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Hu J, Wang J, Muhammad T, Tuerdiyusufu D, Yang T, Li N, Yang H, Wang B, Yu Q. Functional analysis of fasciclin-like arabinogalactan in carotenoid synthesis during tomato fruit ripening. Plant Physiol Biochem 2024; 210:108589. [PMID: 38593485 DOI: 10.1016/j.plaphy.2024.108589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Carotenoids are important pigmented nutrients synthesized by tomato fruits during ripening. To reveal the molecular mechanism underlying carotenoid synthesis during tomato fruit ripening, we analyzed carotenoid metabolites and transcriptomes in six development stages of tomato fruits. A total of thirty different carotenoids were detected and quantified in tomato fruits from 10 to 60 DPA. Based on differential gene expression profiles and WGCNA, we explored several genes that were highly significant and negatively correlated with lycopene, all of which encode fasciclin-like arabinogalactan proteins (FLAs). The FLAs are involved in plant signal transduction, however the functional role of these proteins has not been studied in tomato. Genome-wide analysis revealed that cultivated and wild tomato species contained 18 to 22 FLA family members, clustered into four groups, and mainly evolved by means of segmental duplication. The functional characterization of FLAs showed that silencing of SlFLA1, 5, and 13 were found to contribute to the early coloration of tomato fruits, and the expression of carotenoid synthesis-related genes was up-regulated in fruits that changed phenotypically, especially in SlFLA13-silenced plants. Furthermore, the content of multiple carotenoids (including (E/Z)-phytoene, lycopene, γ-carotene, and α-carotene) was significantly increased in SlFLA13-silenced fruits, suggesting that SlFLA13 has a potential inhibitory function in regulating carotenoid synthesis in tomato fruits. The results of the present study broaden the idea of analyzing the biological functions of tomato FLAs and preliminary evidence for the inhibitory role of SlFLA13 in carotenoid synthesis in fruit, providing the theoretical basis and a candidate for improving tomato fruit quality.
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Affiliation(s)
- Jiahui Hu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Tayeb Muhammad
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Diliaremu Tuerdiyusufu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Haitao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Liang J, Fang Y, An C, Yao Y, Wang X, Zhang W, Liu R, Wang L, Aslam M, Cheng Y, Qin Y, Zheng P. Genome-wide identification and expression analysis of the bHLH gene family in passion fruit (Passiflora edulis) and its response to abiotic stress. Int J Biol Macromol 2023; 225:389-403. [PMID: 36400210 DOI: 10.1016/j.ijbiomac.2022.11.076] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
Passion fruit is a tropical fruit crop with significant agricultural, economic and ornamental values. The growth and development of passion fruit are greatly affected by climatic conditions. In plants, the basic helix-loop-helix (bHLH) gene family plays essential roles in the floral organ and fruit development, as well as stress response. However, the characteristics and functions of the bHLH genes of passion fruit remain unclear. Here, 138 passion fruit bHLH members were identified and classified into 20 subfamilies. The structural analysis illustrated that PebHLH proteins of the specific subfamily are relatively conserved. Collinearity analysis indicated that the expansion of the PebHLH gene family mainly took place by segmental duplication, and the structural diversity of duplicated genes might contribute to their functional diversity. PebHLHs, which potentially regulate different floral organ and fruit development, were further screened out, and many of these genes were differentially expressed under various stress treatments. The co-presence of different cis-regulatory elements involved in developmental regulation, hormone and stress responses in the promoter regions of PebHLHs might be closely related to their diverse regulatory roles. Overall, this study will be helpful for further functional investigation of PebHLHs and provides clues for improvement of the passion fruit breeding.
