Characterization of 20 complete plastomes from the tribe Laureae (Lauraceae) and distribution of small inversions
Autoři:
Sangjin Jo aff001; Young-Kee Kim aff001; Se-Hwan Cheon aff001; Qiang Fan aff002; Ki-Joong Kim aff001
Působiště autorů:
School of Life Sciences, Korea University, Seoul, Korea
aff001; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
aff002
Vyšlo v časopise:
PLoS ONE 14(11)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0224622
Souhrn
Lindera Thunb. (Lauraceae) consists of approximately 100 species, mainly distributed in the temperate and tropical regions of East Asia. In this study, we report 20 new, complete plastome sequences including 17 Lindera species and three related species, Actinodaphne lancifolia, Litsea japonica and Sassafras tzumu. The complete plastomes of Lindera range from 152,502 bp (L. neesiana) to 154,314 bp (L. erythrocarpa) in length. Eleven small inversion (SI) sites are documented among the plastomes. Six of the 11 SI sites are newly reported and they locate in rpoB-trnC, psbC-trnS, petA-psbJ, rpoA and ycf2 regions. The distribution patterns of SIs are useful for species identification. An average of 83 simple sequence repeats (SSRs) were detected in each plastome. The mono-SSRs accounted for 72.7% of total SSRs, followed by di- (12.4%), tetra- (9.4%), tri- (4.2%), and penta-SSRs (1.3%). Of these SSRs, 64.6% were distributed in an intergenic spacer (IGS) region. In addition, 79.8% of the SSRs are located in a large single copy (LSC) region. In contrast, almost no SSRs are distributed in inverted repeat (IR) regions. The SSR loci are useful to identifying species but the phylogenetic value is low because the majority of them show autapomorphic status or highly homoplastic characteristics. The nucleotide diversity (Pi) values also indicated the conserved nature of the IR region compared to LSC and small single copy (SSC) regions. Five spacer regions with high Pi values, trnH-psbA, petA-psbJ and ndhF-rpl32, rpl32-trnL and Ψycf1-ndhF, have a potential use for the molecular identification study of Lindera and related species. Lindera species form a paraphyletic group in the plastome tree because of the inclusion of related genera such as Actinodaphne, Laurus, Litsea and Neolitsea. A former member of tribe Laureae, Sassafras, forms a clade with the tribe Cinnamomeae. The SIs do not affect the phylogenetic relationship of Laureae. This result indicated that ancient plastome captures may have contribute to the mixed intergeneric relationship of Laureae. Alternatively, the result may indicate that the morphological characters defined the genera of Lauraceae originated for several times.
Klíčová slova:
Sequence alignment – Phylogenetics – Phylogenetic analysis – Trees – Sequence databases – Flowering plants – Introns – Microsatellite loci
Zdroje
1. APG IV. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc. 2016; 181: 1–20.
2. Christenhusz MJ, Byng JW. The number of known plants species in the world and its annual increase. Phytotaxa. 2016; 261:201–217.
3. Xiwen L, Jie L, Puhua H, Fa'nan W, Hongbin C, van der Werff H. Lauraceae. In: Zhengyi W, Raven PH, editors. Flora of China. 7: Science Press, Missouri Botanical Garden Press; 2007. pp. 102–254.
4. Renner SS, Chanderbali AS. What is the relationship among Hernandiaceae, Lauraceae, and Monimiaceae, and why is this question so difficult to answer? Int J Plant Sci. 2000; 161: S109–S19.
5. Michalak I, Zhang LB, Renner SS. Trans‐Atlantic, trans‐Pacific and trans‐Indian Ocean dispersal in the small Gondwanan Laurales family Hernandiaceae. J Biogeogr. 2010; 37: 1214–1226.
6. Chanderbali AS, van der Werff H, Renner SS. Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes. Ann Mo Bot Gard. 2001; 88: 104–134.
7. Byng JW. The Flowering Plants Handbook: A practical guide to families and genera of the world. Hertford: Plant Gateway Ltd; 2014.
8. van der Werff H. Lauraceae. In: Committee FoNAE, editor. Flora of North America. 3: Oxford University Press on Demand; 1997. pp. 26–36.
