See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/281542833 Chloroplast phylogenomics resolves key relationships in ferns ARTICLE in JOURNAL OF SYSTEMATICS AND EVOLUTION · SEPTEMBER 2015 Impact Factor: 1.49 · DOI: 10.1111/jse.12180 CITATIONS READS 2 176 5 AUTHORS, INCLUDING: Jinmei lu Ning Zhang Chinese Academy of Sciences U.S. Food and Drug Administration 10 PUBLICATIONS 126 CITATIONS 14 PUBLICATIONS 193 CITATIONS SEE PROFILE SEE PROFILE Jun Wen De-Zhu Li Smithsonian Institution Chinese Academy of Sciences Kunming … 254 PUBLICATIONS 7,029 CITATIONS 340 PUBLICATIONS 2,700 CITATIONS SEE PROFILE SEE PROFILE All in-text references underlined in blue are linked to publications on ResearchGate, Available from: Jinmei lu letting you access and read them immediately. Retrieved on: 17 March 2016 Journal of Systematics JSE and Evolution doi: 10.1111/jse.12180 Research Article Chloroplast phylogenomics resolves key relationships in ferns † † Jin-Mei Lu1 , Ning Zhang2 , Xin-Yu Du1, Jun Wen2*, and De-Zhu Li1* 1Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China 2Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA † These authors contributed equally to this work. *Authors for correspondence. Jun Wen. E-mail: [email protected]. Tel.: 1-202-633-4881. Fax: 1-202-786-2563. De-Zhu LI. E-mail: [email protected]. Tel./Fax: 86-871-65223503. Received 1 July 2015; Accepted 27 August 2015; Article first published online 1 September 2015 Abstract Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae (Koidz.) Ching (eupolypod I) and Woodwardia unigemmata (Makino) Nakai (eupolypod II), and constructed the phylogeny of ferns based on both 48 genes and 64 genes. The trees based on 48 genes and 64 genes are identical in topology, differing only in support values for four nodes, three of which showed higher support values for the 48-gene dataset. Equisetum L. was resolved as the sister to the Psilotales–Ophioglossales clade, and Equisetales–Psilotales–Ophioglossales clade was sister to the clade of the leptosporangiate and marattioid ferns. The sister relationship between the tree fern clade and polypods was supported by 82% and 100% bootstrap values in the 64-gene and 48-gene trees, respectively. Within polypod ferns, Pteridaceae was sister to the clade of Dennstaedtiaceae and eupolypods with a high support value, and the relationship of Dennstaedtiaceae–eupolypods was strongly supported. With recent parallel advances in the phylogenetics of ferns using nuclear data, chloroplast phylogenomics shows great potential in providing a framework for testing the impact of reticulate evolution in the early evolution of ferns. Key words: chloroplast genome, chloroplast phylogenomics, ferns, phylogenetics, polypods. The plant chloroplast genome (or plastome) is of a moderate 1998; Wolf et al., 2003; Roper et al., 2007; Gao et al., 2009). size and can be easily sequenced. In general, there is good co- With the advent of next-generation sequencing, 15 complete linearity among chloroplast genomes of different plant taxa, chloroplast genomes have been sequenced since 2011 (Table 1; facilitating comparative analyses (Jansen et al., 2007). The also see Banks et al., 2011; Wolf et al., 2011; Gao et al., 2013; molecular evolutionary rates of the coding and non-coding Grewe et al., 2013; Kim & Kim, 2014; Kim et al., 2014; Zhong regions of chloroplast genomes are of significant difference, et al., 2014). Moreover, five partial chloroplast genomes were and thus can provide a large degree of genetic variation for recently submitted to GenBank, and these included: Ceratop- comparative phylogenetic studies at different taxonomic teris richardii Brongn. (KM052729), Cystopteris protrusa ranks (Clegg et al., 1994). These advantages have allowed the (Weath.) Blasdell (KP136830), Dipteris conjugata Reinw. wide use of chloroplast DNA sequences in phylogenetic (KP136829), Plagiogyria formosana Nakai (KP136831), and studies of plants (Jansen et al., 2007; Moore et al., 2007, 2010; Polypodium glycyrrhiza D. C. Eaton (KP136832). Gao et al., 2010). The chloroplast genome size is generally approximately Previously, studies on whole chloroplast genomes of ferns 131–168 kb in ferns (Grewe et al., 2013; Zhong et al., 