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144 results on '"He, Yehua"'

5. The pineapple reference genome: Telomere‐to‐telomere assembly, manually curated annotation, and comparative analysis.

Author

Feng, Junting, Zhang, Wei, Chen, Chengjie, Liang, Yinlong, Li, Tangxiu, Wu, Ya, Liu, Hui, Wu, Jing, Lin, Wenqiu, Li, Jiawei, He, Yehua, He, Junhu, and Luan, Aiping

Subjects
TROPICAL fruit, TRANSCRIPTION factors, DATABASES, GENOMICS, FUNCTIONAL analysis, PINEAPPLE
Abstract

Pineapple is the third most crucial tropical fruit worldwide and available in five varieties. Genomes of different pineapple varieties have been released to date; however, none of them are complete, with all exhibiting substantial gaps and representing only two of the five pineapple varieties. This significantly hinders the advancement of pineapple breeding efforts. In this study, we sequenced the genomes of three varieties: a wild pineapple variety, a fiber pineapple variety, and a globally cultivated edible pineapple variety. We constructed the first gap‐free reference genome (Ref) for pineapple. By consolidating multiple sources of evidence and manually revising each gene structure annotation, we identified 26,656 protein‐coding genes. The BUSCO evaluation indicated a completeness of 99.2%, demonstrating the high quality of the gene structure annotations in this genome. Utilizing these resources, we identified 7,209 structural variations across the three varieties. Approximately 30.8% of pineapple genes were located within ±5 kb of structural variations, including 30 genes associated with anthocyanin synthesis. Further analysis and functional experiments demonstrated that the high expression of AcMYB528 aligns with the accumulation of anthocyanins in the leaves, both of which may be affected by a 1.9‐kb insertion fragment. In addition, we developed the Ananas Genome Database, which offers data browsing, retrieval, analysis, and download functions. The construction of this database addresses the lack of pineapple genome resource databases. In summary, we acquired a seamless pineapple reference genome with high‐quality gene structure annotations, providing a solid foundation for pineapple genomics and a valuable reference for pineapple breeding. [ABSTRACT FROM AUTHOR]

Published
2024
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6. AcMYB266, a key regulator of the red coloration in pineapple peel: a case of subfunctionalization in tandem duplicated genes

Author

Zhang, Wei, primary, Wu, Jing, additional, Liu, Chaoyang, additional, Yi, Wen, additional, Xie, Jingyao, additional, Wu, Ya, additional, Xie, Tao, additional, Ma, Jun, additional, Zhong, Ziqin, additional, Yang, Mingzhe, additional, He, Junhu, additional, Chen, Chengjie, additional, Luan, Aiping, additional, and He, Yehua, additional

Published
2024
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16. Genome-Wide Identification and Characterization of Gibberellic Acid-Stimulated Arabidopsis Gene Family in Pineapple (Ananas comosus).

Author

Yang, Mingzhe, Liu, Chaoyang, Zhang, Wei, Wu, Jing, Zhong, Ziqin, Yi, Wen, Liu, Hui, Leng, Yan, Sun, Weisheng, Luan, Aiping, and He, Yehua

Subjects
PINEAPPLE, GENE families, HERBACEOUS plants, GOLGI apparatus, TANDEM repeats, ARABIDOPSIS
Abstract

The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays a crucial role in growth, development, and stress response, and it is specific to plants. This gene family has been extensively studied in various plant species, and its functional role in pineapple has yet to be characterized. In this study, 15 AcGASA genes were identified in pineapple through a genome-wide scan and categorized into three major branches based on a phylogenetic tree. All AcGASA proteins share a common structural domain with 12 cysteine residues, but they exhibit slight variations in their physicochemical properties and motif composition. Predictions regarding subcellular localization suggest that AcGASA proteins are present in the cell membrane, Golgi apparatus, nucleus, and cell wall. An analysis of gene synteny indicated that both tandem and segmental repeats have a significant impact on the expansion of the AcGASA gene family. Our findings demonstrate the differing regulatory effects of these hormones (GA, NAA, IAA, MeJA, and ABA) on the AcGASA genes. We analyzed the expression profiles of GASA genes in different pineapple tissue parts, and the results indicated that AcGASA genes exhibit diverse expression patterns during the development of different plant tissues, particularly in the regulation of floral organ development. This study provides a comprehensive understanding of GASA family genes in pineapple. It serves as a valuable reference for future studies on the functional characterization of GASA genes in other perennial herbaceous plants. [ABSTRACT FROM AUTHOR]

Published
2023
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24. The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color

