Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses

Wang, W., Hwang, C., Lin, T. & Hwang, S. Y. Historical biogeography and phylogenetic relationships of the genus Chamaecyparis (Cupressaceae) inferred from chloroplast DNA polymorphism. Plant Syst. Evol. 241, 13–28. https://doi.org/10.1007/s00606-003-0031-0 (2003).

CAS  Article  Google Scholar 

Liao, P. C., Lin, T. P. & Hwang, S. Y. Reexamination of the pattern of geographical disjunction of Chamaecyparis (Cupressaceae) in North America and East Asia. Bot. Stud. 51, 511–520 (2010).

CAS  Google Scholar 

Li, C. F. et al. Chamaecyparis montane cloud forest in Taiwan: ecology and vegetation classification. Ecol. Res. 30, 771–791. https://doi.org/10.1007/s11284-015-1284-0 (2015).

Article  Google Scholar 

IUCN Red List of Threatened Species. https://www.iucnredlist.org/ (2013).

Horng, F. W., Ma, F. C., Yu, H. M., Hsui, Y. R. & Chang, H. M. An estimation of original Chamaecyparis forest area in Taiwan and its implication for conservation. Q. J. Chin. For. 17, 143–153 (2000).

Google Scholar 

Koch, G., Richter, H. G. & Schmitt, U. Design and application of CITESwoodID computer-aided identification and description of CITES-protected timbers. IAWA J. 32, 213–220. https://doi.org/10.1163/22941932-90000052 (2011).

Article  Google Scholar 

Sarmiento, C. et al. Pl@ntwood: a computer-assisted identification tool for 110 species of Amazon trees based on wood anatomical features. IAWA J. 32, 221–232. https://doi.org/10.1163/22941932-90000053 (2011).

MathSciNet  Article  Google Scholar 

Gasson, P. How precise can wood identification be? Wood anatomy’s role in support of the legal timber trade, especially cites. IAWA J. 32, 137–154. https://doi.org/10.1163/22941932-90000049 (2011).

Article  Google Scholar 

Jiao, L., Yin, Y., Cheng, Y. & Jiang, X. DNA barcoding for identification of the endangered species Aquilaria sinensis: comparison of data from heated or aged wood samples. Holzforschung 68, 487–494. https://doi.org/10.1515/hf-2013-0129 (2014).

CAS  Article  Google Scholar 

Jiao, L. et al. DNA barcode authentication and library development for the wood of six commercial Pterocarpus species: the critical role of xylarium specimens. Sci. Rep. 8, 1945. https://doi.org/10.1038/s41598-018-20381-6 (2018).

ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

Nithaniyal, S. et al. DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India. PLoS ONE 9, e107669. https://doi.org/10.1371/journal.pone.0107669 (2014).

ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

Liu, J. et al. Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification. Mol. Ecol. Resour. 18, 1115–1131. https://doi.org/10.1111/1755-0998.12903 (2018).

CAS  Article  Google Scholar 

Kress, W. J. Plant DNA barcodes: applications today and in the future. J. Syst. Evol. 55, 291–307. https://doi.org/10.1111/jse.12254 (2017).

Article  Google Scholar 

CBOL Plant Working Group. A DNA barcode for land plants. Proc. Natl. Acad. Sci. U S A 106, 12794–12797. https://doi.org/10.1111/1755-0998.12194 (2009).

CAS  Article  PubMed Central  Google Scholar 

Hollingsworth, P. M., Graham, S. W. & Little, D. P. Choosing and using a plant DNA barcode. PLoS ONE 6, e19254. https://doi.org/10.1371/journal.pone.0019254 (2011).

ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

Li, D. Z. et al. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc. Natl. Acad. Sci. USA 108(19641–19646), 2011. https://doi.org/10.1073/pnas.1104551108 (2011).

Article  Google Scholar 

Purty, R. S. & Chatterjee, S. DNA Barcoding: an effective technique in molecular taxonomy. Austin J. Biotechnol. Bioeng. 3, 1059 (2016).

Google Scholar 

Kane, N. et al. Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. Am. J. Bot. 99, 320–329. https://doi.org/10.3732/ajb.1100570 (2012).

