Resources from the Literature

The following list is a collection of papers on genomic and transcriptomic resources for halophytes, not limited to a particular species. Because it is based on a search of PubMed, there may be some important articles not included. Results are shown in reverse chronological order. Note: mangroves and members of the Brassicaceae are excluded but are covered elsewhere on the site.


  1. Zhao, L, Yang, Z, Guo, Q, Mao, S, Li, S, Sun, F et al. (2017) Transcriptomic Profiling and Physiological Responses of Halophyte Kochia sieversiana Provide Insights into Salt Tolerance. Front Plant Sci 8:1985. doi: 10.3389/fpls.2017.01985. PubMed PMID:29225608 PubMed Central PMC5705942.
  2. Lu, L, Li, X, Hao, Z, Yang, L, Zhang, J, Peng, Y et al. (2017) Phylogenetic studies and comparative chloroplast genome analyses elucidate the basal position of halophyte Nitraria sibirica (Nitrariaceae) in the Sapindales. Mitochondrial DNA A DNA Mapp Seq Anal :1-11. doi: 10.1080/24701394.2017.1350954. PubMed PMID:28712318 .
  3. Kakeshpour, T, Monfared, SR, Ebrahimi, A, Beyraghdar Kashkooli, A, Ebrahimie, E (2017) Expression analyses of salinity stress- associated ESTs in Aeluropus littoralis. Gene Expr. Patterns 25-26:76-84. doi: 10.1016/j.gep.2017.06.005. PubMed PMID:28625895 .
  4. Gharat, SA, Parmar, S, Tambat, S, Vasudevan, M, Shaw, BP Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes. PLoS ONE 11:e0163485. doi: 10.1371/journal.pone.0163485. PubMed PMID:27682829 PubMed Central PMC5040429.
  5. Bedre, R, Mangu, VR, Srivastava, S, Sanchez, LE, Baisakh, N (2016) Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity. BMC Genomics 17:657. doi: 10.1186/s12864-016-3017-3. PubMed PMID:27542721 PubMed Central PMC4992267.
  6. Liu, J, Zhou, Y, Luo, C, Xiang, Y, An, L (2016) De Novo Transcriptome Sequencing of Desert Herbaceous Achnatherum splendens (Achnatherum) Seedlings and Identification of Salt Tolerance Genes. Genes (Basel) 7:. doi: 10.3390/genes7040012. PubMed PMID:27023614 PubMed Central PMC4846842.
  7. Jin, H, Dong, D, Yang, Q, Zhu, D (2016) Salt-Responsive Transcriptome Profiling of Suaeda glauca via RNA Sequencing. PLoS ONE 11:e0150504. doi: 10.1371/journal.pone.0150504. PubMed PMID:26930632 PubMed Central PMC4773115.
  8. Gharat, SA, Shaw, BP (2016) Computational prediction and experimental validation of a novel miRNA in Suaeda maritima, a halophyte. Genet. Mol. Res. 15:. doi: 10.4238/gmr.15017527. PubMed PMID:26909919 .
  9. Tiwari, V, Patel, MK, Chaturvedi, AK, Mishra, A, Jha, B (2016) Functional Characterization of the Tau Class Glutathione-S-Transferases Gene (SbGSTU) Promoter of Salicornia brachiata under Salinity and Osmotic Stress. PLoS ONE 11:e0148494. doi: 10.1371/journal.pone.0148494. PubMed PMID:26885663 PubMed Central PMC4757536.
  10. Skorupa, M, Gołębiewski, M, Domagalski, K, Kurnik, K, Abu Nahia, K, Złoch, M et al. (2016) Transcriptomic profiling of the salt stress response in excised leaves of the halophyte Beta vulgaris ssp. maritima. Plant Sci. 243:56-70. doi: 10.1016/j.plantsci.2015.11.007. PubMed PMID:26795151 .
  11. Mondal, TK, Ganie, SA, Debnath, AB (2015) Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice. PLoS ONE 10:e0140675. doi: 10.1371/journal.pone.0140675. PubMed PMID:26506249 PubMed Central PMC4623511.
  12. Zhang, L, Hao, J, Bao, M, Hasi, A, Niu, Y (2015) Cloning and characterization of a Ca(2+)/H(+) exchanger from the halophyte Salicornia europaea L. Plant Physiol. Biochem. 96:321-8. doi: 10.1016/j.plaphy.2015.08.011. PubMed PMID:26332662 .
