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Major publications：

• 1. Shi T, Huneau C, Zhang Y, Li Y, Chen JM^*, Salse J^*, Wang QF^*. 2022. The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution. Nature Plants, 8(7): 764-777.
  2. Zhang Y, Yang XY, Van de Peer Y, Chen JM^*, Marchal K^*, Shi T^*. 2022. Evolution of isoform-level gene expression patterns across tissues during lotus species divergence. The Plant Journal, 112(3): 830-846.
  3. Chen LY^#, Lu B^#, Morales-Briones DF^#, Moody ML, Liu F, Hu GW, Huang CH*, Chen JM^*, Wang QF^*. 2022. Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments. Molecular Biology and Evolution, 39(5): 1–18.
  4. Zhang Y^#, Li H^#, Yang XY, Chen, JM^*, Shi T^*. 2022. Expression rewiring and methylation of non-coding RNAs involved in rhizome phenotypic variations of lotus ecotypes. Computational and Structural Biotechnology Journal, 20: 2848-2860.
  5. Li ZZ^#, Lehtonen S^#, Martins K, Wang QF, Chen JM^*. 2022. Complete genus-level plastid phylogenomics of Alismataceae with revisited historical biogeography. Molecular Phylogenetics and Evolution, 166:107334.
  6. Li ZZ, Lehtonen S, Gichira AW, Martins K, Efremov A, Wang QF, Chen JM^*. 2022. Plastome phylogenomics and historical biogeography of aquatic plant genus Hydrocharis (Hydrocharitaceae). BMC Plant Biology, 22(1): 1-11.
  7. Li ZZ, Wang QF, Chen JM^*. 2022. Ottelia songmingensis, a new rank and combination of Hydrocharitaceae from China. Phytotaxa, 554(1): 101–102.
  8. Ngarega BK, Nzei JM, Saina JK, Halmy MWA, Chen JM, Li, ZZ^*. 2022. Mapping the habitat suitability of Ottelia species in Africa. Plant Diversity, 44(5): 468–480.
  9. Gao ZY, Liang YT, Wang YH, Xiao YJ, Chen JM, Yang XY^*, Shi T^*. 2022. Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations. Frontiers in Plant Science, 13: 973347.
  10. Qian ZH, Li Y, Yang JS, Shi T, Li ZZ^*,Chen JM^*. 2022. The chromosome-level genome of a free-floating aquatic weed Pistia stratiotes provides insights into its rapid invasion. Molecular Ecology Resources, 22(7): 2732–2743.
  11. Yang JS, Qian ZH, Shi T, Li ZZ^*, Chen JM^*. 2022. Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness. DNA Research, 29(4): 1–11.
  12. Li ZZ, Gichira AW, Muchuku JK, Li W, Wang GX^*, Chen JM^*. 2021. Plastid phylogenomics and biogeography of the genus Monochoria (Pontederiaceae). Journal of Systematics and Evolution, 59(5):1027-1039.
  13. Nzei JM, Ngarega BK, Mwanzia VM, Musili PM, Wang QF, Chen JM^*. 2021. The past, current, and future distribution modeling of four water lilies (Nymphaea) in Africa indicates varying suitable habitats and distribution in climate change. Aquatic Botany, 173: 103416.
  14. Ngarega BK, Gichira AW, Karichu MJ, Gituru RW, Wang QF, Chen JM, Li ZZ^*. 2021. Genetic diversity and population structure of Ottelia ulvifolia (Hydrocharitaceae) from three freshwater ecoregions in Zambia. Aquatic Botany, 173: 103412.
  15. Li H^#, Yang XY^#, Wang QF, Chen JM^*, Shi T^*. 2021. Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus). Molecular Ecology, 30(12): 2831-2845.
  16. Li H, Yang XY, Zhang, Y, Gao ZY, Liang YT, Chen JM^*, Shi T^*. 2021. Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera. Scientific Data, 8(1): 38.
  17. Gao ZY, Li H, Yang XY, Yang PF, Chen JM^*, Shi T^*. 2021. Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera). Plant Molecular Biology, 106: 207-220.