CAS  Article  PubMed  Google Scholar 

Bock, D. G., Kane, N. C., Ebert, D. P. & Rieseberg, L. H. Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol. 201, 1021–1030. https://doi.org/10.1111/nph.12560 (2014).

CAS  Article  PubMed  Google Scholar 

Ji, Y. et al. Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae). Mol. Ecol. Resour. 19, 1333–1345. https://doi.org/10.1111/1755-0998.13050 (2019).

CAS  Article  PubMed  Google Scholar 

Li, X. et al. Plant DNA barcoding: from gene to genome. Biol. Rev. 90, 157–166. https://doi.org/10.1111/brv.12104 (2015).

Article  PubMed  Google Scholar 

Niu, Z. et al. Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots. Sci. Rep. 7, 2073. https://doi.org/10.1038/s41598-017-02252-8 (2017).

CAS  Article  Google Scholar 

Zhu, S. et al. Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes. Acta. Pharm. Sin. B. 8, 969–980. https://doi.org/10.1016/j.apsb.2018.05.009 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Fu, C. N. et al. Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide. Sci. Rep. 9, 2773. https://doi.org/10.1038/s41598-019-39161-x (2019).

ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

Dodsworth, S. Genome skimming for next-generation biodiversity analysis. Trends Plant Sci. 20, 525–527. https://doi.org/10.1016/j.tplants.2015.06.012 (2015).

CAS  Article  PubMed  Google Scholar 

Guo, W. et al. Predominant and substoichiometric isomers of the plastid genome coexist within Juniperus plants and have shifted multiple times during cupressophyte evolution. Genome Biol. Evol. 6, 580–590. https://doi.org/10.1093/gbe/evu046 (2014).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Wu, C. S. & Chaw, S. M. Large-scale comparative analysis reveals the mechanisms driving plastomic compaction, reduction, and inversions in conifers II (cupressophytes). Genome Biol. Evol. 8, 3740–3750. https://doi.org/10.1093/gbe/evw278 (2016).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Qu, X. J., Wu, C. S., Chaw, S. M. & Yi, T. S. Insights into the existence of isomeric plastomes in Cupressoideae (Cupressaceae). Genome Biol. Evol. 9, 1110–1119. https://doi.org/10.1093/gbe/evx071 (2017).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A. & Janzen, D. H. Use of DNA barcodes to identify flowering plants. Proc. Natl. Acad. Sci. USA 102, 8369–8374. https://doi.org/10.1073/pnas.0503123102 (2005).

ADS  CAS  Article  PubMed  Google Scholar 

Pang, X. et al. Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis. PLoS ONE 7, e48833. https://doi.org/10.1371/journal.pone.0048833 (2012).

ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

Loera-Sánchez, M., Studer, B. & Kölliker, R. DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses. BMC Res. Notes 13, 35. https://doi.org/10.1186/s13104-020-4897-5 (2020).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Zonneveld, B. J. M. Conifer genome sizes of 172 species, covering 64 of 67 genera, range from 8 to 72 picogram. Nord. J. Bot. 30, 490–502. https://doi.org/10.1111/j.1756-1051.2012.01516.x (2012).

Article  Google Scholar 

Preuten, T. et al. Fewer genes than organelles: extremely low and variable gene copy numbers in mitochondria of somatic plant cells. Plant J. 64, 948–959. https://doi.org/10.1111/j.1365-313X.2010.04389.x (2010).

CAS  Article  PubMed  Google Scholar 

Shen, J., Zhang, Y., Havey, M. J. & Shou, W. Copy numbers of mitochondrial genes change during melon leaf development and are lower than the numbers of mitochondria. Hortic. Res. 6, 95. https://doi.org/10.1038/s41438-019-0177-8 (2019).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Sloan, D. B. One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure. New Phytol. 200, 978–985. https://doi.org/10.1111/nph.12395 (2013).

CAS  Article  PubMed  Google Scholar 

Gualberto, J. M. & Newton, K. J. Plant mitochondrial genomes: dynamics and mechanisms of mutation. Annu. Rev. Plant Biol. 68, 225–252. https://doi.org/10.1146/annurev-arplant-043015-112232 (2017).

