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| 1 | The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing显示文摘Mangroves invade some very marginal habitats for woody plants—at the interface between land and sea.Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication ~70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid(AA) usage as well as unusual AA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves' highly specialized traits(vivipary and red bark) thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future. | Shaohua Xu Ziwen He Zhang Zhang Zixiao Guo Wuxia Guo Haomin Lyu Jianfang Li Ming Yang Zhenglin Du Yelin Huang Renchao Zhou Cairong Zhong David E. Boufford Manuel Lerdau Chung-I Wu Norman C. Duke Suhua Shi | 2017 | National Science Review2017，4，5： | 7 |
| 2 | Monoterpene emission from ponderosa pine显示文摘 | Lerdau M T Ditts S B Westberg H | 1994 | Journal of Geophysical Research1994，99，16： | 1 |
| 3 | Plant chemical defense : Monoterpenes and the growth - defferentiation balance hypothesis 显示文摘 | Lerdau M Litvak M Monson R | 1994 | Trends Ecol1994，9，： | 1 |
| 4 | Ecological controls over monoterpene emission from Douglas fir (Pseudotsuga menziesii)显示文摘 | Lerdau M Matson P Fall R | 1995 | Ecology1995，76，： | 1 |
| 5 | Controls over monoterpene emission from boreal forest conifers显示文摘 | Lerdau M Litvak M E Palmer P | 1997 | Tree physiology1997，17，： | 1 |
| 6 | Relationship between leaf nitrogen and photosynthetic rate for three NAI-ME and three NADP-ME C4 grasses显示文摘 | Taub D R Lerdau M T | | 0，，： | 1 |
| 7 | Leaf and shoot level plasticity in response to different nutrient and water availabilities显示文摘 | Funk J L Jones C G Lerdau M T | 2007 | Tree Physiology2007，27，12： | 1 |
| 8 | New Directions: VOCs and biosphere–atmosphere feedbacks显示文摘 | J.D Fuentes B.P Hayden M Garstang M Lerdau D Fitzjarrald D.D Baldocchi R Monson B Lamb C Geron | 2000 | Atmospheric Environment2000，，1： | 1 |
| 9 | The evolution of function in plant secondary metabolites显示文摘 | Nina Theis Manuel Lerdau | 2003 | International Journal of Plant Science2003，164，3： | 1 |
| 10 | The ecology and evolution of plant secondary metabolites显示文摘 | THEIS N LERDAU M | 2003 | Int J Plant Sci2003，164，3： | 1 |
| 11 | Plant chemical defense: monoterpenes and the growth-differentiation balance hypothesis 显示文摘 | Lerdau M Litvak M Monson R | 1994 | Trends in Ecology and Evolution1994，9，2： | 1 |
| 12 | Ecological and evolutionary aspects of isoprene emission from plants显示文摘 | Peter C. Harley Russell K. Monson Manuel T. Lerdau | 1999 | Oecologia1999，，2： | 1 |
| 13 | Monoterpene emis-sion from ponderosa pine?显示文摘 | LERDAU M DILTS S B WESTBERG H | 1994 | Journal of Geophysical Research-atmospheres1994，99，8： | 1 |
| 14 | The evolution of function in plant secondary metabolites 显示文摘 | Theis N Lerdau M | 2003 | International Journal of Plant Sciences2003，164，53： | 1 |
| 15 | Tansley Review:The ecology and evolution oflight-dependent and light-independent volatile organic carbon emis-sion by plants显示文摘 | LERDAU M GRAY D | 2003 | New Phytologist2003，157，： | 1 |
| 16 | Carbon isotope analysis of acetaldehyde emitted from leaves following mechanical stress and anoxia显示文摘 | JARDINE K KARL T LERDAU M | 2009 | Plant Biology2009，11，4： | 1 |
| 17 | The evolution of function in plant secondary metabolites显示文摘 | THEIS N LERDAU M | 2003 | Int J Plant Sci2003，164，3： | 1 |
| 18 | Plant production and emission of volatile organic compounds显示文摘 | Lerdau M Guenther A Monson R | 1997 | Bioscience1997，47，6： | 1 |
| 19 | Trace gas emissions and species-dependent ecosystem services显示文摘 | Lerdau M Slobodkin L | 2002 | Trends in Ecology & Evolution2002，17，7： | 1 |
| 20 | The Evolution of Function in Plant Secondary Metabolites 显示文摘 | THEIS N LERDAU M | 2003 | Int J Plant Sci2003，164，3： | 1 |
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