  18. Li ZZ, Ngarega BK, Lehtonen S, Gichira AW, Karichu MJ, Wang QF, Chen JM^*. 2020. Cryptic diversity within the African aquatic plant Ottelia ulvifolia (Hydrocharitaceae) revealed by population genetic and phylogenetic analyses. Journal of plant research, 133, 373-381.
  19. Shi T, Rahmani RS, Gugger PF, Wang MH, Li H, Zhang Y, Li ZZ, Wang QF^*, Van de Peer Y^*, Kathleen M^*, Chen JM^*. 2020. Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants. Molecular Biology and Evolution, 37(8): 2394-2413.
  20. Shi T^*, Chen JM*. 2020. A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication. Genome Biology, 21: 295.
  21. Li ZZ, Lehtonen S, Martins K, Gichira AW, Wu S, Li W, Hu GW, Liu Y, Zou CY, Wang QF, Chen JM^*. 2020. Phylogenomics of the aquatic plant genus Ottelia (Hydrocharitaceae): implications for historical biogeography. Molecular Phylogenetics and Evolution, 152: 106939.
  22. Islam MR, Zhang Y, Li ZZ, Liu H, Chen JM^*, Yang XY^*. 2020. Genetic diversity, population structure, and historical gene flow of Nelumbo lutea in USA using microsatellite markers. Aquatic Botany, 160: 103162.
  23. Mekbib Y, Huang SX, Ngarega BK, Li ZZ, Shi T, Ou, KF, Liang YT, Chen JM^*, Yang XY^* .2020. The level of genetic diversity and differentiation of tropical lotus, Nelumbo nucifera Gaertn.(Nelumbonaceae) from Australia, India, and Thailand. Botanical studies, 61(1): 1-11.
  24. Li ZZ^#, Islam MR^#, Huang SX, Yang D, Mekbib Y, Svetlana P, Sun HB, Chen JM^*, Yang XY^*. 2020. Genetic diversity comparisons of wild populations of Nelumbo nucifera (Nelumbonaceae) in Russia and China using microsatellite markers. Plant Systematics and Evolution, 306: 1-12.
  25. Li ZZ, Wu S, Zou CY, Liu Y, Hu GW, Lehtonen S, Wang QF, Chen JM^*. 2019. Ottelia fengshanensis, a new bisexual species of Ottelia (Hydrocharitaceae) from southwestern China. PhytoKeys, 135: 1-10.
  26. Li ZZ^#, Lu MX^#, Gichira AW, Islam MR, Wang QF, Chen JM^*. 2019. Genetic diversity and population structure of Ottelia acuminata var. jingxiensis, an endangered endemic aquatic plant from southwest China. Aquatic Botany, 152: 20-26.
  27. Li ZZ, Liao K, Zou CY, Liu Y, Hu GW, Wang, QF^*, Chen, JM^*. (2018). Ottelia guanyangensis (Hydrocharitaceae), a new species from southwestern China. Phytotaxa, 361(3): 294-300.
  28. Li ZZ, Gichira AW, Wang QF, Chen JM^*. 2018. Genetic diversity and population structure of the endangered basal angiosperm Brasenia schreberi (Cabombaceae) in China. PeerJ, 6: e5296.
  29. Li ZZ^#, Saina JK^#, Gichira AW, Kyalo CM, Wang QF^*,Chen JM^*. 2018. Comparative genomics of the balsaminaceae sister genera Hydrocera triflora and Impatiens pinfanensis. International Journal of Molecular Sciences, 19(1)： 319.
  30. He DX^#, Gichira AW^#, Li ZZ, Nzei JM, Guo, YH, Wang QF, Chen, JM^*. 2018. Intergeneric relationships within the early-diverging angiosperm family Nymphaeaceae based on chloroplast phylogenomics. International Journal of Molecular Sciences, 19(12): 3780.
  31. He DX, Guo P, Gugger PF, Guo YH, Liu X^*, Chen, JM^*. 2018. Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae) with comparative transcriptomics. PeerJ, 6: e4448.
