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Eshel G, Duppen N, Wang G, Oh D, Kazachkova Y, Herzyk P, Amtmann A, Gordon M, Chalifa‐Caspi V, Oscar MA, Bar‐David S, Marshall‐Colon A, Dassanayake M, Barak S. Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica. THE NEW PHYTOLOGIST 2022; 236:1006-1026. [PMID: 35909295 PMCID: PMC9804903 DOI: 10.1111/nph.18411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A. hierochuntica reference transcriptome and identified extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat, and detecting positively selected genes in A. hierochuntica. The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat 'stress-ready' state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype. We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.
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Affiliation(s)
- Gil Eshel
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Nick Duppen
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Guannan Wang
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Dong‐Ha Oh
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Yana Kazachkova
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Pawel Herzyk
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Anna Amtmann
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Michal Gordon
- Bioinformatics Core Facility, The National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8410501Israel
| | - Vered Chalifa‐Caspi
- Bioinformatics Core Facility, The National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8410501Israel
| | - Michelle Arland Oscar
- Blaustein Center for Scientific CooperationBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Shirli Bar‐David
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Amy Marshall‐Colon
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Maheshi Dassanayake
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Simon Barak
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
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Miryeganeh M, Marlétaz F, Gavriouchkina D, Saze H. De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. THE NEW PHYTOLOGIST 2022; 233:2094-2110. [PMID: 34532854 PMCID: PMC9293310 DOI: 10.1111/nph.17738] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/02/2021] [Indexed: 05/27/2023]
Abstract
Mangroves are adapted to harsh environments, such as high ultraviolet (UV) light, low nutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources. We performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant mangrove species. We also performed the first genome-guided transcriptome assembly for mangrove species. The 309 Mb of the genome is predicted to encode 34 403 genes and has a repeat content of 48%. Depending on its growing environment, the natural B. gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. Moreover, high-salinity environments induced genome-wide DNA hypermethylation of transposable elements (TEs) in the B. gymnorhiza. DNA hypermethylation was concurrent with the transcriptional regulation of chromatin modifier genes, suggesting robust epigenome regulation of TEs in the B. gymnorhiza genome under high-salinity environments. The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating, harsh natural environments.
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
| | - Ferdinand Marlétaz
- Department of Genetics, Evolution and Environment (GEE)University College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Daria Gavriouchkina
- Molecular Genetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
| | - Hidetoshi Saze
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
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Guedes FADF, Rossetto PDB, Guimarães F, Wilwerth MW, Paes JES, Nicolás MF, Reinert F, Peixoto RS, Alves-Ferreira M. Characterization of Laguncularia racemosa transcriptome and molecular response to oil pollution. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 205:36-50. [PMID: 30317019 DOI: 10.1016/j.aquatox.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Mangroves are ecosystems of economic and ecological importance. Laguncularia racemosa (Combretaceae), popularly known as white mangrove, is a species that greatly contributes to the community structure of neotropical and West African mangrove forests. Despite the significance of these ecosystems, they have been destroyed by oil spills that can cause yellowing of leaves, increased sensitivity to other stresses and death of trees. However, the molecular response of plants to oil stress is poorly known. In this work, Illumina reads were de novo assembled into 46,944 transcripts of L. racemosa roots and leaves, including putative isoform variants. In addition to improving the genomic information available for mangroves, the L. racemosa assembled transcriptome allowed us to identify reference genes to normalize quantitative real-time PCR (qPCR) expression data from oil-stressed mangrove plants, which were used in RNASeq validation. The analysis of expression changes induced by the oil exposure revealed 310 and 286 responsive transcripts of leaves and roots, respectively, mainly up-regulated. Enriched GO categories related to chloroplasts and photosynthesis were found among both leaf and root oil-responsive transcripts, while "response to heat" and "response to hypoxia" were exclusively enriched in leaves and roots, respectively. The comparison of L. racemosa 12-h-oil-stressed leaf expression profile to previous Arabidopsis heat-stress studies and co-expression evidence also pointed to similarities between the heat and oil responses, in which the HSP-coding genes seem to play a key role. A subset of the L. racemosa oil-responsive root genes exhibited similar up-regulation profiles to their Arabidopsis homologs involved in hypoxia responses, including the HRA1 and LBD41 TF-coding genes. Genes linked to the ethylene pathway such as those coding for ERF TFs were also modulated during the L. racemosa root response to oil stress. Taken together, these results show that oil contamination affects photosynthesis, protein metabolism, hypoxia response and the ethylene pathway in L. racemosa 12-h-oil-exposed leaves and roots.
