Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification

Genomic insights into rapid speciation within the world's largest tree genus Syzygium

Acknowledgements Y.W.L. was supported by a postgraduate scholarship research grant from the Ministry of National Development, Singapore awarded through the National Parks Board, Singapore (NParks; NParks’ Garden City Fund). Principal research funding from NParks and the School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, is acknowledged. We thank Peter Preiser, Associate Vice President for Biomedical and Life Sciences, for facilitating NTU support, and Kenneth Er, CEO of NParks, for facilitating research funding through that organisation. V.A.A. and C.L. were funded by SBS, NTU for a one-year research leave. V.A.A. and C.L. also acknowledge support from the United States National Science Foundation (grants 2030871 and 1854550, respectively). S.R. was supported by a postdoctoral research fellowship under the NTU Strategic Plant Programme. S.R. and N.R.W.C. acknowledge funding from NTU start-up and the Academy of Finland (decisions 318288, 319947) grants to J.S. Fieldwork conducted by Y.W.L. was supported by an Indonesian Government RISTEK research permit (Application ID: 1517217008) and an Access License from the Sabah State government [JKM/MBS.1000-2/2JLD.7(84)]. T.N.C.V. is grateful to the Assemblée de la Province Nord and Assemblée de la Province Sud (New Caledonia) for facilitating relevant collection permits. A.N. was partly supported by the Research Project Promotion Grant (Strategic Research Grant No. 17SP01302) from the University of the Ryukyus, and partly by the Environment Research and Technology Development Fund (JPMEERF20204003) from the Environmental Restoration and Conservation Agency of Japan. Fieldwork in Fiji conducted by R.B. was hosted and facilitated by Elina Nabubuniyaka-Young (The Pacific Community’s Centre for Pacific Crops and Trees, Fiji). We thank the NTU-Smithsonian Partnership for tree data obtained for the Bukit Timah Nature Reserve (BTNR) long-term forest dynamics plots. Administrative support provided by Mui Hwang Khoo-Woon and Peter Ang at the molecular laboratory of the Singapore Botanic Gardens (SBG) is acknowledged. Rosie Woods and Imalka Kahandawala (DNA and Tissue Bank, Royal Botanic Gardens, Kew) facilitated additional DNA samples. Daniel Thomas (SBG) and Yan Yu (Sichuan University) commented on biogeographical analyses. NovogeneAIT in Singapore is acknowledged for personalised sequencing service.Peer reviewedPublisher PD

Genomic insights into rapid speciation within the world's largest tree genus Syzygium

The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium. Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.Peer reviewe

Essential Oil Compounds of Andaliman (Zanthoxylum acanthopodium DC.) Fruit Varieties and Their Utilization as Skin Anti-Aging Using Molecular Docking

Exposure to UV/infrared (IR) radiation is the main extrinsic factor that changes skin morphology and affects the increase in reactive oxygen species (ROS) in skin aging. Ten varieties of andaliman (Zanthoxylum acanthopodium DC.) fruit are presumed to have skin anti-aging compounds via an enzyme-inhibition mechanism. This study aims to compare ten essential oils (EOs) of andaliman fruit varieties, group them according to their varieties, and obtain the chemical components that can be used as potential skin anti-aging agents using molecular docking. EOs were isolated by hydrodistillation, and the determination of the chemical compounds was performed using gas chromatography-mass spectrometry (GC-MS). Using the Orange data mining software, a heatmap was used for grouping and showing the abundance of the compounds of ten varieties. Finally, molecular docking was conducted using the software AutoDockTools 1.5.7. There were 97 chemical components in the ten EOs of andaliman fruit varieties, with the main chemical components being geranyl acetate (29.87%) and D-limonene (26.49%), and they were grouped into three clusters. The chemical components that are prospective candidates as skin anti-aging agents are geranyl acetate and D-limonene, found in abundance in the Sihalus variety of andaliman fruit. These can be developed for applications in the pharmaceutical industry

