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Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Journal of Integrative Plant Biology 2024年第4期66卷 824-843页

作者： Weihong Wu Xiao Feng Nan Wang Shao Shao Min Liu Fa Si Linhao Chen Chuanfeng Jin Shaohua Xu Zixiao Guo cairong zhong Suhua Shi Ziwen He State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life SciencesSun Yat-sen UniversityGuangzhou 510275China Greater Bay Area Institute of Precision Medicine School of Life SciencesFudan UniversityGuangzhou 511462China Hainan Academy of Forestry(Hainan Academy of Mangrove) Haikou 571100China

Nypa fruticans(Wurmb),a mangrove palm species with origins dating back to the Late Cretaceous period,is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of ***,we present a chromosome-level genome sequence and assembly for *** integrated the genomes of *** and other palm family members for a comparative genomic analysis,which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago,shaping the distinctive characteristics observed in this *** also inferred a low mutation rate for the *** genome,which underwent strong purifying selection and evolved slowly,thus contributing to its stability over a long evolutionary ***,ancient duplicates were preferentially retained,with critical genes having experienced positive selection,enhancing waterlogging tolerance in ***,we discovered that the pseudogenization of Early Methionine-labelled 1(EM1)and EM6 in *** underly its crypto-vivipary characteristics,reflecting its intertidal *** study provides valuable genomic insights into the evolutionary history,genome stability,and adaptive evolution of the mangrove *** results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

关键词： crypto-vivipary genome stability long-term adaptation mangrove Nypa fruticans palm

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使君子科3种红树植物叶绿体基因组密码子使用偏好性分析

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植物资源与环境学报 2024年第2期33卷 1-12页

作者：钟才荣何斯敏方赞山张颖海南省林业科学研究院(海南省红树林研究院) 海南海口571129 岭南师范学院湛江市红树林生态系统保护与修复重点实验室红树林珍稀濒危物种保护与利用工程技术研究中心广东湛江524048

为探究使君子科(Combretaceae)红树植物叶绿体基因组密码子使用偏好性及其影响因子,对拉关木(Laguncularia racemosa ***.)、红榄李〔Lumnitzera littorea(Jack)Voigt〕、榄李(Lumnitzera racemosa Willd.)叶绿体基因组的52个共有蛋白质编码序列(CDS)进行密码子第1、第2、第3位碱基的GC含量(分别为GC 1、GC 2、GC 3)、密码子总GC含量(GC all)、有效密码子数(ENC)和相对同义密码子使用度(RSCU)分析;在此基础上,对每种植物的GC 1、GC 2、GC 3、GC all和ENC值进行相关性分析,并对每种植物叶绿体基因组进行中性绘图、ENC-plot、PR2-plot和最优密码子分析;此外,还基于rbcL基因序列和叶绿体基因组共有CDS的RSCU值对使君子科11种植物进行聚类分析。结果表明:3种植物叶绿体基因组GC all值的均值为38.0%~38.2%,GC 1、GC 2和GC 3值的均值均低于50%,均表现为GC 1值的均值最大、GC 3值的均值最小,且GC 3值的均值明显低于GC 1和GC 2值的均值,并与二者呈不显著正相关;ENC值的均值为47.2~47.3,且3种植物叶绿体基因组中ENC值大于45的基因占比均高于70%。3种植物叶绿体基因组中的高频密码子均有29个,以A或U结尾的高频密码子占比达96.6%。中性绘图、ENC-plot和PR2-plot分析结果表明3种植物叶绿体基因组密码子使用偏好性主要受自然选择的影响。拉关木、红榄李和榄李叶绿体基因组的最优密码子分别有8、6和10个,且多以A或U结尾;共有最优密码子有4个,分别为CGA、AGA、GGA、ACA。聚类分析结果表明红榄李和榄李均首先聚在一起,说明二者的亲缘关系较近。综上所述,3种红树植物叶绿体基因组密码子偏好以A或U结尾,且密码子使用偏好性主要受自然选择的影响。

关键词：红树植物叶绿体基因组密码子使用偏好性最优密码子自然选择

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Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees

