| [1] |
Ismail AM, Heuer S, Thomson MJ, Wissuwa M. 2007. Genetic and genomic approaches to develop rice germplasm for problem soils. Plant Molecular Biology 65:547−70 doi: 10.1007/s11103-007-9215-2 |
| [2] |
Shahbaz M, Ashraf M. 2013. Improving salinity tolerance in cereals. Critical Reviews in Plant Sciences 32:237−49 doi: 10.1080/07352689.2013.758544 |
| [3] |
Dong Y, Hu G, Yu J, Thu SW, Grover CE, et al. 2020. Salt-tolerance diversity in diploid and polyploid cotton (Gossypium) species. The Plant Journal 101:1135−51 doi: 10.1111/tpj.14580 |
| [4] |
Foolad MR. 2004. Recent advances in genetics of salt tolerance in tomato. Plant Cell, Tissue and Organ Culture 76:101−19 doi: 10.1023/B:TICU.0000007308.47608.88 |
| [5] |
Guan R, Qu Y, Guo Y, Yu L, Liu Y, et al. 2014. Salinity tolerance in soybean is modulated by natural variation in GmSALT3. The Plant Journal 80:937−50 doi: 10.1111/tpj.12695 |
| [6] |
Chen R, Cheng Y, Han S, Van Handel B, Dong L, et al. 2017. Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar–sea rice 86. BMC Genomics 18:655 doi: 10.1186/s12864-017-4037-3 |
| [7] |
Wang J, Qin H, Zhou S, Wei P, Zhang H, et al. 2020. The ubiquitin-binding protein OsDSK2a mediates seedling growth and salt responses by regulating gibberellin metabolism in rice. The Plant Cell 32:414−28 doi: 10.1105/tpc.19.00593 |
| [8] |
Rana MM, Takamatsu T, Baslam M, Kaneko K, Itoh K, et al. 2019. Salt tolerance improvement in rice through efficient SNP marker-assisted selection coupled with speed-breeding. International Journal of Molecular Sciences 20:2585 doi: 10.3390/ijms20102585 |
| [9] |
Aycan M, Nahar L, Baslam M, Mitsui T. 2023. B-type response regulator hst1 controls salinity tolerance in rice by regulating transcription factors and antioxidant mechanisms. Plant Physiology and Biochemistry 196:542−55 doi: 10.1016/j.plaphy.2023.02.008 |
| [10] |
Yokoi S, Bressan RA, Hasegawa PM. 2002. Salt stress tolerance of plants. Working Report. Japan International Research Center for Agricultural Sciences. 23: 25-33 |
| [11] |
Munns R, Tester M. 2008. Mechanisms of salinity tolerance. Annual Review of Plant Biology 59:651−81 doi: 10.1146/annurev.arplant.59.032607.092911 |
| [12] |
Zhu JK. 2016. Abiotic stress signaling and responses in plants. Cell 167:313−24 doi: 10.1016/j.cell.2016.08.029 |
| [13] |
Flowers TJ, Colmer TD. 2008. Salinity tolerance in halophytes. New Phytologist 179:945−63 doi: 10.1111/j.1469-8137.2008.02531.x |
| [14] |
Zhang H, Han B, Wang T, Chen S, Li H, et al. 2012. Mechanisms of plant salt response: insights from proteomics. Journal of proteome research 11:49−67 doi: 10.1021/pr200861w |
| [15] |
Nilam R, Jyoti P, Sumitra C. 2018. Pharmacognostic and phytochemical studies of Ipomoea pes-caprae, an halophyte from Gujarat. Journal of Pharmacognosy and Phytochemistry 7:11−18 |
| [16] |
Akinniyi G, Lee J, Kim H, Lee JG, Yang I. 2022. A medicinal halophyte Ipomoea pes-caprae (Linn.) R. Br.: A review of its botany, traditional uses, phytochemistry, and bioactivity. Marine Drugs 20:329 doi: 10.3390/md20050329 |
| [17] |
Giovannini P, Howes MJR. 2017. Medicinal plants used to treat snakebite in Central America: Review and assessment of scientific evidence. Journal of Ethnopharmacology 199:240−56 doi: 10.1016/j.jep.2017.02.011 |
| [18] |
Ameamsri U, Tanee T, Chaveerach A, Peigneur S, Tytgat J, et al. 2021. Anti-inflammatory and detoxification activities of some Ipomoea species determined by ion channel inhibition and their phytochemical constituents. Science Asia 47:321−29 doi: 10.2306/scienceasia1513-1874.2021.042 |
| [19] |
Liu Y, Dai XB, Zhao LK, Huo KS, Jin PF, et al. 2020. RNA-seq reveals the salt tolerance of Ipomoea pes-caprae, a wild relative of sweet potato. Journal of Plant Physiology 255:153276 doi: 10.1016/j.jplph.2020.153276 |