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Affiliation(s)
- Jianxiang Liang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunying Fang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang An
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yuanbin Yao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning 530004, China
| | - Wenbin Zhang
- Xinluo Breeding Center for Excellent Germplasms, Longyan 361000, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lulu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan Cheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China; Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ping Zheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Zhang D, Yu Z, Hu S, Liu X, Zeng B, Gao W, Qin H, Ma X, He Y. Genome-wide identification of members of the Skp1 family in almond ( Prunus dulcis), cloning and expression characterization of PsdSSK1. Physiol Mol Biol Plants 2023; 29:35-49. [PMID: 36733834 PMCID: PMC9886703 DOI: 10.1007/s12298-023-01278-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/04/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Skp1 (S-phase kinase-associated protein 1) is the core gene of SCF ubiquitin ligase, which mediates protein degradation, thereby regulating biological processes such as cell cycle progression, transcriptional regulation, and signal transduction. A variety of plant Skp1 gene family studies have been reported. However, the almond Skp1 gene family has not yet been studied. In this study, we identified 18 members of the Prunus dulcis PdSkp1 family that were unevenly distributed across six chromosomes of the almond genome. Phylogenetic tree analysis revealed that the PdSkp1 members can be divided into three groups: I, II, and III. PdSkp1 members in each subfamily have relatively conserved motif types and exon/intron numbers. There were three pairs of fragment duplication genes and one pair of tandem repeat genes, and their functions were highly evolutionarily conserved. Transcriptome data showed that PdSkp1 is expressed in almond flower tissues, and that its expression shows significant change during cross-pollination. Fluorescence quantitative results showed that eight PdSkp1 genes had different expression levels in five tissues of almond, i.e., branches, leaves, flower buds, flesh, and cores. In addition, we cloned a PsdSSK1 gene based on PdSkp1. The cloned PsdSSK1 showed the same protein sequence as PdSkp1-12. Results of qPCR and western blot analysis showed high expression of PsdSSK1 in almond pollen. In conclusion, we report the first clone of the key gene SSK1 that controls self-incompatibility in almonds. Our research lays a foundation for future functional research on PdSkp1 members, especially for exploring the mechanism of almond self-incompatibility. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01278-9.
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Affiliation(s)
- Dongdong Zhang
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Zhenfan Yu
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Shaobo Hu
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Xingyue Liu
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
- GuangZhou Institute of Forestry and Landscape Architecture, GuangZhou, China
| | - Bin Zeng
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Wenwen Gao
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - HuanXue Qin
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Xintong Ma
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Yawen He
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
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Jia C, Guo B, Wang B, Li X, Yang T, Li N, Wang J, Yu Q. The LEA gene family in tomato and its wild relatives: genome-wide identification, structural characterization, expression profiling, and role of SlLEA6 in drought stress. BMC Plant Biol 2022; 22:596. [PMID: 36536303 PMCID: PMC9762057 DOI: 10.1186/s12870-022-03953-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Late embryogenesis abundant (LEA) proteins are widely distributed in higher plants and play crucial roles in regulating plant growth and development processes and resisting abiotic stress. Cultivated tomato (Solanum lycopersicum) is an important vegetable crop worldwide; however, its growth, development, yield, and quality are currently severely constrained by abiotic stressors. In contrast, wild tomato species are more tolerant to abiotic stress and can grow normally in extreme environments. The main objective of this study was to identify, characterize, and perform gene expression analysis of LEA protein families from cultivated and wild tomato species to mine candidate genes and determine their potential role in abiotic stress tolerance in tomatoes. RESULTS Total 60, 69, 65, and 60 LEA genes were identified in S. lycopersicum, Solanum pimpinellifolium, Solanum pennellii, and Solanum lycopersicoides, respectively. Characterization results showed that these genes could be divided into eight clusters, with the LEA_2 cluster having the most members. Most LEA genes had few introns and were non-randomly distributed on chromosomes; the promoter regions contained numerous cis-acting regulatory elements related to abiotic stress tolerance and phytohormone responses. Evolutionary analysis showed that LEA genes were highly conserved and that the segmental duplication event played an important role in evolution of the LEA gene family. Transcription and expression pattern analyses revealed different regulatory patterns of LEA genes between cultivated and wild tomato species under normal conditions. Certain S. lycopersicum LEA (SlLEA) genes showed similar expression patterns and played specific roles under different abiotic stress and phytohormone treatments. Gene ontology and protein interaction analyses showed that most LEA genes acted in response to abiotic stimuli and water deficit. Five SlLEA proteins were found to interact with 11 S. lycopersicum WRKY proteins involved in development or resistance to stress. Virus-induced gene silencing of SlLEA6 affected the antioxidant and reactive oxygen species defense systems, increased the degree of cellular damage, and reduced drought resistance in S. lycopersicum. CONCLUSION These findings provide comprehensive information on LEA proteins in cultivated and wild tomato species and their possible functions under different abiotic and phytohormone stresses. The study systematically broadens our current understanding of LEA proteins and candidate genes and provides a theoretical basis for future functional studies aimed at improving stress resistance in tomato.
