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      The Complete Plastomes of Five Hemiparasitic Plants ( Osyris wightiana, Pyrularia edulis, Santalum album, Viscum liquidambaricolum, and V. ovalifolium): Comparative and Evolutionary Analyses Within Santalales

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          Abstract

          Most species of Santalales (the sandalwood order) are hemiparasites, including both facultative and obligate hemiparasites. Despite its rich diversity, only a small fraction of the species in the sandalwood order have sequenced plastomes. The evolution of parasitism–associated plastome reduction in Santalales remains under-studied. Here, we report the complete plastomes of three facultative hemiparasites ( Pyrularia edulis, Cervantesiaceae; Osyris wightiana, and Santalum album, Santalaceae), and two obligate hemiparasites ( Viscum liquidambaricolum and Viscum ovalifolium, Viscaceae). Coupled with publicly available data, we investigated the dynamics of plastome degradation in Santalales hemiparasites. Our results indicate that these hemiparasites can be characterized by various degrees of plastome downsizing, structural rearrangement, and gene loss. The loss or pseudogenization of ndh genes was commonly observed in Santalales hemiparasites, which may be correlated to the lifestyle shift from photoautotroph to hemiparasitism. However, the obligate hemiparasites did not exhibit a consistently higher level of gene loss or pseudogenization compared to facultative hemiparasites, which suggests that the degree of plastome reduction is not correlated with the trophic level facultative or obligate hemiparasitism. Instead, closely related taxa tend to possess highly similar plastome size, structure, and gene content. This implies the parasitism-associated plastome degradation in Santalales may evolve in a lineage-specific manner.

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          A rapid DNA isolation procedure for small quantities of fresh leaf tissue

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            Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.

            Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematics. Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly. We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths. We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae). Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40× and 30×, respectively. Divergence from the reference significantly affected plastome assembly, but relatively similar references are available for most seed plants. Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism. The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths. Nearly 160000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.
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              Comparative organization of chloroplast genomes.

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                Author and article information

                Contributors
                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                16 June 2020
                2020
                : 11
                : 597
                Affiliations
                [1] 1Institute of Ecology and Geobotany, Yunnan University , Kunming, China
                [2] 2CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, China
                [3] 3Department of Botany and Plant Sciences, University of California, Riverside , Riverside, CA, United States
                [4] 4CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan, China
                [5] 5Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, China
                Author notes

                Edited by: Federico Luebert, University of Chile, Chile

                Reviewed by: Liping Zeng, University of California, Riverside, United States; Deise J. P. Goncalves, The University of Texas at Austin, United States

                *Correspondence: Wenhua Su, whsu@ 123456ynu.edu.cn
                Hengchang Wang, hcwang@ 123456wbgcas.cn

                This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics

                Article
                10.3389/fgene.2020.00597
                7308561
                20e0a135-235c-49b9-8348-16cf17c959be
                Copyright © 2020 Guo, Liu, Zhang, Su, Landis, Zhang, Wang and Ji.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 09 April 2019
                : 18 May 2020
                Page count
                Figures: 3, Tables: 2, Equations: 0, References: 74, Pages: 11, Words: 0
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 31590823
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 31060052
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 31872673
                Funded by: National Natural Science Foundation of China-Yunnan Joint Fund 10.13039/501100011002
                Award ID: U1802287
                Categories
                Genetics
                Original Research

                Genetics
                parasitism,plastome degradation,gene loss,pseudogenization,cervantesiaceae,santalaceae,viscaceae
                Genetics
                parasitism, plastome degradation, gene loss, pseudogenization, cervantesiaceae, santalaceae, viscaceae

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