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Affiliation(s)
- Fernanda Alves de Freitas Guedes
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Priscilla de Barros Rossetto
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Fábia Guimarães
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Maurício Wolf Wilwerth
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Jorge Eduardo Santos Paes
- Centro de Pesquisa e Desenvolvimento Leopoldo Américo Miguez de Mello, PETROBRAS/CENPES, Cidade Universitária, Av. Horácio de Macedo, nº 950, 21941-915, Rio de Janeiro, RJ, Brazil.
| | - Marisa Fabiana Nicolás
- Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, n(o)333 - Quitandinha, 25651-075, Petrópolis, RJ, Brazil.
| | - Fernanda Reinert
- Laboratório de Ecofisiologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Raquel Silva Peixoto
- Laboratório de Ecologia Microbiana Molecular, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco K, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Márcio Alves-Ferreira
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
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Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis. Sci Rep 2017; 7:10031. [PMID: 28855698 PMCID: PMC5577154 DOI: 10.1038/s41598-017-10730-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/14/2017] [Indexed: 12/11/2022] Open
Abstract
Salinity affects growth and development of plants, but mangroves exhibit exceptional salt tolerance. With direct exposure to salinity, mangrove roots possess specific adaptations to tolerate salt stress. Therefore, studying the early effects of salt on mangrove roots can help us better understand the tolerance mechanisms. Using two-month-old greenhouse-grown seedlings of the mangrove tree Avicennia officinalis subjected to NaCl treatment, we profiled gene expression changes in the roots by RNA-sequencing. Of the 6547 genes that were differentially regulated in response to salt treatment, 1404 and 5213 genes were significantly up- and down-regulated, respectively. By comparative genomics, 93 key salt tolerance-related genes were identified of which 47 were up-regulated. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in ethylene and auxin signaling were up-regulated while those involved in ABA signaling were down-regulated. These results imply that ABA-independent signaling pathways also play a major role in salt tolerance of A. officinalis. Further, ethylene response factors (ERFs) were abundantly expressed upon salt treatment and the Arabidopsis mutant aterf115, a homolog of AoERF114 is characterized. Overall, our results would help in understanding the possible molecular mechanism underlying salt tolerance in plants.
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Guo W, Wu H, Zhang Z, Yang C, Hu L, Shi X, Jian S, Shi S, Huang Y. Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments. FRONTIERS IN PLANT SCIENCE 2017; 8:795. [PMID: 28559911 PMCID: PMC5432612 DOI: 10.3389/fpls.2017.00795] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/27/2017] [Indexed: 05/08/2023]
Abstract
Mangroves are woody plants that grow at the interface between land and sea in tropical and subtropical latitudes, where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures, and muddy, anaerobic soils. Rhizophoraceae is a key mangrove family, with highly developed morphological and physiological adaptations to extreme conditions. It is an ideal system for the study of the origin and adaptive evolution of mangrove plants. In this study, we characterized and comprehensively compared the transcriptomes of four mangrove species, from all four mangrove genera, as well as their closest terrestrial relative in Rhizophoraceae, using RNA-Seq. We obtained 41,936-48,845 unigenes with N50 values of 982-1,185 bp and 61.42-69.48% annotated for the five species in Rhizophoraceae. Orthology annotations of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Clusters of Orthologous Groups revealed overall similarities in the transcriptome profiles among the five species, whereas enrichment analysis identified remarkable genomic characteristics that are conserved across the four mangrove species but differ from their terrestrial relative. Based on 1,816 identified orthologs, phylogeny analysis and divergence time estimation revealed a single origin for mangrove species in Rhizophoraceae, which diverged from the terrestrial lineage ~56.4 million years ago (Mya), suggesting that the transgression during the Paleocene-Eocene Thermal Maximum may have been responsible for the entry of the mangrove lineage of Rhizophoraceae into intertidal environments. Evidence showed that the ancestor of Rhizophoraceae may have experienced a whole genome duplication event ~74.6 Mya, which may have increased the adaptability and survival chances of Rhizophoraceae during and following the Cretaceous-Tertiary extinction. The analysis of positive selection identified 10 positively selected genes from the ancestor branch of Rhizophoraceae mangroves, which were mainly associated with stress response, embryo development, and regulation of gene expression. Positive selection of these genes may be crucial for increasing the capability of stress tolerance (i.e., defense against salt and oxidative stress) and development of adaptive traits (i.e., vivipary) of Rhizophoraceae mangroves, and thus plays an important role in their adaptation to the stressful intertidal environments.