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Affiliation(s)
- Chunping Jia
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Bin Guo
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Xin Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
- College of Life Science and Technology, Xinjiang University, Urumqi, China.
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Yu Z, Zhang D, Zeng B, Liu X, Yang J, Gao W, Ma X. Characterization of the WRKY gene family reveals its contribution to the adaptability of almond ( Prunus dulcis). PeerJ 2022; 10:e13491. [PMID: 35811825 PMCID: PMC9261925 DOI: 10.7717/peerj.13491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/03/2022] [Indexed: 01/17/2023] Open
Abstract
Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT-PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
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Affiliation(s)
- Zhenfan Yu
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Dongdong Zhang
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Bin Zeng
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Xingyue Liu
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China,GuangZhou Institute of Forestry and Landscape Architecture, GuangZhou, China
| | - Jiahui Yang
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Wenwen Gao
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Xintong Ma
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
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Valouzi H, Shahmohammadi N, Golnaraghi A, Moosavi MR, Ohshima K. Genetic diversity and evolutionary analyses of potyviruses infecting narcissus in Iran. J Plant Pathol 2021; 104:237-250. [PMID: 34866893 PMCID: PMC8628840 DOI: 10.1007/s42161-021-00985-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Potyviruses are among the most important pathogens of dicotyledonous and monocotyledonous ornamentals and crop plants. In this study, leaf samples were collected from symptomatic narcissus plants and weeds in Fars and Tehran provinces of Iran. Enzyme-linked immunosorbent assay using broad-spectrum potyvirus antibodies gave a positive reaction with 38 out of 61 narcissus samples tested (62.3%); the results were confirmed by reverse-transcription polymerase chain reaction using universal NIb primers, and for thirty samples, by sequencing and phylogenetic studies. The results suggested the infection of almost all positive samples with narcissus yellow stripe virus (NYSV); only one sample seemed to be infected with narcissus late season yellows virus (NLSYV). The 3'-end of the genome of the NLSYV isolate and six NYSV isolates, encompassing the complete coat protein gene, was amplified and sequenced using species-specific and universal potyvirus primers. Sequence analysis indicated the presence of NLSYV and NYSV, not previously identified from Western Asia. No evidence of recombination was found in Iranian isolates. Based on phylogenetic analyses, isolates of NLSYV and NYSV clustered into five and three phylogroups, respectively, where all the Iranian isolates fell into distinct subpopulations in groups NLSYV-I and NYSV-II. Multiple sequence alignments showed some phylogroup-specific amino acid substitutions for both viruses. Phylogroup IV and II populations had higher nucleotide diversities as compared with other populations of NLSYV and NYSV, respectively. Our findings revealed the presence of negative selection in the populations of both viruses. Almost no statistically significant gene flow was found between populations of these viruses. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s42161-021-00985-0.
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Affiliation(s)
- Hajar Valouzi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Niayesh Shahmohammadi
- Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Alireza Golnaraghi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Department of Biodiversity, BoomZista Institute, Vancouver, British Columbia Canada
| | - Mohammad Reza Moosavi
- Department of Plant Pathology, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, 1-banchi, Honjo-manchi, Saga, 804-8502 Japan
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Cheng Z, Zhang X, Yao W, Zhao K, Liu L, Fan G, Zhou B, Jiang T. Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar. BMC Plant Biol 2021; 21:110. [PMID: 33627082 PMCID: PMC7903804 DOI: 10.1186/s12870-021-02872-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 02/02/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. RESULTS On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. CONCLUSION Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.