CAS  Article  PubMed  Google Scholar 

Kozik, A. et al. The alternative reality of plant mitochondrial DNA: one ring does not rule them all. PLoS Genet. 15, e1008373. https://doi.org/10.1371/journal.pgen.1008373 (2019).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Ruhsam, M. et al. Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?. Mol. Ecol. Resour. 15, 1067–1078. https://doi.org/10.1111/1755-0998.12375 (2015).

CAS  Article  PubMed  Google Scholar 

Chen, Q., Wu, X. & Zhang, D. Comparison of the abilities of universal, super, and specific DNA barcodes to discriminate among the original species of Fritillariae cirrhosae bulbus and its adulterants. PLoS ONE 15, e0229181. https://doi.org/10.1371/journal.pone.0229181 (2020).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Weng, M. L., Blazier, J. C., Govindu, M. & Jansen, R. K. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Mol. Biol. Evol. 31, 645–659. https://doi.org/10.1093/molbev/mst257 (2014).

CAS  Article  PubMed  Google Scholar 

Vieira Ldo, N. et al. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection. PLoS ONE 9, e90618. https://doi.org/10.1371/journal.pone.0090618 (2014).

ADS  Article  PubMed  Google Scholar 

Hamsher, S. E. et al. Extensive chloroplast genome rearrangement amongst three closely relatedHalamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants. PLoS ONE 14, e0217824. https://doi.org/10.1371/journal.pone.0217824 (2019).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Garcia, S., Kovařík, A., Leitch, A. R. & Garnatje, T. Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database. Plant J. 89, 1020–1030. https://doi.org/10.1111/tpj.13442 (2017).

CAS  Article  PubMed  Google Scholar 

Liere, K. & Börner, T. Development-dependent changes in the amount and structural organization of plastid DNA. In Plastid Development in Leaves during Growth and Senescence (ed. Biswal, B., K. Krupinska, K. & Biswal, U. C.) 215–237 (Amsterdam Springer, 2013).

Li, J., Su, Y. & Wang, T. The repeat sequences and elevated substitution rates of the chloroplast accD gene in cupressophytes. Front. Plant Sci. 9, 533. https://doi.org/10.3389/fpls.2018.00533 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Sudianto, E. & Chaw, S. M. Two independent plastid accD transfers to the nuclear genome of Gnetum and other insights on acetyl-coA carboxylase evolution in gymnosperms. Genome Biol. Evol. 11, 1691–1705. https://doi.org/10.1093/gbe/evz059 (2019).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Deguilloux, M. F., Pemonge, M. H. & Petit, R. J. Novel perspectives in wood certification and forensics: dry wood as a source of DNA. Proc. Biol. Sci. 269, 1039–1046. https://doi.org/10.1098/rspb.2002.1982 (2002).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bul. 19, 11–15 (1987).

Google Scholar 

Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 (2014).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477. https://doi.org/10.1089/cmb.2012.0021 (2012).

MathSciNet  CAS  Article  PubMed  PubMed Central  Google Scholar 

Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421. https://doi.org/10.1186/1471-2105-10-421 (2009).

CAS  Article  Google Scholar 

Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18. https://doi.org/10.1186/2047-217X-1-18 (2012).

Article  PubMed  PubMed Central  Google Scholar 

Ronen, R., Boucher, C., Chitsaz, H. & Pevzner, P. SEQuel: improving the accuracy of genome assemblies. Bioinformatics 28, i188-196. https://doi.org/10.1093/bioinformatics/bts219 (2012).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Tillich, M. et al. GeSeq-versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45, W6–W11. https://doi.org/10.1093/nar/gkx391 (2017).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. https://doi.org/10.1093/nar/gkm160 (2007).

ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645. https://doi.org/10.1101/gr.092759.109 (2009).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780. https://doi.org/10.1093/molbev/mst010 (2013).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313. https://doi.org/10.1093/bioinformatics/btu033 (2014).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).

CAS  Article  PubMed  PubMed Central  Google Scholar 

Darling, A. E., Mau, B. & Perna, N. T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5, e11147. https://doi.org/10.1371/journal.pone.0011147 (2010).

ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

Rozas, J. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34, 3299–3302. https://doi.org/10.1093/molbev/msx248 (2017).

CAS  Article  Google Scholar 

Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(1792–1797), 2004. https://doi.org/10.1093/nar/gkh340 (2004).

CAS  Article  Google Scholar