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Can Plastid Genome Sequencing Be Used for Species Identification in the Lauraceae?

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Can Plastid Genome Sequencing Be Used for Species Identification in the Lauraceae? Edinburgh Research Explorer Can plastid genome sequencing be used for species identification in the Lauraceae? Citation for published version: Liu, ZF, Ma, H, Ci, X-Q, Li, L, Song, Y, Liu, B, Li, HW, Wang, SL, Qu, XJ, Hu, J-L, Zhang, XY, Conran, JG, Twyford, AD, Yang, J-B, Hollingsworth, P & Li, J 2021, 'Can plastid genome sequencing be used for species identification in the Lauraceae?', Botanical journal of the linnean society. https://doi.org/10.1093/botlinnean/boab018 Digital Object Identifier (DOI): 10.1093/botlinnean/boab018 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Botanical journal of the linnean society General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 06. Oct. 2021 applyparastyle “fig//caption/p[1]” parastyle “FigCapt” Botanical Journal of the Linnean Society, 2021, XX, 1–14. With 4 figures. Can plastid genome sequencing be used for species identification in Lauraceae? Downloaded from https://academic.oup.com/botlinnean/advance-article/doi/10.1093/botlinnean/boab018/6179569 by guest on 06 April 2021 ZHI-FANG LIU1,2,13, HUI MA1, XIU-QIN CI1,3, LANG LI1,3, YU SONG4, BING LIU5,6, Keywords=Keywords=Keywords_First=Keywords HSI-WEN LI7, SHU-LI WANG1,2,8, XIAO-JIAN QU9, JIAN-LIN HU1,2, HeadA=HeadB=HeadA=HeadB/HeadA XIAO-YAN ZHANG1,2, JOHN G. CONRAN10, ALEX D. TWYFORD11,*, JUN-BO YANG12,*, HeadB=HeadC=HeadB=HeadC/HeadB PETER M. HOLLINGSWORTH13,* and JIE LI1,3,* HeadC=HeadD=HeadC=HeadD/HeadC 1 Extract3=HeadA=Extract1=HeadA Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China REV_HeadA=REV_HeadB=REV_HeadA=REV_HeadB/HeadA 2University of Chinese Academy of Sciences, Beijing, China REV_HeadB=REV_HeadC=REV_HeadB=REV_HeadC/HeadB 3Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China REV_HeadC=REV_HeadD=REV_HeadC=REV_HeadD/HeadC 4Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of REV_Extract3=REV_HeadA=REV_Extract1=REV_HeadA Sciences, Mengla, China 5 BOR_HeadA=BOR_HeadB=BOR_HeadA=BOR_HeadB/HeadA State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China BOR_HeadB=BOR_HeadC=BOR_HeadB=BOR_HeadC/HeadB 6Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China BOR_HeadC=BOR_HeadD=BOR_HeadC=BOR_HeadD/HeadC 7Herbarium (KUN), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China BOR_Extract3=BOR_HeadA=BOR_Extract1=BOR_HeadA 8Tibet Agriculture & Animal Husbandry University, Nyingchi, China EDI_HeadA=EDI_HeadB=EDI_HeadA=EDI_HeadB/HeadA 9Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong EDI_HeadB=EDI_HeadC=EDI_HeadB=EDI_HeadC/HeadB Normal University, Ji’nan, China 10Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of EDI_HeadC=EDI_HeadD=EDI_HeadC=EDI_HeadD/HeadC Biological Sciences, University of Adelaide, Adelaide, Australia EDI_Extract3=EDI_HeadA=EDI_Extract1=EDI_HeadA 11Institute of Evolutionary Biology, Ashworth Laboratories, The University of Edinburgh, Edinburgh, UK CORI_HeadA=CORI_HeadB=CORI_HeadA=CORI_HeadB/HeadA 12Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China CORI_HeadB=CORI_HeadC=CORI_HeadB=CORI_HeadC/HeadB 13Genetics and Conservation Section, Royal Botanic Garden Edinburgh, Edinburgh, UK CORI_HeadC=CORI_HeadD=CORI_HeadC=CORI_HeadD/HeadC Received 23 June 2020; revised 27 December 2020; accepted for publication 25 January 2021 CORI_Extract3=CORI_HeadA=CORI_Extract1=CORI_HeadA ERR_HeadA=ERR_HeadB=ERR_HeadA=ERR_HeadB/HeadA ERR_HeadB=ERR_HeadC=ERR_HeadB=ERR_HeadC/HeadB Using DNA barcoding for species identification remains challenging for many plant groups. New sequencing ERR_HeadC=ERR_HeadD=ERR_HeadC=ERR_HeadD/HeadC approaches such as complete plastid genome sequencing may provide some increased power and practical benefits ERR_Extract3=ERR_HeadA=ERR_Extract1=ERR_HeadA for species identification beyond standard plant DNA barcodes. We undertook a case study comparing standard DNA barcoding to plastid genome sequencing for species discrimination in the ecologically and economically important INRE_HeadA=INRE_HeadB=INRE_HeadA=INRE_HeadB/HeadA