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2019年11月17日

【期刊论文】Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas

Mao-Sheng Chen, Mei-Li Zhao, Gui-Juan Wang, Hui-Ying He, Xue Bai, Bang-Zhen Pan, Qiantang Fu, Yan-Bin Tao, Mingyong Tang, Jorge Martínez-Herrera, Zeng-Fu Xu, Mao-Sheng Chen, Mei-Li Zhao, Gui-Juan Wang, Hui-Ying He, Xue Bai, Bang-Zhen Pan, Qiantang Fu, Yan-Bin Tao, Mingyong Tang, Jorge Martínez-Herrera, Zeng-Fu Xu

BMC Plant Biology,2019,19(1):468

2019年11月04日

摘要

In higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture in Jatropha curcas L., a perennial woody plant belonging to Euphorbiaceae. Two inflorescence branching mutants were identified in germplasm collection of Jatropha. The duo xiao hua (dxh) mutant has a seven-order branch inflorescence, and the gynoecy (g) mutant has a three-order branch inflorescence, while WT Jatropha has predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them, Jatropha ADENOSINE KINASE 2 (JcADK2), ADENINE PHOSPHORIBOSYL TRANSFERASE 1 (JcAPT1), CYTOKININ OXIDASE 3 (JcCKX3), ISOPENTENYLTRANSFERASE 5 (JcIPT5), LONELY GUY 3 (JcLOG3) and JcLOG5 may participate in cytokinin metabolic pathway in Jatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching in Jatropha. In addition, comparative transcriptome analysis showed that Arabidopsis homologous genes Jatropha AGAMOUS-LIKE 6 (JcAGL6), JcAGL24, FRUITFUL (JcFUL), LEAFY (JcLFY), SEPALLATAs (JcSEPs), TERMINAL FLOWER 1 (JcTFL1), and WUSCHEL-RELATED HOMEOBOX 3 (JcWOX3), were differentially expressed in inflorescence

关键词: Transcriptome, inflorescence branching, cytokinin

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2020年04月20日

【期刊论文】Transcriptomic investigation of immune responses of the Apis cerana cerana larval gut infected by Ascosphaera apis

Rui Guo, Dafu Chen, Qingyun Diao, Cuiling Xiong, Yanzhen Zheng, Chunsheng Hou

Journal of Invertebrate Pathology,2019,166(1):170210-170

2019年09月08日

摘要

Chalkbrood is the most common fungal disease in honeybees. The objective of this study was to reveal immune responses in the Apis cerana cerana larval gut following Ascosphaera apis invasion. Combining a previously assembled transcriptome of A. c. cerana larval gut and the high-throughput sequencing data obtained in this study, 6152 differentially expressed genes (DEGs) were clustered into eight profiles. Trend analysis showed three significant up-regulated profiles (p ≤ 0.05) and three down-regulated profiles. Gene Ontology (GO) term analysis suggested that DEGs within significant up-regulated and down-regulated clusters were enriched in 46 and 38 functional groups, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated a majority of DEGs were involved in ribosome structure or function, carbon metabolism, biosynthesis of amino acids, and oxidative phosphorylation. In addition, 142 and 14 DEGs were annotated in the cellular immune- and humoral immune-related pathways, respectively. Further investigation indicated that DEGs up-regulated in cellular immune and humoral immune pathways outnumbered those that were downregulated. Moreover, immune responses of A. c. cerana and Apis mellifera ligustica larvae were compared and studied to decipher resistance of eastern honeybee larvae to A. apis. These results demonstrated that a large number of genes involved in immunity-related pathways were activated by A. apis. Our findings provided valuable information for elucidating the molecular mechanisms underlying immune responses of A. c. cerana larvae to A. apis infection and pathogen-host interactions during chalkbrood infection.

关键词: Chalkbrood, Apis cerana cerana, Larval gut, Ascosphaera apis, Immune response, Transcriptome

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2020年05月06日

【期刊论文】A comprehensive transcriptome data of normal and Nosema ceranae-stressed midguts of Apis mellifera ligustica workers

Huazhi Chen, Yu Du, Cuiling Xiong, Yanzhen Zheng, Dafu Chen, Rui Guo

Data in Brief,2019,26(1):1-5

2019年08月22日

摘要

Honeybees are pivotal pollinators of crops and wild flora, and of great importance in supporting critical ecosystem balance. Nosema ceranae, a unicellular fungal parasite that infects midgut epithelial cells of honeybees, can dramatically reduce honeybee population and productivity. Here, midguts of Apis mellifera ligustica workers at 7 d and 10 d post inoculation (dpi) with sucrose solution (Ac7CK and Ac10CK) and midguts at 7 dpi and 10 dpi with sucrose solution containing N. ceranae spores (Ac7T and Ac10T) were sequenced using strand-specific cDNA library construction and next-generation sequencing. A total of 1956129858 raw reads were gained in this article, and after quality control, 1946489304 high-quality clean reads with a mean Q30 of 93.82% were obtained. The rRNA-removed clean reads were then aligned to the reference genome of Apis mellifera with TopHat2. For more insight please see “Genome-wide identification of long non-coding RNAs and their regulatory networks involved in Apis mellifera ligustica response to Nosema ceranae infection” [1]. Raw data were deposited in NCBI Sequence Read Archive (SRA) database under the BioProject number PRJNA406998. These data can be used for comparative analysis to identify differentially expressed coding RNAs and non-coding RNAs involved in host responses to N. ceranae stress, and for investigation of molecular mechanisms regulating N. ceranae-response.

关键词: Apis mellifera ligustica, Nosema ceranae, Midgut, Transcriptome

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2020年05月06日

【期刊论文】MicroRNA dataset of normal and Nosema ceranae-infected midguts of Apis cerana cerana workers

Yu Du, Dingding Zhou, Huazhi Chen, Cuiling Xiong, Yanzhen Zheng, Dafu Chen, Rui Guo

Data in Brief,2019,26(1):1-6

2019年09月14日

摘要

N osema ceranae is a widespread fungal pathogen of honeybees, which is infective to all castes in the colony, including queens, drones and workers. Nosemosis caused by N. ceranae poses a big challenge for apiculture all over the world. In this articleHere, midguts of normal and N. ceranae-infected Apis cerana cerana workers at 7 (10) days post infection (dpi) were sequenced utilizing small RNA sequencing (sRNA-seq). Totally, 150.54 Mb raw reads were produced in this article, and 144.26 Mb high-quality clean reads with a mean ratio of 95.83% were obtained after strict filtering and quality control. For more insight please see “Comparative identification of microRNAs in Apis cerana cerana workers' midguts responding to Nosema ceranae invasion” [1]. Raw data are available in NCBI Sequence Read Archive (SRA) database under the BioProject number PRJNA487111. Our data can be used for investigating differentially expressed microRNAs (miRNAs) and piRNAs and their regulatory roles engaged in A. c. cerana response to N. ceranae infection, and for offering potential candidates for uncovering the molecular mechanisms regulating eastern honeybee-microsporidian interactions.

关键词: Apis cerana cerana, Nosema ceranae, Midgut, MicroRNA, Transcriptome

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