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Marine Life Science & Technology 2023年第2期5卷 155-168页

作者： Xiao Feng Guohong Li Weihong Wu Haomin Lyu Jiexin Wang Cong Liu cairong zhong Suhua Shi Ziwen He State Key Laboratory of Biocontrol Guangdong Key Laboratory of Plant ResourcesSchool of Life SciencesSouthern Marine Science and Engineering Guangdong Laboratory(Zhuhai)Sun Yat-sen UniversityGuangzhou 510275China Greater Bay Area Institute of Precision Medicine(Guangzhou) Fudan UniversityGuangzhou 511458China Hainan Academy of Forestry(Hainan Academy of Mangrove) Haikou 571100China

Mangroves are adapted to intertidal zones,which present extreme environmental *** are among the most prominent transcription factors(TFs)in higher plants and act through various interconnected networks to regulate responses to multiple abiotic ***,based on omic data,we investigated the landscape and evolutionary patterns of WRKYs in the main mangrove genus *** found that both the number and the proportion of TFs and WRKYs in Avicennia species exceeded their inland relatives,indicating a signifcant expansion of WRKYs in *** identifed 109 WRKY genes in the representative species Avicennia *** genomic analysis showed that two recent wholegenome duplication(WGD)events played a critical role in the expansion of WRKYs,and 88%of Avicennia marina WRKYs(AmWRKYs)have been retained following these *** comparative transcriptomics on roots under experimental salt gradients,we inferred that there is high divergence in the expression of WGD-retained ***,we found that the expression of 16 AmWRKYs was stable between freshwater and moderately saline water but increased when the trees were exposed to high *** particular,14 duplicates were retained following the two recent WGD events,indicating potential neo-and *** also found that WRKYs could interact with other upregulated genes involved in signalling pathways and natural antioxidant biosynthesis to enhance salt tolerance,contributing to the adaptation to intertidal *** omic data of the WRKY family in *** broadens the understanding of how a TF family relates to the adaptive evolution of mangroves.

关键词： Adaptation Avicennia Mangrove Transcription factor Whole-genome duplication WRKY

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Extensive gene flow in secondary sympatry after allopatric speciation

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National Science Review 2022年第12期9卷 24-36页

作者： Xinfeng Wang Ziwen He Zixiao Guo Ming Yang Shaohua Xu Qipian Chen Shao Shao Sen Li cairong zhong Norman C.Duke Suhua Shi State Key Laboratory of Biocontrol Guangdong Key Laboratory of Plant Resources School of Life SciencesSouthern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Sun Yat-sen University Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering School of Life Sciences Fudan University Department of Laboratory Medicine& Pathology University of Washington Hainan Academy of Forestry (Hainan Academy of Mangrove) Centre for Tropical Water and Aquatic Ecosystem Research James Cook University

In the conventional view,species are separate gene pools delineated by reproductive isolation(RI).In an alternative view,species may also be delineated by a small set of ’speciation genes’ without full RI,a view that has gained broad acceptance.A recent survey,however,suggested that the extensive literature on’speciation with gene flow’ is mostly(if not all) about exchanges in the early stages of *** is no definitive evidence that the observed gene flow actually happened after speciation is ***,we wish to know whether ’good species’(defined by the ’secondary sympatry’ test) do continue to exchange genes and,importantly,under what conditions such exchanges can be *** novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species(Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in *** became sympatric in northeastern Australia but remain distinct ***,their genomes harbor～4000-10 000 introgression blocks averaging only about 3-4 *** fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable ’genomic islets,’～1.4 Kb in size,often harbor diverging genes of flower or gamete *** fine-grained introgression in secondary sympatry may help settle the debate about sympatric ***-allopatric *** conclusion,true’good species’ may often continue to exchange genes but the opportunity for detection is highly constrained.