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Affiliation(s)
- Zihan Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xuemei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Kai Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Lin Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Gaofeng Fan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
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Wang L, Ding X, Gao Y, Yang S. Genome-wide identification and characterization of GRAS genes in soybean (Glycine max). BMC Plant Biol 2020; 20:415. [PMID: 32891114 PMCID: PMC7487615 DOI: 10.1186/s12870-020-02636-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/30/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND GRAS proteins are crucial transcription factors, which are plant-specific and participate in various plant biological processes. Thanks to the rapid progress of the whole genome sequencing technologies, the GRAS gene families in different plants have been broadly explored and studied. However, comprehensive research on the soybean (Glycine max) GRAS gene family is relatively lagging. RESULTS In this study, 117 Glycine max GRAS genes (GmGRAS) were identified. Further phylogenetic analyses showed that the GmGRAS genes could be categorized into nine gene subfamilies: DELLA, HAM, LAS, LISCL, PAT1, SCL3, SCL4/7, SCR and SHR. Gene structure analyses turned out that the GmGRAS genes lacked introns and were relatively conserved. Conserved domains and motif patterns of the GmGRAS members in the same subfamily or clade exhibited similarities. Notably, the expansion of the GmGRAS gene family was driven both by gene tandem and segmental duplication events. Whereas, segmental duplications took the major role in generating new GmGRAS genes. Moreover, the synteny and evolutionary constraints analyses of the GRAS proteins among soybean and distinct species (two monocots and four dicots) provided more detailed evidence for GmGRAS gene evolution. Cis-element analyses indicated that the GmGRAS genes may be responsive to diverse environmental stresses and regulate distinct biological processes. Besides, the expression patterns of the GmGRAS genes were varied in various tissues, during saline and dehydration stresses and during seed germination processes. CONCLUSIONS We conducted a systematic investigation of the GRAS genes in soybean, which may be valuable in paving the way for future GmGRAS gene studies and soybean breeding.
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Affiliation(s)
- Liang Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingqi Gao
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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Guterres A, de Oliveira RC, Fernandes J, de Lemos ERS. The mystery of the phylogeographic structural pattern in rodent-borne hantaviruses. Mol Phylogenet Evol 2019; 136:35-43. [PMID: 30914396 DOI: 10.1016/j.ympev.2019.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/19/2022]
Abstract
Hantaviruses (order Bunyavirales, family Hantaviridae) are important zoonotic pathogens. Because of the great diversity of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. To understand the mechanisms behind the evolutionary history of hantaviruses through virus-reservoir interactions, it is important to know how the radiation and diversity of hantaviruses occurred. In this paper, we evaluate the pattern of hantavirus diversification based on a complete S segment representing major groups of hantaviruses found in the Americas. Phylogenetic analyses revealed a high degree of phylogeographic structure and a surprising pattern of geographical distribution of New World hantaviruses. The available data suggest that hantaviruses related to the Arvicolinae rodent subfamily in North America probably emerged and initially adapted from a shared common ancestor of the Tula virus. The first clade of hantaviruses associated with Neotominae occupied a stem lineage, especially those that emerged in Central America or Mexico. Hantaviruses from Central America and Mexico found in Neotominae rodents spread northward and probably gave rise to the first phylogroup of hantaviruses associated with Sigmodontinae in North America. Two preferential host-switching transmissions in hantaviruses apparently gave rise to two different paraphyletic group in Neotominae and Sigmodontinae. Our study supports a probable epicenter of diversification in Central America and/or Mexico for hantaviruses related to both the Neotominae and Sigmodontinae subfamilies.
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Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
| | - Renata Carvalho de Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Elba Regina Sampaio de Lemos
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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Durães-Carvalho R, Salemi M. In-depth phylodynamics, evolutionary analysis and in silico predictions of universal epitopes of Influenza A subtypes and Influenza B viruses. Mol Phylogenet Evol 2018; 121:174-182. [PMID: 29355604 DOI: 10.1016/j.ympev.2018.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/26/2017] [Accepted: 01/10/2018] [Indexed: 12/11/2022]
Abstract
This study applied High-Performance Computing to explore the high-resolution phylodynamics and the evolutionary dynamics of Influenza viruses (IVs) A and B and their subtypes in-depth to identify peptide-based candidates for broad-spectrum vaccine targets. For this purpose, we collected all the available Hemagglutinin (HA) and Neuraminidase (NA) nucleotide and amino acid sequences (more than 100,000) of IVs isolated from all the reservoirs and intermediate hosts species, from all geographic ranges and from different isolation sources, covering a period of almost one century of sampling years. We highlight that despite the constant changes in Influenza evolutionary dynamics over time, which are responsible for the generation of novel strains, our study identified the presence of highly conserved peptides distributed in all the HA and NA found in H1-H18 and N1-N11 IAV subtypes and IBVs. Additionally, predictions through computational methods showed that these peptides could have a strong affinity to bind to HLA-A∗02:01/HLA-DRB1∗01:01 major histocompatibility complex (MHC) class I and II molecules, therefore acting as a double ligand. Moreover, epitope prediction in antigens from pathogens responsible for secondary bacterial infection was also studied. These findings show that the regions mapped here may potentially be explored as universal epitope-based candidates to develop therapies leading to a broader response against the infection induced by all circulating IAVs, IBVs and Influenza-associated bacterial infections.