Author

Feng, Lijun, primary, Wang, Juntao, additional, Mao, Meiqin, additional, Yang, Wei, additional, Adje, Mark Owusu, additional, Xue, Yanbin, additional, Zhou, Xuzixin, additional, Zhang, Huiling, additional, Luo, Jiaheng, additional, Tang, Ruimin, additional, Tan, Lin, additional, Lin, Dongpu, additional, Zhang, Xiaopeng, additional, Zang, Yaoqiang, additional, He, Yehua, additional, Chen, Changming, additional, Luan, Aiping, additional, Lin, Wenqiu, additional, Xu, Wentian, additional, Li, Xi, additional, Sun, Lingxia, additional, Jiang, Fuxing, additional, and Ma, Jun, additional

Published
2022
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25. Validation of Reference Genes for Quantitative Real-Time PCR Normalization in Ananas comosus var. bracteatus During Chimeric Leaf Development and Response to Hormone Stimuli

Author

Mao, Meiqin, primary, Xue, Yanbin, additional, He, Yehua, additional, Zhou, Xuzixing, additional, Hu, Hao, additional, Liu, Jiawen, additional, Feng, Lijun, additional, Yang, Wei, additional, Luo, Jiaheng, additional, Zhang, Huiling, additional, Li, Xi, additional, and Ma, Jun, additional

Published
2021
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27. Comparative transcriptome analysis of a fan-shaped inflorescence in pineapple

Author

He, Yehua and Xie, Tao

Subjects
pineapple, transcriptome analysis, fan-shaped inflorescence, RNA-Seq technique, DEGs
Abstract

Filesare transcriptome data and pictures of pineapple fan-shaped inflorescence. As follows: Figure S1: A PCA analysis with the expression of all samples, Figure S2: KEGG pathways of plant hormone signal transduction between the two pineapples, Table S1: Statistical results of comparison rate between reads and reference genome, Table S2: Expression of genes in the 18 libraries in pineapple based on the results of RNA-Seq, Table S3: Statistical table of FPKM distribution of genes, Table S4: Information of DEGs between the two pineapples, Table S5: Information of DEGs between different tissues within each pineapple, Table S6: KEGG enrichment analysis of all DEGs, Table S7: List of all TFs and DETFs, Table S8: List and statistics of overlapped TFs between the two pineapples, Table S9: Differentially expressed and overlapped IDGs between the two pineapples, Table S10: Differentially expressed BPGs, Table S11: Sequences of the primers used in this study for qRT-PCR.

Published
2021
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29. Identification of a novel promoter region responsible for the embryo-specific expression of SERK1in pineapple

Author

Xie, Tao, Zhang, Wei, Chen, Chengjie, Wang, Xiaoshuang, Zhang, Jing, Luan, Aiping, and He, Yehua

Abstract

Somatic embryogenesis (SE) is a key regeneration process in plant. AcSERK1is a gene specifically expressed in the early stage of SE in pineapple (Ananas comosus), suggesting that the promoter of SERK1might contain specific cis-acting element regulating SE. To identify embryonic cell-specific element in the SERK1promoter, a series of binary plant transformation vectors with GUS (β-glucuronidase) reporter gene were systematically analyzed by transient gene expression system in wild-type and transgenic pineapple embryogenic callus. Histochemical and quantitative GUS assays demonstrated that the activity of the AcSERK1upstream regulatory sequence lacking − 921 to -911 or -910 to -880 was significantly reduced in the embryonic callus of the pineapple, and these two regions were needed for the embryonic cell-specific. Besides, a promoter lacking − 943 to -922 was shown to significantly increase GUS activity in embryogenic callus, suggesting repressive elements exist in this region. Our data of stable transformation assays confirmed again the 5’ upstream regulatory sequence (-921 to -880) of the AcSERK1gene is an essential functional region. Our findings lay the basis for better understanding of the molecular mechanisms of AcSERK1gene in the regulation in early stage of SE.

Published
2023
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32. Metabolome and Transcriptome Profiling Reveals Anthocyanin Contents and Anthocyanin-Related Genes of Chimeric Leaves in Ananas comosus Var. Bracteatus

Author

Zhou, Xuzixin, primary, Xue, Yanbin, additional, Mao, Meiqin, additional, He, Yehua, additional, Adjei, Mark Owusu, additional, Yang, Wei, additional, Hu, Hao, additional, Liu, Jiawen, additional, Feng, Lijun, additional, Zhang, Huiling, additional, Luo, Jiaheng, additional, Li, Xi, additional, Sun, Lingxia, additional, Huang, Zhuo, additional, and Ma, Jun, additional

Published
2020
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41. Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus

Author

Xue, Yanbin, primary, Ma, Jun, additional, He, Yehua, additional, Yu, Sanmiao, additional, Lin, Zhen, additional, Xiong, Yingyuan, additional, Rafique, Fatima, additional, Jiang, Fuxing, additional, Sun, Lingxia, additional, Ma, Mingdong, additional, Zhou, Yujue, additional, Li, Xi, additional, and Huang, Zhuo, additional

Published
2019
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