关键词： mangroves population genomics speciation introgression species hybridization

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Speciation with gene flow via cycles of isolation and migration:insights from multiple mangrove taxa

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National Science Review 2019年第2期6卷 275-288页

作者： Ziwen He Xinnian Li Ming Yang Xinfeng Wang cairong zhong Norman C.Duke Chung-I Wu Suhua Shi State Key Laboratory of Biocontrol Guangdong Key Lab of Plant Resources Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education InstitutesSchool of Life Sciences Sun Yat-Sen University Department of Ecology and Evolution University of Chicago CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences Hainan Dongzhai Harbor National Nature Reserve Administration Centre for Tropical Water and Aquatic Ecosystem Research James Cook University

Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca,narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding mn(m > 1) species after n cycles.

关键词： speciation gene flow allopatry geographical isolation mangrove

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Convergent adaptation of the genomes of woody plants at the land–sea interface

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National Science Review 2020年第6期7卷 978-993页

作者： Ziwen He Shaohua Xu Zhang Zhang Wuxia Guo Haomin Lyu cairong zhong David E.Boufford Norman C.Duke The International Mangrove Consortium Suhua Shi State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes School of Life Sciences Sun Yat-Sen University Hainan Dongzhai Harbor National Nature Reserve Administration Harvard University Herbaria Centre for Tropical Water and Aquatic Ecosystem Research James Cook University the Consortium of 26 Institutions

Sequencing multiple species that share the same ecological niche may be a new frontier for genomic *** such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method(convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with Ptrue(probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid(AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.

关键词： convergent evolution genome mangrove adaptive evolution woody plants

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1990年—2020年广西北仑河口红树林扰动研究

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遥感学报 2022年第6期26卷 1112-1120页

作者：陈高钟才荣李明玉余洲刘心雨贾明明延边大学地理与海洋科学学院延吉133002 海南省林业科学研究院(海南省红树林研究院) 海口571100 中国科学院东北地理与农业生态研究所湿地生态与环境重点实验室长春130102

监测国家级自然保护区内红树林的扰动,可为滨海湿地生态系统的管理和保护提供数据支撑和决策支持。本研究使用谷歌云平台GEE(Google Earth Engine)建立Landsat长时间序列卫星数据集,结合LandTrendr算法研究了广西北仑河口红树林自然保护... 详细信息

监测国家级自然保护区内红树林的扰动,可为滨海湿地生态系统的管理和保护提供数据支撑和决策支持。本研究使用谷歌云平台GEE(Google Earth Engine)建立Landsat长时间序列卫星数据集,结合LandTrendr算法研究了广西北仑河口红树林自然保护区1990年—2020年红树林的扰动情况。结果表明:(1)1990年—2020年,共有45.94 ha的红树林发生了扰动,其中2001年保护区内红树林扰动面积最大,为12.91 ha;(2)1990年—2020年,轻微扰动和中度扰动所占比例较大,分别为57.5%和29.17%,严重扰动所占比例最少,只有13.33%;(3)红树林变化像元的总体识别精度达到88.56%,对扰动年份检测的总体精度达到87%,Kappa系数为0.76。本研究基于LandTrendr算法解析了30年间北仑河口保护区内红树林发生扰动的年份、频率和面积,结合实际情况分析了导致扰动的因素,认为人类活动是北仑河口红树林扰动的次要原因,自然因素,如虫灾,台风等是导致扰动的主要原因。本研究的结论和方法可为红树林保护区管理处制定科学合理的保护和恢复政策提供重要的决策支持。

关键词：遥感红树林保护区谷歌地球引擎GEE(Google Earth Engine) LandTrendr算法

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3种红树植物的移植技术

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林业科技通讯 2022年第8期 76-78页

作者：钟才荣方赞山海南省林业科学研究院海南省红树林研究院海口571100

根据红树植物桐花树、海莲和秋茄的生境需求和生长特点,在前期开展移植工作的基础上,总结了3种红树植物的移植季节,以及3种红树植物苗木、幼树、壮龄树和老龄树在移植过程中的修剪、断根与打包、假植和种植的方法和关键技术,为今后到红... 详细信息