  13. Tiwari, V, Chaturvedi, AK, Mishra, A, Jha, B (2015) Introgression of the SbASR-1 gene cloned from a halophyte Salicornia brachiate enhances salinity and drought endurance in transgenic groundnut (arachis hypogaea)and acts as a transcription factor [corrected]. PLoS ONE 10:e0131567. doi: 10.1371/journal.pone.0131567. PubMed PMID:26158616 PubMed Central PMC4497679.
  14. Ben-Saad, R, Meynard, D, Ben-Romdhane, W, Mieulet, D, Verdeil, JL, Al-Doss, A et al. (2015) The promoter of the AlSAP gene from the halophyte grass Aeluropus littoralis directs a stress-inducible expression pattern in transgenic rice plants. Plant Cell Rep. 34:1791-806. doi: 10.1007/s00299-015-1825-6. PubMed PMID:26123290 .
  15. Diray-Arce, J, Clement, M, Gul, B, Khan, MA, Nielsen, BL (2015) Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. BMC Genomics 16:353. doi: 10.1186/s12864-015-1553-x. PubMed PMID:25943316 PubMed Central PMC4422317.
  16. Wang, J, Li, B, Meng, Y, Ma, X, Lai, Y, Si, E et al. (2015) Transcriptomic profiling of the salt-stress response in the halophyte Halogeton glomeratus. BMC Genomics 16:169. doi: 10.1186/s12864-015-1373-z. PubMed PMID:25880042 PubMed Central PMC4363069.
  17. Chen, Y, Zong, J, Tan, Z, Li, L, Hu, B, Chen, C et al. (2015) Systematic mining of salt-tolerant genes in halophyte-Zoysia matrella through cDNA expression library screening. Plant Physiol. Biochem. 89:44-52. doi: 10.1016/j.plaphy.2015.02.007. PubMed PMID:25689412 .
  18. Yuan, F, Lyu, MJ, Leng, BY, Zheng, GY, Feng, ZT, Li, PH et al. (2015) Comparative transcriptome analysis of developmental stages of the Limonium bicolor leaf generates insights into salt gland differentiation. Plant Cell Environ. 38:1637-57. doi: 10.1111/pce.12514. PubMed PMID:25651944 .
  19. Tsutsumi, K, Yamada, N, Cha-um, S, Tanaka, Y, Takabe, T (2015) Differential accumulation of glycinebetaine and choline monooxygenase in bladder hairs and lamina leaves of Atriplex gmelini under high salinity. J. Plant Physiol. 176:101-7. doi: 10.1016/j.jplph.2014.12.009. PubMed PMID:25588694 .
  20. Zhang, X, Liao, M, Chang, D, Zhang, F (2014) Comparative transcriptome analysis of the Asteraceae halophyte Karelinia caspica under salt stress. BMC Res Notes 7:927. doi: 10.1186/1756-0500-7-927. PubMed PMID:25515859 PubMed Central PMC4320537.
  21. Chaturvedi, AK, Patel, MK, Mishra, A, Tiwari, V, Jha, B (2014) The SbMT-2 gene from a halophyte confers abiotic stress tolerance and modulates ROS scavenging in transgenic tobacco. PLoS ONE 9:e111379. doi: 10.1371/journal.pone.0111379. PubMed PMID:25340650 PubMed Central PMC4207811.
  22. Li, Y, Takano, T, Liu, S (2014) Discovery and characterization of two novel salt-tolerance genes in Puccinellia tenuiflora. Int J Mol Sci 15:16469-83. doi: 10.3390/ijms150916469. PubMed PMID:25238412 PubMed Central PMC4200785.
  23. Li, J, Sun, X, Yu, G, Jia, C, Liu, J, Pan, H et al. (2014) Generation and analysis of expressed sequence tags (ESTs) from halophyte Atriplex canescens to explore salt-responsive related genes. Int J Mol Sci 15:11172-89. doi: 10.3390/ijms150611172. PubMed PMID:24960361 PubMed Central PMC4100206.
  24. Tiwari, V, Chaturvedi, AK, Mishra, A, Jha, B (2014) The transcriptional regulatory mechanism of the peroxisomal ascorbate peroxidase (pAPX) gene cloned from an extreme halophyte, Salicornia brachiata. Plant Cell Physiol. 55:201-17. doi: 10.1093/pcp/pct172. PubMed PMID:24285755 .
  25. Singh, N, Mishra, A, Jha, B (2014) Over-expression of the peroxisomal ascorbate peroxidase (SbpAPX) gene cloned from halophyte Salicornia brachiata confers salt and drought stress tolerance in transgenic tobacco. Mar. Biotechnol. 16:321-32. doi: 10.1007/s10126-013-9548-6. PubMed PMID:24197564 .
