1
|
Le S, Le TV. Genetic diversity and population structure of natural provenances of Sonneratia caseolaris in Vietnam. J Genet Eng Biotechnol 2024; 22:100356. [PMID: 38494260 PMCID: PMC10903747 DOI: 10.1016/j.jgeb.2024.100356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/29/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Sommeratia caseolaris is considered the most important mangrove species for reforestation and conservation programs. Therefore, the knowledge of genetic diversity and the population structure of the species has important implications both for the conservation of existing genetic resources and development programs. In the present study, the genetic diversity and structure population of eight populations of S. caseolaris from the Northern to the Southern Coast of Vietnam were determined using nine ISSR molecular markers. RESULTS Eight populations of the mangrove species Sonneratia caseolaris were sampled across the natural range in Vietnam to evaluate the genetic diversity of the species. Nine ISSR markers were used to analyse 30 individuals from each population. There were moderate to high levels of genetic diversity (I = 0.447; h = 0.300). PCoA analysis gave very similar results to UPGMA dendrogram construction with the eight populations clustered into three genetic groups which mostly aligned with geographical distances among them. AMOVA analysis results indicated that most (81 %) of the genetic variation was within populations. CONCLUSION The current study also indicates the high level of genetic variation existing among and within the natural population of S. caseolaris in Vietnam. These results open new perspectives towards the conservation of the species' genetic resources and their future use in conservation and reforestation programs.
Collapse
Affiliation(s)
- Son Le
- Institute of Forest Tree Improvement and Biotechnology, Vietnamese Academy of Forest Sciences, 46, Ducthang, Bac Tuliem, 10000 Hanoi, Viet Nam; University of Tasmania, Hobart 7001, TAS, Australia.
| | - Thanh Van Le
- Research Institute for Forest Ecology and Environment, Vietnamese Academy of Forest Sciences, 46, Ducthang, Bac Tuliem, 10000 Hanoi, Viet Nam.
| |
Collapse
|
2
|
Sun J, Liu Z, Quan J, Li L, Zhao G, Lu J. RNA-seq Analysis Reveals Alternative Splicing Under Heat Stress in Rainbow Trout (Oncorhynchus mykiss). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:5-17. [PMID: 34787764 DOI: 10.1007/s10126-021-10082-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss) is one of the most economically important cold-water farmed species in the world, and transcriptomic studies in response to heat stress have been conducted and will be studied in depth. Alternative splicing (AS), a post-transcriptional regulatory process that regulates gene expression and increases proteomic diversity, is still poorly understood in rainbow trout under heat stress. In the present study, 18,623 alternative splicing events were identified from 9936 genes using RNA transcriptome sequencing technology (RNA-Seq) and genomic information. A total of 2731 differential alternative splicing (DAS) events were found among 2179 differentially expressed genes (DEGs). Gene ontology analysis revealed that the DEGs were mainly enriched in cellular metabolic process, cell part, and organic cyclic compound binding under heat stress. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis displayed that the DEGs were enriched for 39 pathways, and some key pathways, such as lysine degradation, are involved in the regulation of heat stress in liver tissues of rainbow trout. The results were validated by qRT-PCR, confirming reliability of our bioinformatics analysis.
Collapse
Affiliation(s)
- Jun Sun
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China.
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Junhao Lu
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| |
Collapse
|
3
|
Yan X, Bai D, Song H, Lin K, Pang E. Alternative splicing during fruit development among fleshy fruits. BMC Genomics 2021; 22:762. [PMID: 34702184 PMCID: PMC8547070 DOI: 10.1186/s12864-021-08111-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/20/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known about alternative splicing during fruit development in fleshy fruits. RESULTS We studied the alternative splicing at the immature and ripe stages during fruit development in cucumber, melon, papaya and peach. We found that 14.96-17.48% of multiexon genes exhibited alternative splicing. Intron retention was not always the most frequent event, indicating that the alternative splicing pattern during different developmental process differs. Alternative splicing was significantly more prevalent at the ripe stage than at the immature stage in cucumber and melon, while the opposite trend was shown in papaya and peach, implying that developmental stages adopt different alternative splicing strategies for their specific functions. Some genes involved in fruit ripening underwent stage-specific alternative splicing, indicating that alternative splicing regulates fruits ripening. Conserved alternative splicing events did not appear to be stage-specific. Clustering fruit developmental stages across the four species based on alternative splicing profiles resulted in species-specific clustering, suggesting that diversification of alternative splicing contributes to lineage-specific evolution in fleshy fruits. CONCLUSIONS We obtained high quality transcriptomes and alternative splicing events during fruit development across the four species. Dynamics and nonconserved alternative splicing were discovered. The candidate stage-specific AS genes involved in fruit ripening will provide valuable insight into the roles of alternative splicing during the developmental processes of fleshy fruits.