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Affiliation(s)
- Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Haidan Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Zhang Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Chao Yang
- Department of Neurosurgery, First Affiliated Hospital of Sun Yat-sen UniversityGuangzhou, China
| | - Ling Hu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Xianggang Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Shuguang Jian
- Chinese Academy of Sciences, South China Botanical GardenGuangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
- *Correspondence: Yelin Huang
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The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses. Funct Integr Genomics 2016; 16:465-80. [DOI: 10.1007/s10142-016-0501-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 12/23/2022]
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Small RNA transcriptomes of mangroves evolve adaptively in extreme environments. Sci Rep 2016; 6:27551. [PMID: 27278626 PMCID: PMC4899726 DOI: 10.1038/srep27551] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/20/2016] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are key players in plant stress responses. Here, we present the sRNA transcriptomes of mangroves Bruguiera gymnorrhiza and Kandelia candel. Comparative computational analyses and target predictions revealed that mangroves exhibit distinct sRNA regulatory networks that differ from those of glycophytes. A total of 32 known and three novel miRNA families were identified. Conserved and mangrove-specific miRNA targets were predicted; the latter were widely involved in stress responses. The known miRNAs showed differential expression between the mangroves and glycophytes, reminiscent of the adaptive stress-responsive changes in Arabidopsis. B. gymnorrhiza possessed highly abundant but less conserved TAS3 trans-acting siRNAs (tasiRNAs) in addition to tasiR-ARFs, with expanded potential targets. Our results indicate that the evolutionary alteration of sRNA expression levels and the rewiring of sRNA-regulatory networks are important mechanisms underlying stress adaptation. We also identified sRNAs that are involved in salt and/or drought tolerance and nutrient homeostasis as possible contributors to mangrove success in stressful environments.
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Jyothi-Prakash PA, Mohanty B, Wijaya E, Lim TM, Lin Q, Loh CS, Kumar PP. Identification of salt gland-associated genes and characterization of a dehydrin from the salt secretor mangrove Avicennia officinalis. BMC PLANT BIOLOGY 2014; 14:291. [PMID: 25404140 PMCID: PMC4247641 DOI: 10.1186/s12870-014-0291-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 10/15/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND Salt stress is a major challenge for growth and development of plants. The mangrove tree Avicennia officinalis has evolved salt tolerance mechanisms such as salt secretion through specialized glands on its leaves. Although a number of structural studies on salt glands have been done, the molecular mechanism of salt secretion is not clearly understood. Also, studies to identify salt gland-specific genes in mangroves have been scarce. RESULTS By subtractive hybridization (SH) of cDNA from salt gland-rich cell layers (tester) with mesophyll tissues as the driver, several Expressed Sequence Tags (ESTs) were identified. The major classes of ESTs identified include those known to be involved in regulating metabolic processes (37%), stress response (17%), transcription (17%), signal transduction (17%) and transport functions (12%). A visual interactive map generated based on predicted functional gene interactions of the identified ESTs suggested altered activities of hydrolase, transmembrane transport and kinases. Quantitative Real-Time PCR (qRT-PCR) was carried out to validate the expression specificity of the ESTs identified by SH. A Dehydrin gene was chosen for further experimental analysis, because it is significantly highly expressed in salt gland cells, and dehydrins are known to be involved in stress remediation in other plants. Full-length Avicennia officinalis Dehydrin1 (AoDHN1) cDNA was obtained by Rapid Amplification of cDNA Ends. Phylogenetic analysis and further characterization of this gene suggested that AoDHN1 belongs to group II Late Embryogenesis Abundant proteins. qRT-PCR analysis of Avicennia showed up-regulation of AoDHN1 in response to salt and drought treatments. Furthermore, some functional insights were obtained by growing E. coli cells expressing AoDHN1. Growth of E. coli cells expressing AoDHN1 was significantly higher than that of the control cells without AoDHN1 under salinity and drought stresses, suggesting that the mangrove dehydrin protein helps to mitigate the abiotic stresses. CONCLUSIONS Thirty-four ESTs were identified to be enriched in salt gland-rich tissues of A. officinalis leaves. qRT-PCR analysis showed that 10 of these were specifically enriched in the salt gland-rich tissues. Our data suggest that one of the selected genes, namely, AoDHN1 plays an important role to mitigate salt and drought stress responses.