9. Ohba H. Lauraceae. In: Iwatsuki K, Boufford DE, Ohba H, editors. Flora of Japan. IIa: Kodansha LTD; 2006. pp. 240–53.
10. Chung MG. LAURACEAE Juss. In: Park CW, editor. The Genera of Vascular Plants of Korea: Academy Publishing Co.; 2007.
11. APG II. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc. 2013; 141: 399–436.
12. Wicke S, Schneeweiss GM, Müller KF, Quandt D. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol. 2011; 76: 273–97. doi: 10.1007/s11103-011-9762-4 21424877
13. Chen X, Yang J, Zhang H, Bai R, Zhang X, Bai G, et al. The complete chloroplast genome of Calycanthus chinensis, an endangered species endemic to China. Conserv Genet Resour. 2019; 11: 55–58.
14. Song Y, Dong W, Liu B, Xu C, Yao X, Gao J, et al. Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae. Front Plant Sci. 2015; 6: 662. doi: 10.3389/fpls.2015.00662 26379689
15. Song Y, Yao X, Tan Y, Gan Y, Corlett RT. Complete chloroplast genome sequence of the avocado: gene organization, comparative analysis, and phylogenetic relationships with other Lauraceae. Can J For Res. 2016; 46: 1293–1301.
16. Hinsinger DD, Strijk JS. Toward phylogenomics of Lauraceae: The complete chloroplast genome sequence of Litsea glutinosa (Lauraceae), an invasive tree species on Indian and Pacific Ocean islands. Plant Gene. 2017; 9: 71–79.
17. Chen C, Zheng Y, Liu S, Zhong Y, Wu Y, Li J, et al. The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species. PeerJ. 2017; 5: e3820. doi: 10.7717/peerj.3820 28948105
18. Li Y, Xu W, Zou W, Jiang D, Liu X. Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species. Bot Stud. 2017; 58: 37. doi: 10.1186/s40529-017-0192-8 28905330
19. Song Y, Yao X, Tan Y, Gan Y, Yang J, Corlett RT. Comparative analysis of complete chloroplast genome sequences of two subtropical trees, Phoebe sheareri and Phoebe omeiensis (Lauraceae). Tree Genet Genomes. 2017; 13: 120. doi: 10.1007/s11295-017-1196-y
20. Song Y, Yu W-B, Tan Y, Liu B, Yao X, Jin J, et al. Evolutionary comparisons of the chloroplast genome in Lauraceae and insights into loss events in the Magnoliids. Genome Biol Evol. 2017; 9: 2354–2364. doi: 10.1093/gbe/evx180 28957463
21. Wu C-S, Wang T-J, Wu C-W, Wang Y-N, Chaw S-M. Plastome evolution in the sole hemiparasitic genus laurel dodder (Cassytha) and insights into the plastid phylogenomics of Lauraceae. Genome Biol Evol. 2017; 9: 2604–2614. doi: 10.1093/gbe/evx177 28985306
22. Song Y, Yao X, Liu B, Tan Y, Corlett RT. Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae. Holzforschung. 2018; 72: 337–345.
23. Zhao M-L, Song Y, Ni J, Yao X, Tan Y-H, Xu Z-F. Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae). Sci Rep. 2018; 8: 8844. doi: 10.1038/s41598-018-27090-0 29891996
24. Wu C-C, Chu F-H, Ho C-K, Sung C-H, Chang S-H. Comparative analysis of the complete chloroplast genomic sequence and chemical components of Cinnamomum micranthum and Cinnamomum kanehirae. Holzforschung. 2017; 71: 189–197.
25. Rabah SO, Lee C, Hajrah NH, Makki RM, Alharby HF, Alhebshi AM, et al. Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew. The Plant Genome. 2017; 10. doi: 10.3835/plantgenome2017.03.0020 29293812
26. Li J, Christophel D, Conran J, Li H-W. Phylogenetic relationships within the ‘core’Laureae (Litseacomplex, Lauraceae) inferred from sequences of the chloroplast gene matK and nuclear ribosomal DNA ITS regions. Plant Syst Evol. 2004; 246: 19–34.
27. Li J, Conran JG, Christophel DC, Li Z-M, Li L, Li H-W. Phylogenetic Relationships of the Litsea Complex and Core Laureae (Lauraceae) Using ITS and ETS Sequences and Morphology. Ann Mo Bot Gard. 2008; 95: 580–599.