  32. Chen JM^#, Du ZY^#, Long ZC, Gichira AW, Wang QF*. 2017. Molecular divergence among varieties of Ottelia acuminata (Hydrocharitaceae) in the Yunnan-Guizhou Plateau. Aquatic Botany, 140: 62-68.
  33. Li ZZ, Sun SS, Wang QF^*, Chen JM^*. 2017. RNA-Seq analysis of the distylous plant Nymphoides peltata identified ortholog genes between long-and short-styled flowers. Frontiers in Ecology and Evolution, 5, 59.
  34. Liao YY, Gichira AW, Wang QF^*, Chen JM^*. 2016. Molecular phylogeography of four endemic Sagittaria species (Alismataceae) in the Sino-Japanese floristic region of east Asia. Botanical Journal of the Linnean Society, 180(1)： 6-20.
  35. Chen JM, Werth S, Sork VL^*. 2016. Comparison of phylogeographical structures of a lichen‐forming fungus and its green algal photobiont in western North America. Journal of Biogeography, 43(5): 932-943.
  36. Sork VL^*, Gugger PF, Chen JM, Werth S. 2016. Evolutionary lessons from California plant phylogeography. Proceedings of the National Academy of Sciences, 113(29): 8064-8071.
  37. Sun SS, Gugger PF, Wang QF^*, Chen JM^*. 2016. Identification of a R2R3-MYB gene regulating anthocyanin biosynthesis and relationships between its variation and flower color difference in lotus (Nelumbo Adans.). PeerJ, 4: e2369.
  38. Chen JM^#, Du ZY^#, Yuan YY, Wang QF. 2014. Phylogeography of an alpine aquatic herb Ranunculus bungei (Ranunculaceae) on the Qinghai–Tibet Plateau. Journal of Systematics and Evolution, 52(3): 313-325.
  39. Chen JM, Du ZY, Sun SS, Gituru RW, Wang QF. 2013. Chloroplast DNA phylogeography reveals repeated range expansion in a widespread aquatic herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and adjacent areas. PLoS one, 8(4): e60948.
  40. Li WG, Chen WB, Qi XF, Wang QF, Chen JM^*. 2013. Variation of cytosine methylation in response to water availability in two contrasting growth types of an amphibious plant Alternanthera philoxeroides. Biochemical Systematics and Ecology, 50: 175-181.
  41. Liao YY, Yue XL, Guo YH, Gituru WR, Wang QF^*, Chen JM^*. 2013. Genotypic diversity and genetic structure of populations of the distylous aquatic plant Nymphoides peltata (Menyanthaceae) in China. Journal of Systematics and Evolution, 51(5): 536-544.
  42. Chen LY, Chen JM, Gituru RW, Wang QF. 2013. Eurasian origin of Alismatidae inferred from statistical dispersal–vicariance analysis. Molecular phylogenetics and evolution, 67(1): 38-42.
  43. Chen LY, Chen JM, Gituru, RW, Wang QF*. 2012. Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae. BMC Evolutionary Biology, 12(1): 1-12.
  44. Chen LY, Chen JM, Gituru RW, Temam TD, Wang QF. 2012. Generic phylogeny and historical biogeography of Alismataceae, inferred from multiple DNA sequences. Molecular phylogenetics and evolution, 63(2): 407-416.
  45. Liao YY, Yang XY, Motley TJ, Chen JM^*, Wang QF^*. 2011. Phylogeographic analysis reveals two cryptic species of the endangered fern Ceratopteris thalictroides (L.) Brongn.(Parkeriaceae) in China. Conservation genetics, 12: 1357-1365.
  46. Zhao SY, Chen JM^*, Wang QF^*, Liu F, Guo YH, Gituru WR. 2010. The extent of clonality and genetic diversity in Sagittaria lichuanensis (Alismataceae), an endemic marsh herb in China. Botanical Studies, 51(3): 363–369.
  47. Du ZY, Yang CF, Chen JM^*, Guo YH^*. 2010. Identification of hybrids in broad-leaved Potamogeton species (Potamogetonaceae) in China using nuclear and chloroplast DNA sequences data. Plant Systematics and Evolution, 287: 57–63.