| [20] |
Cheng Y, Zhou Q, Li W, Cheng H, Mohammadi MA, et al. 2021. De novo transcriptome assembly and gene expression profiling of Ipomoea pes-caprae L. under heat and cold stresses. Scientia Horticulturae 289:110379 doi: 10.1016/j.scienta.2021.110379 |
| [21] |
Zheng J, Su H, Lin R, Zhang H, Xia K, et al. 2019. Isolation and characterization of an atypical LEA gene (IpLEA) from Ipomoea pes-caprae conferring salt/drought and oxidative stress tolerance. Scientific Reports 9:14838 doi: 10.1038/s41598-019-50813-w |
| [22] |
Zhang M, Zhang H, Zheng JX, Mo H, Xia KF, et al. 2018. Functional identification of salt-stress-related genes using the FOX hunting system from Ipomoea pes-caprae. International Journal of Molecular Sciences 19:3446 doi: 10.3390/ijms19113446 |
| [23] |
Ye K, Dong C, Hu B, Yuan J, Sun J, et al. 2023. The genome size, chromosome number and the seed adaption to long-distance dispersal of Ipomoea pes-caprae (L.). Frontiers in Plant Science 14:1074935 doi: 10.3389/fpls.2023.1074935 |
| [24] |
Wang Y, Xu J, Hu B, Dong C, Sun J, et al. 2023. Assembly, annotation, and comparative analysis of Ipomoea chloroplast genomes provide insights into the parasitic characteristics of Cuscuta species. Frontiers in Plant Science 13:1074697 doi: 10.3389/fpls.2022.1074697 |
| [25] |
Xie T, Zheng JF, Liu S, Peng C, Zhou YM, et al. 2015. De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. Molecular Plant 8:489−92 doi: 10.1016/j.molp.2014.12.015 |
| [26] |
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, et al. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27:722−36 doi: 10.1101/gr.215087.116 |
| [27] |
Guan D, McCarthy SA, Wood J, Howe K, Wang Y, et al. 2020. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics 36:2896−98 doi: 10.1093/bioinformatics/btaa025 |
| [28] |
Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, et al. 2015. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biology 16:259 doi: 10.1186/s13059-015-0831-x |
| [29] |
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, et al. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356:92−95 doi: 10.1126/science.aal3327 |
| [30] |
Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238 doi: 10.1186/s13059-019-1832-y |
| [31] |
Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113 doi: 10.1186/1471-2105-5-113 |
| [32] |
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312−13 doi: 10.1093/bioinformatics/btu033 |
| [33] |
Tarailo-Graovac M, Chen N. 2004. Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics 5:4.10.1−4.10.14 doi: 10.1002/0471250953.bi0410s25 |
| [34] |
Qiao X, Li Q, Yin H, Qi K, Li L, et al. 2019. Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants. Genome Biology 20:38 doi: 10.1186/s13059-019-1650-2 |
| [35] |
Vinocur B, Altman A. 2005. Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Current Opinion in Biotechnology 16:123−32 doi: 10.1016/j.copbio.2005.02.001 |
| [36] |
Xiong L, Zhu JK. 2002. Molecular and genetic aspects of plant responses to osmotic stress. Plant, Cell & Environment 25:131−39 doi: 10.1046/j.1365-3040.2002.00782.x |
| [37] |
Ahmad R, Hussain S, Anjum MA, Khalid MF, Saqib M, et al. 2019. Oxidative stress and antioxidant defense mechanisms in plants under salt stress. In Plant abiotic stress tolerance: Agronomic, molecular and biotechnological approaches, eds. Hasanuzzaman M, Hakeem K, Nahar K, Alharby H. Cham: Springer. pp. 191−205. https://doi.org/10.1007/978-3-030-06118-0_8 |
| [38] |
Zhang M, Liang X, Wang L, Cao Y, Song W, et al. 2019. A HAK family Na+ transporter confers natural variation of salt tolerance in maize. Nature Plants 5:1297−308 doi: 10.1038/s41477-019-0565-y |