2014; and lycophytes have been relatively few in comparison with Table 1), and the genome size variation is mostly due to length those on seed plants and those studies largely focused on variation in the inverted repeat (IR) and the small single copy chloroplast genome sequencing of a single species (Wakasugi (SSC) section (Grewe et al., 2013). Although the number of et al., 1998; Wolf et al., 2003; Roper et al., 2007; Tsuji et al., genes (117–124 coding genes) and gene order are relatively 2007). However, as of June 2015, the National Center for conserved in chloroplast genomes of ferns, there are some Biotechnology Information’s database included 26 chloroplast differences among taxa (Table 1). A few studies on the genomes of ferns and five of lycophytes (Table 1; Fig. 1). Early chloroplast evolutionary genomics of ferns have been production of chloroplast genomes for ferns and lycophytes published in recent years (Gao et al., 2010, 2011, 2013; Karol involved more tedious Sanger sequencing (Wakasugi et al., et al., 2010; Wolf et al., 2011; Grewe et al., 2013; Kim et al., 2014; © 2015 Institute of Botany, Chinese Academy of Sciences September 2015 | Volume 53 | Issue 5 | 448–457 www.jse.ac.cn Table 1 General characteristics of chloroplast genomes of ferns and selected outgroups † Taxon Reference Accession Size, GC % LSC IR SSC Coding, Coding, Non- Non- Genes Protein rRNA tRNA Intron no. bp bp % coding, coding, bp % Ferns Equisetum Karol et al., 2010 NC_014699 133 309 33.40 93 542 10 149 19 469 84 365 63.29 48 944 36.71 121 84 4 33 18 arvense L. Equisetum Kim et al., 2014 JN968380 132 726 34.00 92 961 10 144 19 477 84 465 63.64 48 261 36.36 121 84 4 33 18 arvense L. Equisetum hyemale Grewe et al., 2013 NC_020146 131 760 33.74 92 580 10 093 18 994 84 612 64.22 47 148 35.78 122 85 4 33 17 Mankyua Kim & Kim, unpublished data NC_017006 146 221 37.97 106 096 9756 20 613 81 447 55.70 64 774 44.30 123 87 4 32 18 ‡ chejuense Mankyua chejuense Kim et al., 2014 KP205433 146 225 38.00 106 099 9756 20 614 82 056 56.12 64 169 43.88 124 88 4 32 19 Ophioglossum Grewe et al., 2013 NC_020147 138 270 42.20 99 058 9775 19 662 83 529 60.41 54 741 39.59 120 84 4 32 19 californicum Chloroplast phylogenomics in ferns Psilotum nudum Wakasugi et al., 1998 NC_003386 138 829 36.03 84 617 18 954 16 304 90 274 65.03 48 555 34.97 119Ã 84Ã 43219 Psilotum nudum Grewe et al., 2013 KC117179 138 909 36.00 84 674 18 953 16 329 85 345 61.44 53 564 38.56 119 82 4 33 20 Tmesipteris Zhong et al., 2014 KJ569699 139 736 36.10 85 629 18 914 16 279 79 507 56.90 60 229 43.10 116 81 4 31 17 elongata P. A. Dangeard Angiopteris Zhu & Mower, unpublished NC_026300 153 596 35.50 89 708 21 676 20 536 87 132 56.73 66 464 43.27 122 86 4 32 19 angustifolia data Angiopteris evecta Roper et al., 2007 NC_008829 153 901 49.50 89 709 21 053 22 086 82 600 53.67 71 301 46.33 121 86 4 31 18 Osmundastrum Kim et al., 2014 NC_024157 142 812 40.20 100 294 10 109 22 300 80 239 56.19 62 573 43.81 121 84 4 33 21 cinnamomeum Diplopterygium Kim et al., 2014 NC_024158 151 007 40.20 99 857 14 584 21 982 84 623 56.04 66 384 43.96 119 85 4 30 20 glaucum Lygodium Gao et al., 2013 NC_022136 157 260 40.64 85 448 25 080 21 652 92 740 58.97 64 520 41.03 117 86 4 27 20 japonicum Lygodium Kim et al., 2014 KF225593 157 142 41.00 85 432 25 038 21 634 91 810 58.42 65 332 41.58 117 86 4 27 19 japonicum Marsilea crenata C. Gao et al., 2013 NC_022137 151 628 42.22 87 828 20 795 22 210 91 301 60.21 60 327 39.79 117 86 4 27 21 Presl Dicksonia Zhong et al., 2014 KJ569698 168 244 41.50 85 817 30 201 22 025 96 942 57.62 71 302 42.38 118 85 4 29 15 J. Syst. Evol. squarrosa (Forst. f.) Sw. Alsophila spinulosa Gao et al., 2009 NC_012818 156 661 40.40 86 308 24 365 21 623 91 947 58.69 64 714 41.31 118 86 4 28 21 (Wall. ex Hook.) R. M. Tryon 53 (5): 448 Pteridium Der, 2010 NC_014348 152 362 41.50 84 335 23 384 21 259 92 311 60.59 60 051 39.41 117 84 4 29 21 aquilinum subsp. aquilinum Adiantum capillus- Wolf et al., 2003 NC_004766 150 568 42.00 82 282 23 447 21 392 91 562 60.81 59 006 39.19 117 84 4 29 20 veneris – 457, 2015 Cheilanthes Wolf et al., 2011 NC_014592 155 770 42.70 83 059 25 694 21 323 92 140 59.15 63 630 40.85 118 85 4 29 22 lindheimeri Continued 449 J.