PENGEMBANGAN KAWASAN WISATA ALAM KEBUN RAYA DAN KEBUN BINATANG (KRKB) GEMBIRA LOKA UNTUK WISATAWAN DIFABEL

Gembira Loka botanical garden and zoo is a tourism product (supply) and the ex-situ conservation area to prevent the extinction species. Tourist with disabilities is a segment of the tourist market (demand) whose very potential because their numbers have been increasing. The purposes of this research were investigating the appropriateness of tourist with disabilities facilities in the natural tourism area of Gembira Loka botanical garden and zoo, examining the satisfaction level of tourist with disabilities in the natural tourism area of Gembira Loka botanical garden and zoo and formulate the development strategy in the natural tourism area of Gembira Loka botanical garden and zoo for tourist with disabilities. Data research was taken on June 2012 in the natural tourism area Gembira Loka botanical garden and zoo,Yogyakarta. This research uses cluster sampling technique and the census technique. Technique of data collection by observation, in-depth interviews, and literature study. Data analysis technique was performed using Scoring, Customer Satisfaction Index (CSI) and SWOT. The research results showed: First, the appropriateness of tourist with disabilities facilities in the natural tourism area of Gembira Loka botanical garden and zoo for tourist with physical impairment was less appropiate (27), for mental retardation was less appropiate (24), for autist was less appropiate (17) and for deaf-speech impairment was less appropiate (17). Second, the satisfaction level of tourist with disabilities in the natural tourism area of Gembira Loka botanical garden and zoo for mental retardation was not satisfied ( 0.401), deaf-speech impairment was not satisfied (0.387), autist was not satisfied (0.121) and tourist with physical impairment was not satisfied (0.082). Third, the development strategy in the natural tourism area of Gembira Loka botanical garden and zoo for tourist with disabilities are: applying of barrier free natural tourism for tourist with disabilities by improving the quality of attraction, amenity and accessibility, increasing the participation of tourist with disabilities by their family�s relief fund to protect the environment and planning of travel packages environment education and research for tourist with disabilities by promotio

POTENSI MINYAK ATSIRI DAUN ANDALIMAN (Zanthoxylum acanthopodium) SEBAGAI ANTIVIRUS CORONA BERDASARKAN PENAMBATAN MOLEKUL

Andaliman (Zanthoxylum acanthopodium) plant, a unique spice in the Batak tribe limited only to the fruit. The leaves available most of the time and consisting of essential oils, there are no research has been conducted on molecular docking to determine the potential of the drug. The Covid-19 pandemic is still ongoing, so information as Corona antivirus is needed. This study aims to find the differences of chemical components from Andaliman leaves essential oil, classify the varieties, and get potential components as Corona antivirals based on molecular docking. The Andaliman leaves were collected from North Tapanuli District, than isolated using water distillation and Gas chromatography-mass spectrometry (GC-MS). Data analysis using Principal Component Analysis (PCA) with the XL stat 2020. The results showed that three varieties of Andaliman, Siholpu, Siganjangpat, and Variety three are not grouped in one quadrant. There are 53 compounds were detected. The dominant chemical compounds in all varieties are D-Limonene (Siganjangpat: 87.7%, Siholpu: 50.4%, and Variety three: 42.6%). Each variety is characterized by specific compounds, Siholpu by caryophyllene and sabinene; Singanjangpat by D-Limonene; Variety three by neryl acetate and 1,8-cinneol. The chemical component in Andaliman leaves that most potent as Corona antiviral is beta-caryophyllene in the Siholpu variety.

Genomic insights into rapid speciation within the world’s largest tree genus [PREPRINT].

Species radiations have long fascinated biologists, but the contribution of adaptation to observed diversity and speciation is still an open question. Here, we explore this question using the clove genus, Syzygium, the world’s largest genus of tree species comprising approximately 1200 species. We dissect Syzygium diversity through shotgun sequencing of 182 distinct species and 58 additional as-yet unidentified taxa, and assess their genetic diversity against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that Syzygium grande shares a whole genome duplication (WGD) event with other Myrtales. Genomic analyses confirm that Syzygium originated in Sahul (Australia-New Guinea), and later diversified eastward to the Hawaiian Islands and westward in multiple independent migration events. The migrations were associated with bursts of speciation events, visible by poorly resolved branches on phylogenies and networks, some of which were likely confounded by incomplete lineage sorting. Clinal genomic variation in some sublineages follows phylogenetic progression, which coupled with sympatric occurrences of distantly related species suggests that both geographic and ecological speciation have been important in the diversification of Syzygium. Together, these results point to a mixture of both neutral and adaptive drivers having contributed to the radiation of the genus