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Zhang ZR, Yang X, Li WY, Peng YQ, Gao J. Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions. FRONTIERS IN PLANT SCIENCE 2022; 13:965335. [PMID: 36186045 PMCID: PMC9521400 DOI: 10.3389/fpls.2022.965335] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.
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Affiliation(s)
- Zheng-Ren Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Wei-Ying Li
- Southwest Research Center for Landscape Architecture Engineering Technology, State Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yan-Qiong Peng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
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Xu X, Wang BS, Yu H. Intraspecies Genomic Divergence of a Fig Wasp Species Is Due to Geographical Barrier and Adaptation. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.764828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Understanding how intraspecies divergence results in speciation has great importance for our knowledge of evolutionary biology. Here we applied population genomics approaches to a fig wasp species (Valisia javana complex sp 1) to reveal its intraspecies differentiation and the underlying evolutionary dynamics. With re-sequencing data, we prove the Hainan Island population (DA) of sp1 genetically differ from the continental ones, then reveal the differed divergence pattern. DA has reduced SNP diversity but a higher proportion of population-specific structural variations (SVs), implying a restricted gene exchange. Based on SNPs, 32 differentiated islands containing 204 genes were detected, along with 1,532 population-specific SVs of DA overlapping 4,141 genes. The gene ontology (GO) enrichment analysis performed on differentiated islands linked to three significant GO terms on a basic metabolism process, with most of the genes failing to enrich. In contrast, population-specific SVs contributed more to the adaptation than the SNPs by linking to 59 terms that are crucial for wasp speciation, such as host reorganization and development regulation. In addition, the generalized dissimilarity modeling confirms the importance of environment difference on the genetic divergence within sp1. Hence, we assume the genetic divergence between DA and the continent due to not only the strait as a geographic barrier, but also adaptation. We reconstruct the demographic history within sp1. DA shares a similar population history with the nearby continental population, suggesting an incomplete divergence. Summarily, our results reveal how geographic barriers and adaptation both influence the genetic divergence at population-level, thereby increasing our knowledge on the potential speciation of non-model organisms.
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Zhang X, Wang G, Zhang S, Chen S, Wang Y, Wen P, Ma X, Shi Y, Qi R, Yang Y, Liao Z, Lin J, Lin J, Xu X, Chen X, Xu X, Deng F, Zhao L, Lee YL, Wang R, Chen XY, Lin YR, Zhang J, Tang H, Chen J, Ming R. Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution. Cell 2020; 183:875-889.e17. [PMID: 33035453 DOI: 10.1016/j.cell.2020.09.043] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 05/04/2020] [Accepted: 09/17/2020] [Indexed: 01/27/2023]
Abstract
Banyan trees are distinguished by their extraordinary aerial roots. The Ficus genus includes species that have evolved a species-specific mutualism system with wasp pollinators. We sequenced genomes of the Chinese banyan tree, F. microcarpa, and a species lacking aerial roots, F. hispida, and one wasp genome coevolving with F. microcarpa, Eupristina verticillata. Comparative analysis of the two Ficus genomes revealed dynamic karyotype variation associated with adaptive evolution. Copy number expansion of auxin-related genes from duplications and elevated auxin production are associated with aerial root development in F. microcarpa. A male-specific AGAMOUS paralog, FhAG2, was identified as a candidate gene for sex determination in F. hispida. Population genomic analyses of Ficus species revealed genomic signatures of morphological and physiological coadaptation with their pollinators involving terpenoid- and benzenoid-derived compounds. These three genomes offer insights into and genomic resources for investigating the geneses of aerial roots, monoecy and dioecy, and codiversification in a symbiotic system.
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Affiliation(s)
- Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Gang Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303
| | - Shengcheng Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Shuai Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Yibin Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Ping Wen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Yan Shi
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Rui Qi
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Yang Yang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Zhenyang Liao
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Jishan Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Xiuming Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Xuequn Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Xindan Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Fang Deng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Lihua Zhao
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Yi-Lun Lee
- Department of Agronomy, National Taiwan University, Taipei, Taiwan 10617
| | - Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241
| | - Xiao-Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan 10617
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Jin Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303.