  26. Prinz, K, Weising, K, Hensen, I (2013) Habitat fragmentation and recent bottlenecks influence genetic diversity and differentiation of the Central European halophyte Suaeda maritima (Chenopodiaceae). Am. J. Bot. 100:2210-8. doi: 10.3732/ajb.1300097. PubMed PMID:24148614 .
  27. Garg, R, Verma, M, Agrawal, S, Shankar, R, Majee, M, Jain, M et al. (2014) Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. DNA Res. 21:69-84. doi: 10.1093/dnares/dst042. PubMed PMID:24104396 PubMed Central PMC3925395.
  28. Li, B, Duan, H, Li, J, Deng, XW, Yin, W, Xia, X et al. (2013) Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol. Biol. 81:525-39. doi: 10.1007/s11103-013-0010-y. PubMed PMID:23430564 .
  29. Zhang, GH, Wang, H, Wang, XD, Feng, M, Li, HM, Li, SY et al. (2012) [Isolation of the promoter region of HAK gene from Aeluropus littoralis and functional analysis in rice]. Yi Chuan 34:742-8. . PubMed PMID:22698746 .
  30. Baisakh, N, RamanaRao, MV, Rajasekaran, K, Subudhi, P, Janda, J, Galbraith, D et al. (2012) Enhanced salt stress tolerance of rice plants expressing a vacuolar H+ -ATPase subunit c1 (SaVHAc1) gene from the halophyte grass Spartina alterniflora Löisel. Plant Biotechnol. J. 10:453-64. doi: 10.1111/j.1467-7652.2012.00678.x. PubMed PMID:22284568 .
  31. He, H, Yajing, N, Huawen, C, Xingjiao, T, Xinli, X, Weilun, Y et al. (2012) cDNA-AFLP analysis of salt-inducible genes expression in Chrysanthemum lavandulifolium under salt treatment. J. Plant Physiol. 169:410-20. doi: 10.1016/j.jplph.2011.09.013. PubMed PMID:22257748 .
  32. Ayarpadikannan, S, Chung, E, Cho, CW, So, HA, Kim, SO, Jeon, JM et al. (2012) Exploration for the salt stress tolerance genes from a salt-treated halophyte, Suaeda asparagoides. Plant Cell Rep. 31:35-48. doi: 10.1007/s00299-011-1137-4. PubMed PMID:21874516 .
  33. Wu, S, Su, Q, An, LJ (2010) Isolation of choline monooxygenase (CMO) gene from Salicornia europaea and enhanced salt tolerance of transgenic tobacco with CMO genes. Indian J. Biochem. Biophys. 47:298-305. . PubMed PMID:21280567 .
  34. Saad, RB, Romdhan, WB, Zouari, N, Azaza, J, Mieulet, D, Verdeil, JL et al. (2011) Promoter of the AlSAP gene from the halophyte grass Aeluropus littoralis directs developmental-regulated, stress-inducible, and organ-specific gene expression in transgenic tobacco. Transgenic Res. 20:1003-18. doi: 10.1007/s11248-010-9474-6. PubMed PMID:21188636 .
  35. Jha, B, Sharma, A, Mishra, A (2011) Expression of SbGSTU (tau class glutathione S-transferase) gene isolated from Salicornia brachiata in tobacco for salt tolerance. Mol. Biol. Rep. 38:4823-32. doi: 10.1007/s11033-010-0625-x. PubMed PMID:21136169 .
  36. Bellati, J, Alleva, K, Soto, G, Vitali, V, Jozefkowicz, C, Amodeo, G et al. (2010) Intracellular pH sensing is altered by plasma membrane PIP aquaporin co-expression. Plant Mol. Biol. 74:105-18. doi: 10.1007/s11103-010-9658-8. PubMed PMID:20593222 .
  37. Ben Saad, R, Zouari, N, Ben Ramdhan, W, Azaza, J, Meynard, D, Guiderdoni, E et al. (2010) Improved drought and salt stress tolerance in transgenic tobacco overexpressing a novel A20/AN1 zinc-finger "AlSAP" gene isolated from the halophyte grass Aeluropus littoralis. Plant Mol. Biol. 72:171-90. doi: 10.1007/s11103-009-9560-4. PubMed PMID:19838809 .