| [39] |
Hong JP, Takeshi Y, Kondou Y, Schachtman DP, Matsui M, et al. 2013. Identification and characterization of transcription factors regulating Arabidopsis HAK5. Plant and Cell Physiology 54:1478−90 doi: 10.1093/pcp/pct094 |
| [40] |
Rubio F, Fon M, Ródenas R, Nieves-Cordones M, Alemán F, et al. 2014. A low K+ signal is required for functional high-affinity K+ uptake through HAK5 transporters. Physiologia Plantarum 152:558−70 doi: 10.1111/ppl.12205 |
| [41] |
Wang Q, Guan C, Wang P, Lv ML, Ma Q, et al. 2015. AtHKT1;1 and AtHAK5 mediate low-affinity Na+ uptake in Arabidopsis thaliana under mild salt stress. Plant Growth Regulation 75:615−23 doi: 10.1007/s10725-014-9964-2 |
| [42] |
da Silva Barth C, de Souza HGT, Rocha LW, da Silva GF, Dos Anjos MF, et al. 2017. Ipomoea pes-caprae (L.) R. Br (Convolvulaceae) relieved nociception and inflammation in mice–A topical herbal medicine against effects due to cnidarian venom-skin contact. Journal of Ethnopharmacology 200:156−64 doi: 10.1016/j.jep.2017.02.014 |
| [43] |
Eakwaropas P, Ngawhirunpat T, Rojanarata T, Akkaramongkolporn P, Opanasopit P, et al. 2020. Fabrication of electrospun hydrogels loaded with Ipomoea pes-caprae (L.) R. Br extract for infected wound. Journal of Drug Delivery Science and Technology 55:101478 doi: 10.1016/j.jddst.2019.101478 |
| [44] |
Ievinsh G. 2006. Biological basis of biological diversity: physiological adaptations of plants to heterogeneous habitats along a sea coast. Acta Universitatis Latviensis 710:53−79 |
| [45] |
Yang J, Moeinzadeh MH, Kuhl H, Helmuth J, Xiao P, et al. 2017. Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nature Plants 3:696−703 doi: 10.1038/s41477-017-0002-z |
| [46] |
Hao Y, Bao W, Li G, Gagoshidze Z, Shu H, et al. 2021. The chromosome-based genome provides insights into the evolution in water spinach. Scientia Horticulturae 289:110501 doi: 10.1016/j.scienta.2021.110501 |
| [47] |
Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, et al. 2016. Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nature Communications 7:13295 doi: 10.1038/ncomms13295 |
| [48] |
Li M, Yang S, Xu W, Pu Z, Feng J, et al. 2019. The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development. BMC Plant Biology 19:119 doi: 10.1186/s12870-019-1708-z |
| [49] |
Wu S, Lau KH, Cao Q, Hamilton JP, Sun H, et al. 2018. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nature Communications 9:4580 doi: 10.1038/s41467-018-06983-8 |
| [50] |
Wee Y, Bhyan SB, Liu Y, Lu J, Li X, et al. 2019. The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing. Briefings in Functional Genomics 18:1−12 doi: 10.1093/bfgp/ely037 |
| [51] |
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841−42 doi: 10.1093/bioinformatics/btq033 |
| [52] |
Cheng Y, Sun J, Jiang M, Luo Z, Wang Y, et al. 2023. Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes. Horticulture Research 10:uhad161 doi: 10.1093/hr/uhad161 |
| [53] |
Bradshaw AD. 1965. Evolutionary significance of phenotypic plasticity in plants. Advances in Genetics 13:115−55 doi: 10.1016/S0065-2660(08)60048-6 |
| [54] |
Darwin C. 1859. On the origin of species. 1st Edition. UK: Routledge, Abingdon. |
| [55] |
Zuellig MP, Kenney AM, Sweigart AL. 2014. Evolutionary genetics of plant adaptation: insights from new model systems. Current Opinion in Plant Biology 18:44−50 doi: 10.1016/j.pbi.2014.01.001 |
| [56] |
Shen L, Liu Y, Xu B, Wang N, Zhao H, et al. 2017. Comparative genomic analysis reveals the environmental impacts on two Arcticibacter strains including sixteen Sphingobacteriaceae species. Scientific Reports 7:2055 doi: 10.1038/s41598-017-02191-4 |