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Neggad A, Benkaci-Ali F, Alsafra Z, Eppe G. Headspace Solid Phase Microextraction Coupled to GC/MS for the Analysis of Volatiles of Honeys from Arid and Mediterranean Areas of Algeria. Chem Biodivers 2019; 16:e1900267. [PMID: 31419038 DOI: 10.1002/cbdv.201900267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/15/2019] [Indexed: 12/19/2022]
Abstract
The volatile composition of seven honey samples collected from various regions of Algeria and feeding on different plants have been determined. The Headspace Solid-Phase MicroExtraction (HS-SPME) coupled with Gas Chromatography-Mass Spectrometry (GC/MS) was used to achieve the purpose. In this work, different parameters of the HS-SPME analytical method were investigated in order to reach maximal sensitivity, and thus to obtain maximum information about the volatile profile of Algerian honey. These parameters include saline medium, HS extraction temperature, and the nature of the fiber used. The results showed a great diversity in the chemical composition, in total 124 compounds from different chemical classes were identified, including compounds found for the first time in honey. The Ascending Hierarchical Classification (AHC) demonstrated the importance of choosing SPME extraction conditions to find volatile compounds, which could be as specific markers of the floral or geographical origin of honey, the latter was optimized in the parameter PDMS-55 °C.
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Affiliation(s)
- Abdelhamid Neggad
- University of Sciences and Technology Houari Boumediene, Faculty of Chemistry, Laboratory of Functional Organic Analysis, BP 32 El-Alia, 16111, Bab-Ezzouar, Algiers, Algeria
| | - Farid Benkaci-Ali
- University of Sciences and Technology Houari Boumediene, Faculty of Chemistry, Laboratory of Functional Organic Analysis, BP 32 El-Alia, 16111, Bab-Ezzouar, Algiers, Algeria
| | - Zouheir Alsafra
- University of Liege, Laboratoire de Spectrometrie de Masse L.S.M, Allee du 6 Août, Bât B6c, 4000, Liege (Sart-Tilman), Belgium
| | - Gauthier Eppe
- University of Liege, Laboratoire de Spectrometrie de Masse L.S.M, Allee du 6 Août, Bât B6c, 4000, Liege (Sart-Tilman), Belgium
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Barbosa-Cornelio R, Cantor F, Coy-Barrera E, Rodríguez D. Tools in the Investigation of Volatile Semiochemicals on Insects: From Sampling to Statistical Analysis. INSECTS 2019; 10:insects10080241. [PMID: 31390759 PMCID: PMC6723273 DOI: 10.3390/insects10080241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/28/2019] [Accepted: 08/02/2019] [Indexed: 12/16/2022]
Abstract
The recognition of volatile organic compounds (VOCs) involved in insect interactions with plants or other organisms is essential for constructing a holistic comprehension of their role in ecology, from which the implementation of new strategies for pest and disease vector control as well as the systematic exploitation of pollinators and natural enemies can be developed. In the present paper, some of the general methods employed in this field are examined, focusing on their available technologies. An important part of the investigations conducted in this context begin with VOC collection directly from host organisms, using classical extraction methods, by the employment of adsorption materials used in solid-phase micro extraction (SPME) and direct-contact sorptive extraction (DCSE) and, subsequently, analysis through instrumental analysis techniques such as gas chromatography (GC), nuclear magnetic resonance (NMR) and mass spectrometry (MS), which provide crucial information for determining the chemical identity of volatile metabolites. Behavioral experiments, electroantennography (EAG), and biosensors are then carried out to define the semiochemicals with the best potential for performing relevant functions in ecological relationships. Chemical synthesis of biologically-active VOCs is alternatively performed to scale up the amount to be used in different purposes such as laboratory or field evaluations. Finally, the application of statistical analysis provides tools for drawing conclusions about the type of correlations existing between the diverse experimental variables and data matrices, thus generating models that simplify the interpretation of the biological roles of VOCs.
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Affiliation(s)
- Ricardo Barbosa-Cornelio
- Biological Control Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
| | - Fernando Cantor
- Biological Control Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia.
| | - Daniel Rodríguez
- Biological Control Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia.
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