  48. Du ZY, Yang CF, Chen JM^*, Guo YH^*. 2010. Using DNA-based techniques to identify the hybrids among the linear-leaved Potamogeton plants collected in China. Journal of Systematics and Evolution, 48 (4): 265–270.
  49. Liu, F, Liao YY, Li W, Chen JM^*, Wang QF^*, Motley TJ. 2010. The effect of pollination on resource allocation among sexual reproduction, clonal reproduction, and vegetative growth in Sagittaria potamogetifolia (Alismataceae). Ecological research, 25: 495-499.
  50. Liu F, Chen JM^*, Wang QF^*. 2009. Trade-offs between the sexual and asexual reproduction in a monoecious species Sagittaria pygmaea (Alismataceae): the effect of different nutrient levels. Plant Systematics and Evolution, 277: 61–65.
  51. Chen JM, Liu F, Wang QF^*, Motley TJ. 2008. Phylogeography of a marsh herb Sagittaria trifolia (Alismataceae) in China inferred from cpDNA atpB–rbcL intergenic spacers. Molecular phylogenetics and evolution, 48(1): 168-175.
  52. Chen JM, Liu F, Gituru WR, Wang QF^*. 2008. Chloroplast DNA phylogeography of the Chinese endemic alpine quillwort Isoetes hypsophila Hand.-Mazz.(Isoetaceae). International journal of plant sciences,169(6): 792-798.
  53. Tan B, Liu K, Yue XL, Liu F, Chen JM^*, Wang QF^*. 2008. Chloroplast DNA variation and phylogeographic patterns in the Chinese endemic marsh herb Sagittaria potamogetifolia. Aquatic Botany, 89(4): 372-378.
  54. Shi W, Yang CF, Chen JM^*, Guo YH. 2008. Genetic variation among wild and cultivated populations of the Chinese medicinal plant Coptis chinensis (Ranunculaceae). Plant Biology, 10(4): 485-491.
  55. Dong YH, Chen JM^*, Robert GW, Wang F^*. 2008. Genetic variation in the endangered aquatic fern Ceratopteris thalictroides (Parkeriaceae) in China: implications from RAPD and ISSR data. Botanical journal of the Linnean Society, 157(4): 657-671.
  56. Liu F, Yue XL, Chen JM^*, Wang QF^*. 2008. Gender modification in a monoecious species Sagittaria potamogetifolia (Alismataceae). Plant Ecology, 199: 217-223.
  57. Chen JM, Robert GW, Wang QF^*. 2007. A comparison of the extent of genetic variation in the endangered Sagittaria natans and its widespread congener S. trifolia. Aquatic Botany, 87: 1–6.
  58. Dong YH, Chen JM^*, Robert GW, Wang QF^*. 2007. Gene flow in populations of the endangered aquatic fern Ceratopteris pteridoides in China as revealed by ISSR markers. Aquatic Botany, 87: 69–74.
  59. Chen JM, Robert GW, Wang YH, Wang QF^*. 2006. The extent of clonality and genetic diversity in the rare Caldesia grandis (Alismataceae): comparative results for RAPD and ISSR markers. Aquatic Botany, 84: 301–307.
  60. Chen JM, Liu X, Wang JY, Robert GW, Wang QF^*. 2005. Genetic variation within the endangered quillwort Isoetes hypsophila (Isoetaceae) in China as evidenced by ISSR analysis. Aquatic Botany, 82: 89–98.
  61. Chen JM, Robert GW, Wang QF^*. 2005. Evolution of aquatic life-forms in Alismatidae: phylogenetic estimation from chloroplast rbcL gene sequence data. Israel Journal of Plant Sciences, 52: 323–329.
  62. Chen JM, Chen D, Robert GW, Wang QF^*, Guo YH. 2004. Evolution of apocarpy in Alismatidae using phylogenetic evidence from chloroplast rbcL gene sequence data. Botanical Bulletin of Academia Sinica, 45: 33–40.