Collapse
Affiliation(s)
- Xiaomin Yan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Dan Bai
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China.
| |
Collapse
|
4
|
Feng X, Xu S, Li J, Yang Y, Chen Q, Lyu H, Zhong C, He Z, Shi S. Molecular adaptation to salinity fluctuation in tropical intertidal environments of a mangrove tree Sonneratia alba. BMC PLANT BIOLOGY 2020; 20:178. [PMID: 32321423 PMCID: PMC7178616 DOI: 10.1186/s12870-020-02395-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/13/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Mangroves have adapted to intertidal zones - the interface between terrestrial and marine ecosystems. Various studies have shown adaptive evolution in mangroves at physiological, ecological, and genomic levels. However, these studies paid little attention to gene regulation of salt adaptation by transcriptome profiles. RESULTS We sequenced the transcriptomes of Sonneratia alba under low (fresh water), medium (half the seawater salinity), and high salt (seawater salinity) conditions and investigated the underlying transcriptional regulation of salt adaptation. In leaf tissue, 64% potential salinity-related genes were not differentially expressed when salinity increased from freshwater to medium levels, but became up- or down-regulated when salt concentrations further increased to levels found in sea water, indicating that these genes are well adapted to the medium saline condition. We inferred that both maintenance and regulation of cellular environmental homeostasis are important adaptive processes in S. alba. i) The sulfur metabolism as well as flavone and flavonol biosynthesis KEGG pathways were significantly enriched among up-regulated genes in leaves. They are both involved in scavenging ROS or synthesis and accumulation of osmosis-related metabolites in plants. ii) There was a significantly increased percentage of transcription factor-encoding genes among up-regulated transcripts. High expressions of salt tolerance-related TF families were found under high salt conditions. iii) Some genes up-regulated in response to salt treatment showed signs of adaptive evolution at the amino acid level and might contribute to adaptation to fluctuating intertidal environments. CONCLUSIONS This study first elucidates the mechanism of high-salt adaptation in mangroves at the whole-transcriptome level by salt gradient experimental treatments. It reveals that several candidate genes (including salt-related genes, TF-encoding genes, and PSGs) and major pathways are involved in adaptation to high-salt environments. Our study also provides a valuable resource for future investigation of adaptive evolution in extreme environments.
Collapse
Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jianfang Li
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haomin Lyu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve Administration, Haikou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
| |
Collapse
|
5
|
Wang Z, Zhang H, Gong W. Genome-wide identification and comparative analysis of alternative splicing across four legume species. PLANTA 2019; 249:1133-1142. [PMID: 30603789 DOI: 10.1007/s00425-018-03073-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/18/2018] [Indexed: 05/07/2023]
Abstract
MAIN CONCLUSION Alternative splicing EVENTS were genome-wide identified for four legume species, and nitrogen fixation-related gene families and evolutionary analysis was also performed. Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. Investigation of the genome-wide conserved AS events across different species will help with the understanding of the evolution of the functional diversity in legumes, allowing for genetic improvement. Genome-wide identification and characterization of AS were performed using the publically available mRNA, EST, and RNA-Seq data for four important legume species. A total of 15,165 AS genes in Glycine max, 6077 in Cicer arietinum, 7240 in Medicago truncatula, and 7358 in Lotus japonicus were identified. Intron retention (IntronR) was the dominant AS type among the identified events, with IntronR occurring from 53.76% in M. truncatula to 43.91% in C. arietinum. We identified 1159 AS genes that were conserved among four species. Furthermore, nine nitrogen fixation-related gene families with 237 genes were identified, and 80 of them were AS, accounting for the 43.48% in G. max and 27.78% in C. arietinum. An evolutionary analysis showed that these AS genes tended to be located adjacent to each other in the evolutionary tree and are unbalanced in the distribution in the sub-family. This study provides a foundation for future studies on transcription complexity, evolution, and the role of AS on plant functional regulation.
Collapse
Affiliation(s)
- Zan Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.
| | - Han Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Wenlong Gong
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| |
Collapse
|