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Affiliation(s)
- Pavithra A Jyothi-Prakash
- />Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Republic of Singapore
- />NUS Environmental Research Institute (NERI), National University of Singapore, #02-01, T-Lab Building, 5A Engineering Drive 1, Singapore, Republic of Singapore
| | - Bijayalaxmi Mohanty
- />Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Republic of Singapore
| | - Edward Wijaya
- />IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871 Japan
| | - Tit-Meng Lim
- />Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Republic of Singapore
| | - Qingsong Lin
- />Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Republic of Singapore
| | - Chiang-Shiong Loh
- />Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Republic of Singapore
- />NUS Environmental Research Institute (NERI), National University of Singapore, #02-01, T-Lab Building, 5A Engineering Drive 1, Singapore, Republic of Singapore
| | - Prakash P Kumar
- />Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Republic of Singapore
- />Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, Republic of Singapore
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Lin X, Peng F, Huang J, Zhang T, Shi S, Tang T. Isolation and characterization of RARE-1, a Ty1/copia-like retrotransposon domesticated in the genome of Rhizophora apiculata. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.03.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Khraiwesh B, Pugalenthi G, Fedoroff NV. Identification and analysis of red sea mangrove (Avicennia marina) microRNAs by high-throughput sequencing and their association with stress responses. PLoS One 2013; 8:e60774. [PMID: 23593307 PMCID: PMC3620391 DOI: 10.1371/journal.pone.0060774] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/02/2013] [Indexed: 11/18/2022] Open
Abstract
Although RNA silencing has been studied primarily in model plants, advances in high-throughput sequencing technologies have enabled profiling of the small RNA components of many more plant species, providing insights into the ubiquity and conservatism of some miRNA-based regulatory mechanisms. Small RNAs of 20 to 24 nucleotides (nt) are important regulators of gene transcript levels by either transcriptional or by posttranscriptional gene silencing, contributing to genome maintenance and controlling a variety of developmental and physiological processes. Here, we used deep sequencing and molecular methods to create an inventory of the small RNAs in the mangrove species, Avicennia marina. We identified 26 novel mangrove miRNAs and 193 conserved miRNAs belonging to 36 families. We determined that 2 of the novel miRNAs were produced from known miRNA precursors and 4 were likely to be species-specific by the criterion that we found no homologs in other plant species. We used qRT-PCR to analyze the expression of miRNAs and their target genes in different tissue sets and some demonstrated tissue-specific expression. Furthermore, we predicted potential targets of these putative miRNAs based on a sequence homology and experimentally validated through endonucleolytic cleavage assays. Our results suggested that expression profiles of miRNAs and their predicted targets could be useful in exploring the significance of the conservation patterns of plants, particularly in response to abiotic stress. Because of their well-developed abilities in this regard, mangroves and other extremophiles are excellent models for such exploration.
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Affiliation(s)
- Basel Khraiwesh
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
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Oh DH, Dassanayake M, Bohnert HJ, Cheeseman JM. Life at the extreme: lessons from the genome. Genome Biol 2012; 13:241. [PMID: 22390828 DOI: 10.1186/gb-2012-13-3-241] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Extremophile plants thrive in places where most plant species cannot survive. Recent developments in high-throughput technologies and comparative genomics are shedding light on the evolutionary mechanisms leading to their adaptation.
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Affiliation(s)
- Dong-Ha Oh
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 61801, USA
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12
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Oh DH, Dassanayake M, Bohnert HJ, Cheeseman JM. Life at the extreme: lessons from the genome. Genome Biol 2012. [DOI: 10.1186/gb4003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Huang J, Lu X, Yan H, Chen S, Zhang W, Huang R, Zheng Y. Transcriptome characterization and sequencing-based identification of salt-responsive genes in Millettia pinnata, a semi-mangrove plant. DNA Res 2012; 19:195-207. [PMID: 22351699 PMCID: PMC3325082 DOI: 10.1093/dnares/dss004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Semi-mangroves form a group of transitional species between glycophytes and halophytes, and hold unique potential for learning molecular mechanisms underlying plant salt tolerance. Millettia pinnata is a semi-mangrove plant that can survive a wide range of saline conditions in the absence of specialized morphological and physiological traits. By employing the Illumina sequencing platform, we generated ~192 million short reads from four cDNA libraries of M. pinnata and processed them into 108,598 unisequences with a high depth of coverage. The mean length and total length of these unisequences were 606 bp and 65.8 Mb, respectively. A total of 54,596 (50.3%) unisequences were assigned Nr annotations. Functional classification revealed the involvement of unisequences in various biological processes related to metabolism and environmental adaptation. We identified 23,815 candidate salt-responsive genes with significantly differential expression under seawater and freshwater treatments. Based on the reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR analyses, we verified the changes in expression levels for a number of candidate genes. The functional enrichment analyses for the candidate genes showed tissue-specific patterns of transcriptome remodelling upon salt stress in the roots and the leaves. The transcriptome of M. pinnata will provide valuable gene resources for future application in crop improvement. In addition, this study sets a good example for large-scale identification of salt-responsive genes in non-model organisms using the sequencing-based approach.
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Affiliation(s)
- Jianzi Huang
- College of Life Science, Shenzhen University, Shenzhen, China
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