724176 DOI: 10.1074/mcp.ra117.000104] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Indexed: 11/06/2022] Open
Abstract
Varroa destructor is the most economically damaging honey bee pest, weakening colonies by simultaneously parasitizing bees and transmitting harmful viruses. Despite these impacts on honey bee health, surprisingly little is known about its fundamental molecular biology. Here, we present a Varroa protein atlas crossing all major developmental stages (egg, protonymph, deutonymph, and adult) for both male and female mites as a web-based interactive tool (http://foster.nce.ubc.ca/varroa/index.html). We used intensity-based label-free quantitation to find 1,433 differentially expressed proteins across developmental stages. Enzymes for processing carbohydrates and amino acids were among many of these differences as well as proteins involved in cuticle formation. Lipid transport involving vitellogenin was the most significantly enriched biological process in the foundress (reproductive female) and young mites. In addition, we found that 101 proteins were sexually regulated and functional enrichment analysis suggests that chromatin remodeling may be a key feature of sex determination. In a proteogenomic effort, we identified 519 protein-coding regions, 301 of which were supported by two or more peptides and 169 of which were differentially expressed. Overall, this work provides a first-of-its-kind interrogation of the patterns of protein expression that govern the Varroa life cycle and the tools we have developed will support further research on this threatening honey bee pest.
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Affiliation(s)
- Alison McAfee
- From the ‡Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, 2125 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Queenie W T Chan
- From the ‡Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, 2125 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jay Evans
- §Bee Research Laboratory, Beltsville Agricultural Research Center-East, U.S. Department of Agriculture, Beltsville, MD, USA 20705-0000
| | - Leonard J Foster
- §Bee Research Laboratory, Beltsville Agricultural Research Center-East, U.S. Department of Agriculture, Beltsville, MD, USA 20705-0000
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