family Lauraceae, using 191 plastid genomes for 131 species from 25 genera, representing the largest plastome data INRE_HeadB=INRE_HeadC=INRE_HeadB=INRE_HeadC/HeadB set for Lauraceae to date. We found that the plastome sequences were useful in correcting some identification errors INRE_HeadC=INRE_HeadD=INRE_HeadC=INRE_HeadD/HeadC and for finding new and cryptic species. However, plastome data overall were only able to discriminate c. 60% of the species in our sample, with this representing a modest improvement from 40 to 50% discrimination success with INRE_Extract3=INRE_HeadA=INRE_Extract1=INRE_HeadA the standard plant DNA barcodes. Beyond species discrimination, the plastid genome sequences revealed complex App_Head=App_HeadA=App_Head=App_HeadA/App_Head relationships in the family, with 12/25 genera being non-monophyletic and with extensive incongruence relative to BList1=SubBList1=BList1=SubBList nuclear ribosomal DNA. These results highlight that although useful for improving phylogenetic resolution in the family and providing some species-level insights, plastome sequences only partially improve species discrimination, BList1=SubBList3=BList1=SubBList2 and this reinforces the need for large-scale nuclear data to improve discrimination among closely related species. SubBList1=SubSubBList3=SubBList1=SubSubBList2 SubSubBList3=SubBList=SubSubBList=SubBList ADDITIONAL KEYWORDS: cytonuclear discordance – DNA barcoding – nrDNA – phylogenetics – plastomes. SubSubBList2=SubBList=SubSubBList=SubBList SubBList2=BList=SubBList=BList *Corresponding authors. E-mails: [email protected]; Alex. [email protected]; [email protected]; PHollingsworth@ rbge.org.uk. © 2021 The Linnean Society of London, Botanical Journal of the Linnean Society, 2021, XX, 1–14 1 This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact [email protected] 2 Z.-F. LIU ET AL. INTRODUCTION to a range of issues, such as high diversity affecting the reliability of sequence alignments, incomplete The aim of DNA barcoding is to use standardized concerted evolution and frequent paralogy. These DNA sequences to aid in species identification (Hebert issues create a tension between the technical appeal et al., 2003; Hollingsworth, 2011). Various regions have of plastomes and nrDNA in terms of ease of use, vs. been proposed for DNA barcoding in plants (Kress & their suitability as representatives of the evolutionary Erickson, 2007; Lahaye et al., 2008), with the plastid Downloaded from https://academic.oup.com/botlinnean/advance-article/doi/10.1093/botlinnean/boab018/6179569 by guest on 06 April 2021 history of a species. Although the discriminatory loci matK+rbcL adopted as core DNA barcodes (CBOL power of next-generation DNA barcoding in plants Plant Working Group, 2009), with these loci now has been evaluated in some recent studies (e.g. Kane widely used alongside the nuclear region ITS and et al., 2012; Li et al., 2015; Ruhsam et al., 2015; Ji et al., other plastid loci such as trnH–psbA (Chase et al., 2019; Pang et al., 2019), few studies have undertaken 2005; Kress et al., 2005; China Plant BOL Group, 2011; direct comparisons between the suitability of standard Hollingsworth, Graham & Little, 2011). Despite many DNA barcodes and plastomes for genus and species benefits of using these standardized loci for plant DNA identification using multiple individuals per species barcoding, it has long been recognized that no single from a specific family. suite of loci will be suitable across all plant taxa. In Lauraceae were established by de Jussieu (1789) groups where standard DNA barcoding ‘fails’ due to in his Genera Plantarum, based on the type genus technical issues, such as mutations in primer-binding Laurus L. (Linnaeus, 1753). Lauraceae are evergreen regions, or biological issues, such as rapid divergence, or sometimes deciduous shrubs or trees (except for researchers must augment the standard loci with Cassytha L., which is a twining, virtually leafless, additional sequence data. The massive improvements parasitic perennial vine), often with aromatic bark in genomic sequencing technologies allow researchers and
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