  38. Guo, YQ, Tian, ZY, Qin, GY, Yan, DL, Zhang, J, Zhou, WZ et al. (2009) Gene expression of halophyte Kosteletzkya virginica seedlings under salt stress at early stage. Genetica 137:189-99. doi: 10.1007/s10709-009-9384-9. PubMed PMID:19588254 .
  39. Jha, B, Agarwal, PK, Reddy, PS, Lal, S, Sopory, SK, Reddy, MK et al. (2009) Identification of salt-induced genes from Salicornia brachiata, an extreme halophyte through expressed sequence tags analysis. Genes Genet. Syst. 84:111-20. . PubMed PMID:19556705 .
  40. Li, H, Wang, Y, Jiang, J, Liu, G, Gao, C, Yang, C et al. (2009) Identification of genes responsive to salt stress on Tamarix hispida roots. Gene 433:65-71. doi: 10.1016/j.gene.2008.12.007. PubMed PMID:19146931 .
  41. Baisakh, N, Subudhi, PK (2009) Heat stress alters the expression of salt stress induced genes in smooth cordgrass (Spartina alterniflora L.). Plant Physiol. Biochem. 47:232-5. doi: 10.1016/j.plaphy.2008.11.010. PubMed PMID:19109026 .
  42. Pagliano, C, La Rocca, N, Andreucci, F, Deák, Z, Vass, I, Rascio, N et al. (2009) The extreme halophyte Salicornia veneta is depleted of the extrinsic PsbQ and PsbP proteins of the oxygen-evolving complex without loss of functional activity. Ann. Bot. 103:505-15. doi: 10.1093/aob/mcn234. PubMed PMID:19033288 PubMed Central PMC2707329.
  43. Chang-Qing, Z, Shunsaku, N, Shenkui, L, Tetsuo, T (2008) Characterization of two plasma membrane protein 3 genes (PutPMP3) from the alkali grass, Puccinellia tenuiflora, and functional comparison of the rice homologues, OsLti6a/b from rice. BMB Rep 41:448-54. . PubMed PMID:18593528 .
  44. Liu, HH, Liu, J, Fan, SL, Song, MZ, Han, XL, Liu, F et al. (2008) Molecular cloning and characterization of a salinity stress-induced gene encoding DEAD-box helicase from the halophyte Apocynum venetum. J. Exp. Bot. 59:633-44. doi: 10.1093/jxb/erm355. PubMed PMID:18272921 .
  45. Gao, C, Wang, Y, Liu, G, Yang, C, Jiang, J, Li, H et al. (2008) Expression profiling of salinity-alkali stress responses by large-scale expressed sequence tag analysis in Tamarix hispid. Plant Mol. Biol. 66:245-58. doi: 10.1007/s11103-007-9266-4. PubMed PMID:18058243 .
  46. Li, B, Wei, A, Song, C, Li, N, Zhang, J (2008) Heterologous expression of the TsVP gene improves the drought resistance of maize. Plant Biotechnol. J. 6:146-59. doi: 10.1111/j.1467-7652.2007.00301.x. PubMed PMID:17999658 .
  47. Zouari, N, Ben Saad, R, Legavre, T, Azaza, J, Sabau, X, Jaoua, M et al. (2007) Identification and sequencing of ESTs from the halophyte grass Aeluropus littoralis. Gene 404:61-9. doi: 10.1016/j.gene.2007.08.021. PubMed PMID:17916418 .
  48. Li, Q, Yin, H, Li, D, Zhu, H, Zhang, Y, Zhu, W et al. (2007) Isolation and characterization of CMO gene promoter from halophyte Suaeda liaotungensis K. J Genet Genomics 34:355-61. doi: 10.1016/S1673-8527(07)60038-1. PubMed PMID:17498634 .
  49. Chen, SH, Guo, SL, Wang, ZL, Zhao, JQ, Zhao, YX, Zhang, H et al. (2007) Expressed sequence tags from the halophyte Limonium sinense. DNA Seq. 18:61-7. doi: 10.1080/10425170601108555. PubMed PMID:17364815 .
  50. Dyachenko, OV, Zakharchenko, NS, Shevchuk, TV, Bohnert, HJ, Cushman, JC, Buryanov, YI et al. (2006) Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress. Biochemistry Mosc. 71:461-5. . PubMed PMID:16615868 .
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  52. Wang, Y, Chu, Y, Liu, G, Wang, MH, Jiang, J, Hou, Y et al. (2007) Identification of expressed sequence tags in an alkali grass (Puccinellia tenuiflora) cDNA library. J. Plant Physiol. 164:78-89. doi: 10.1016/j.jplph.2005.12.006. PubMed PMID:16545489 .
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