根据红树植物桐花树、海莲和秋茄的生境需求和生长特点,在前期开展移植工作的基础上,总结了3种红树植物的移植季节,以及3种红树植物苗木、幼树、壮龄树和老龄树在移植过程中的修剪、断根与打包、假植和种植的方法和关键技术,为今后到红树植物的移植提供参考。

关键词：红树植物移植打包养护管理

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海南清澜港海南海桑群落中物种生态位特征和种间联结性

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植物资源与环境学报 2023年第5期32卷 70-77页

作者：张孟文钟才荣吕晓波方赞山程成海南省林业科学研究院(海南省红树林研究院) 海南海口571100

对海南清澜港海南海桑(Sonneratia×hainanensis ***,*** et ***)群落现状进行系统调查,采用Levins指数、Pianka指数、Schoener指数和方差比率(VR)等指标以及χ^(2)检验对海南海桑群落中物种生态位特征和种间联结性进行了研究。结果显示... 详细信息

对海南清澜港海南海桑(Sonneratia×hainanensis ***,*** et ***)群落现状进行系统调查,采用Levins指数、Pianka指数、Schoener指数和方差比率(VR)等指标以及χ^(2)检验对海南海桑群落中物种生态位特征和种间联结性进行了研究。结果显示:海南海桑群落共有14种(变种,下同)植物,隶属于8科10属,其中海南海桑的重要值(33.48%)和生态位宽度(Levins指数为14.40)在群落中均排名第1,明显高于其他物种。14种植物共组成91个种对,其中Pianka指数和Schoener指数小于0.5的种对数分别占总种对数的86.8%和92.3%,说明群落中大部分物种间的生态位重叠程度和生态位相似性较低,种间竞争不激烈。海南海桑群落物种间总体表现为不显著负联结,并有84.6%的种对联结性不显著,说明群落物种间联结性不强,具有一定的独立性。海南海桑与其他植物组成的13个种对中,显著联结种对数仅占38.5%,说明海南海桑与群落中大部分物种联结性较弱。综合分析认为,生态位特征和种间联结不是海南海桑濒危的主要因子,可从开展人工辅助育种工作、加大就地保护力度和优化迁地保护策略方面考虑海南海桑种群的保护与恢复。

关键词：红树植物海南清澜港海南海桑群落生态位特征种间关系

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中国孑遗红树植物水椰的资源现状与种群特征

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生态学杂志 2023年第12期42卷 2918-2925页

作者：张孟文钟才荣吕晓波方赞山程成海南省林业科学研究院(海南省红树林研究院) 海口571100

水椰属棕榈科真红树植物,也是孑遗植物,被列为国家二级重点保护植物。中国水椰仅天然分布于海南岛。为探讨其濒危现状和保护策略,本研究采用样方法对水椰群落进行调查,并分析其地理分布、群落特征、种群结构及其空间分布。结果表明:(1)... 详细信息

水椰属棕榈科真红树植物,也是孑遗植物,被列为国家二级重点保护植物。中国水椰仅天然分布于海南岛。为探讨其濒危现状和保护策略,本研究采用样方法对水椰群落进行调查,并分析其地理分布、群落特征、种群结构及其空间分布。结果表明:(1)中国水椰共有6个自然种群,总面积为3.96 hm^(2),种群数量为9319棵,自然分布于海口东寨港的野菠萝岛和道学村、文昌的玉阳公园和头苑村、琼海长坡镇文场村、万宁日月湾,并且仅在日月湾有小面积成片分布,其他种群均为零星分布。(2)水椰样地内共有28种红树植物,形成以水椰+海莲+桐花树、水椰+海莲等为优势种的红树林群落。(3)海口、琼海、万宁水椰的种群结构均为衰退型,而文昌水椰种群为增长型,并且各种群分布格局都为聚集分布。(4)宏观尺度的极端气候变化、过度砍伐与开发利用、小尺度上的个体自身繁殖受限是水椰种群濒危的三大原因。建议通过增加科研技术投入解决种源问题、加大生境修复与就地保护力度、优化迁地保护与野外回归策略等措施扩大其种群数量。

关键词：孑遗植物水椰濒危现状保护策略种群结构

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