28. Nie Z-L, Wen J, Sun H. Phylogeny and biogeography of Sassafras (Lauraceae) disjunct between eastern Asia and eastern North America. Plant Syst Evol. 2007; 267: 191–203.
29. Rohwer JG, Li J, Rudolph B, Schmidt SA, van der Werff H, Li H-w. Is Persea (Lauraceae) monophyletic? Evidence from nuclear ribosomal ITS sequences. Taxon. 2009; 58: 1153–1167.
30. Huang J-F, Li L, van der Werff H, Li H-W, Rohwer JG, Crayn DM, et al. Origins and evolution of cinnamon and camphor: A phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae). Mol Phylogenet Evol. 2016; 96: 33–44. doi: 10.1016/j.ympev.2015.12.007 26718058
31. Kim K-J, Choi K-S, Jansen RK. Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Mol Biol Evol. 2005; 22: 1783–1792. doi: 10.1093/molbev/msi174 15917497
32. Palmer JD, Osorio B, Aldrich J, Thompson WF. Chloroplast DNA evolution among legumes: loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr Genet. 1987; 11: 275–286.
33. Saski C, Lee S-B, Daniell H, Wood TC, Tomkins J, Kim H-G, et al. Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol Biol. 2005; 59: 309–322. doi: 10.1007/s11103-005-8882-0 16247559
34. Palmer JD, Nugent JM, Herbon LA. Unusual structure of geranium chloroplast DNA: a triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families. Proc Natl Acad Sci USA. 1987; 84: 769–773. doi: 10.1073/pnas.84.3.769 16593810
35. Guisinger MM, Kuehl JV, Boore JL, Jansen RK. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol. 2011; 28: 583–600. doi: 10.1093/molbev/msq229 20805190
36. Kim K-J, Lee H-L. Widespread occurrence of small inversions in the chloroplast genomes of land plants. Mol Cells (Springer Science & Business Media BV). 2005; 19: 104–113.
37. Lee H-L, Jansen RK, Chumley TW, Kim K-J. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol. 2007; 24: 1161–1180. doi: 10.1093/molbev/msm036 17329229
38. Cauz-Santos LA, Munhoz CF, Rodde N, Cauet S, Santos AA, Penha HA, et al. The chloroplast genome of Passiflora edulis (Passifloraceae) assembled from long sequence reads: Structural organization and phylogenomic studies in Malpighiales. Front Plant Sci. 2017; 8: 334. doi: 10.3389/fpls.2017.00334 28344587
39. Doyle JJ, Davis JI, Soreng RJ, Garvin D, Anderson MJ. Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proc Natl Acad Sci USA. 1992; 89: 7722–7726. doi: 10.1073/pnas.89.16.7722 1502190
40. Catalano SA, Saidman BO, Vilardi JC. Evolution of small inversions in chloroplast genome: a case study from a recurrent inversion in angiosperms. Cladistics. 2009; 25: 93–104.
41. Graham SW, Reeves PA, Burns AC, Olmstead RG. Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int J Plant Sci. 2000; 161: S83–S96.
42. Sang T, Crawford DJ, Stuessy TF. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am J Bot. 1997; 84:1120–1136. 21708667
43. Bain J, Jansen R. A chloroplast DNA hairpin structure provides useful phylogenetic data within tribe Senecioneae (Asteraceae). Botany. 2006; 84: 862–868.
44. Whitlock BA, Hale AM, Groff PA. Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. PLoS One. 2010; 5: e11533. doi: 10.1371/journal.pone.0011533 20644717
45. Bieniek W, Mizianty M, Szklarczyk M. Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species. Plant Syst Evol. 2015; 301: 1275–1286.
46. Swangpol S, Volkaert H, Sotto RC, Seelanan T. Utility of selected non-coding chloroplast DNA sequences for lineage assessment of Musa interspecific hybrids. BMB Reports. 2007; 40: 577–587.