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Affiliation(s)
- Ricardo Durães-Carvalho
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
| | - Marco Salemi
- Emerging Pathogens Institute, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
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de Souza E Sousa JF, Viana PF, Bertollo LAC, Cioffi MB, Feldberg E. Evolutionary Relationships among Boulengerella Species (Ctenoluciidae, Characiformes): Genomic Organization of Repetitive DNAs and Highly Conserved Karyotypes. Cytogenet Genome Res 2017; 152:194-203. [PMID: 28942442 DOI: 10.1159/000480141] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2017] [Indexed: 11/19/2022] Open
Abstract
Ctenoluciidae is a Neotropical freshwater fish family whose representatives are known as bicudas. The genus Boulengerella contains 5 species, and 4 of them (B. cuvieri, B. lateristriga, B. lucius, and B. maculata) were cytogenetically analyzed in the present study by conventional and molecular procedures. All 4 species have a very similar karyotype, with 2n = 36 chromosomes (14 metacentrics + 16 submetacentrics + 6 subtelocentrics; FN = 72). However, the heterochromatin distribution pattern is species-specific. In all 4 species, the nucleolus organizer region is located in pair 18, as also confirmed by cytogenetic mapping of 18S rDNA. In turn, 5S rRNA genes are present in 2 chromosome pairs: in pair 1 of all 4 species, and in pair 10 of B. lateristriga, B. maculata, and B. cuvieri, but in pair 4 of B. lucius. The telomeric probe highlighted terminal regions in all chromosomes, as well as an interstitial centromeric sequence in pair 3 of the 3 first-mentioned species. Notably, a conspicuous heteromorphic secondary constriction in chromosomes 18 was found only in the males of the 3 species, rendering one of the homologs much larger than the other one. This feature, associated with a large 18S rDNA block and accumulation of telomeric sequences, suggests the presence of an XX/XY sex chromosome system in the analyzed Boulengerella species.
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Affiliation(s)
- José F de Souza E Sousa
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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Li J, Gao Y, Xu T. Comparative genomic and evolution of vertebrate NOD1 and NOD2 genes and their immune response in miiuy croaker. Fish Shellfish Immunol 2015; 46:387-397. [PMID: 26108036 DOI: 10.1016/j.fsi.2015.06.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/16/2015] [Accepted: 06/19/2015] [Indexed: 06/04/2023]
Abstract
The nucleotide-binding oligomerization domain proteins NOD1 and NOD2 are important cytoplasmic pathogen recognition receptors which sense microbial infections molecules to induce innate immune response. In this study, the sequence analysis showed that NOD1 and NOD2 genes in miiuy croaker (miichthys miiuy, mmiNOD1 and mmiNOD2) share some highly conserved motifs that crucial for recognizing the bacterial and viral components. Quantitative expression analysis revealed mmiNOD1 and mmiNOD2 had the highest level of expression in liver. Induction experiments with Vibrio anguillarum indicated the different expression levels of mmiNOD1 and mmiNOD2 in liver, spleen and kidney. The expressions of mmiNOD1 and mmiNOD2 increased more significantly after Poly(I:C) stimulation, meanwhile, we carried out the expression analysis at the transcriptome level and the regulation of microRNAs. In addition, the evolutionary analysis showed that the ancestral lineages of NOD1 in bony fish detected one positively selected site, however, both the current lineages of NOD1 and NOD2 genes in bony fish underwent purifying selection indicating that NOD1 gene in the ancestor of bony fish experienced positive selection. To further understand the evolutionary pattern of NOD1 and NOD2 in vertebrates, we were the first to conduct comparative genomic analysis by comparing the number and synteny of NOD1 and NOD2. Combining the duplication of NOD1, the lost of NOD2 and the more conserved synteny of NOD2 than NOD1, we proposed that the hypothetical evolutionary pattern is different between NOD1 and NOD2.
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Affiliation(s)
- Jinrui Li
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yunhang Gao
- College of Animal Science and Veterinary Medicine, Jilin Agriculture University, Changchun 130118, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China.
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