47. Kelchner SA, Wendel JF. Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr Genet. 1996; 30: 259–262. doi: 10.1007/s002940050130 8753656
48. Borsch T, Quandt D. Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Syst Evol. 2009; 282: 169–199.
49. Yi D-K, Lee H-L, Sun B-Y, Chung MY, Kim K-J. The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids. Mol Cells. 2012; 33: 497–508. doi: 10.1007/s10059-012-2281-6 22555800
50. Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One. 2010; 5: e12762. doi: 10.1371/journal.pone.0012762 20856810
51. Yi D-K, Kim K-J. Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PLoS One. 2012; 7: e35872. doi: 10.1371/journal.pone.0035872 22606240
52. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28: 1647–1649. doi: 10.1093/bioinformatics/bts199 22543367
53. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25: 955–964. doi: 10.1093/nar/25.5.955 9023104
54. Lohse M, Drechsel O, Kahlau S, Bock R. OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013; 41: W575–W581. doi: 10.1093/nar/gkt289 23609545
55. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001; 29: 4633–4642. doi: 10.1093/nar/29.22.4633 11713313
56. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31: 3406–3415. doi: 10.1093/nar/gkg595 12824337
57. Katoh K, Misawa K, Kuma Ki, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002; 30: 3059–3066. doi: 10.1093/nar/gkf436 12136088
58. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol Biol Evol. 2017; 34: 3299–3302. doi: 10.1093/molbev/msx248 29029172
59. Leese F, Mayer C, Held C. Isolation of microsatellites from unknown genomes using known genomes as enrichment templates. Limnol Oceanogr Meth. 2008; 6: 412–426.
60. Darriba D, Taboada GL, Doallo R, Posada D. JmodelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012; 9: 772.
61. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008; 57: 758–771. doi: 10.1080/10635150802429642 18853362
62. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986; 5: 2043–2049. 16453699
63. Kim K-J, Lee H-L. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 2004; 11: 247–261. doi: 10.1093/dnares/11.4.247 15500250
64. Ruhlman TA, Jansen RK. The plastid genomes of flowering plants. In: Maliga P, editor. Chloroplast biotechnology. Totowa, NJ, USA: Humana Press; 2014. pp. 3–38.
65. Rossetto M, Kooyman R, Yap J-YS, Laffan SW. From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly. Proc R Soc B- Biol Sci. 2015; 282: 20151998. doi: 10.1098/rspb.2015.1998 26645199
66. Dong W, Liu J, Yu J, Wang L, Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One. 2012; 7: e35071. doi: 10.1371/journal.pone.0035071 22511980
67. Li R, Ma P-F, Wen J, Yi T-S. Complete sequencing of five Araliaceae chloroplast genomes and the phylogenetic implications. PLoS One. 2013; 8: e78568. doi: 10.1371/journal.pone.0078568 24205264
68. Powell W, Morgante M, McDevitt R, Vendramin G, Rafalski J. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci USA. 1995; 92: 7759–7763. doi: 10.1073/pnas.92.17.7759 7644491
69. Grassi F, Labra M, Scienza A, Imazio S. Chloroplast SSR markers to assess DNA diversity in wild and cultivated grapevines. Vitis. 2002; 41: 157–158.
70. Levinson G, Gutman GA. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol. 1987; 4: 203–221. doi: 10.1093/oxfordjournals.molbev.a040442 3328815
71. Fijridiyanto IA, Murakami N. Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences. J Plant Res. 2009; 122: 283–298. doi: 10.1007/s10265-009-0218-8 19219578
Článok vyšiel v časopise
PLOS One
2019 Číslo 11
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
- Nejasný stín na plicích – kazuistika
- Masturbační chování žen v ČR − dotazníková studie
- Úspěšná resuscitativní thorakotomie v přednemocniční neodkladné péči
- Dlouhodobá recidiva a komplikace spojené s elektivní operací břišní kýly
Najčítanejšie v tomto čísle
- A daily diary study on maladaptive daydreaming, mind wandering, and sleep disturbances: Examining within-person and between-persons relations
- A 3’ UTR SNP rs885863, a cis-eQTL for the circadian gene VIPR2 and lincRNA 689, is associated with opioid addiction
- A substitution mutation in a conserved domain of mammalian acetate-dependent acetyl CoA synthetase 2 results in destabilized protein and impaired HIF-2 signaling
- Molecular validation of clinical Pantoea isolates identified by MALDI-TOF