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Chloroplast genome assembly and phylogenetic analysis of Pterocarpus dalbergioides Roxb., an endemic timber species

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Abstract  

Pterocarpus dalbergioides commonly known as Andaman Padauk is endemic to the Andaman Islands of India and is known for its exquisite timber quality. Due to overexploitation and poor regeneration, the species is classified as vulnerable by International Union for Conservation of Nature (IUCN). There are no genomic resources reported in this species to date. In the present study, a near-complete chloroplast (Cp) genome of P. dalbergioides was assembled from leaf transcriptome data. The size of the assembled Cp genome was 159 kb containing a total of 157 genes. Comparative analysis revealed a congruence in genome size, structure, gene content, and gene order with previously published Pterocarpus Cp genomes. Phylogenetic analysis revealed the closest relationship between P. dalbergioides and Pterocarpus santalinus which were grouped together as sister clades with other Asian species. African and Asian species of Pterocarpus were clearly demarcated in the phylogenetic tree. The availability of the Cp genome of P. dalbergioides will support future studies in systematics, species evolution, population structure analysis, and species discrimination. It will facilitate the development of high-resolution DNA barcodes for timber forensics.

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Data availability

The raw paired-end sequence data were deposited in NCBI’s Short Read Archive with the accession number PRJNA763729.

References 

  • Ankenbrand MJ, Pfaff S, Terhoeven N, Qureischi M, Gündel M, Weiß CL, Hackl T, Förster F (2018) chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data. J Open Source Softw 3:464. https://doi.org/10.2110/joss.00464

    Article  Google Scholar 

  • Asaf S, Waqas M, Khan AL, Khan MA, Kang SM, Imran QM, Shahzad R, Bilal S, Yun BW, Lee IJ (2017) The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species. Front Plant Sci 8:304. https://doi.org/10.3389/fpls.2017.00304

    Article  Google Scholar 

  • Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33(16):2583–2585

    Article  CAS  Google Scholar 

  • Bendich AJ (2004) Circular chloroplast chromosomes: the grand illusion. Plant Cell 16:1661–1666. https://doi.org/10.1105/tpc.160771

    Article  CAS  Google Scholar 

  • Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17(1):134. https://doi.org/10.1186/s13059-016-1004-2

    Article  CAS  Google Scholar 

  • Daniell H, Jin S, Zhu XG, Gitzendanner MA, Soltis DE, Soltis PS (2021) Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. Plant Biotechnol J 19(3):430–447. https://doi.org/10.1111/pbi.13556

    Article  CAS  Google Scholar 

  • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772. https://doi.org/10.1038/nmeth.2109

    Article  CAS  Google Scholar 

  • Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45:18. https://doi.org/10.1093/nar/gkw955

    Article  CAS  Google Scholar 

  • Dobrogojski J, Adamiec M, Luciński R (2020) The chloroplast genome: a review. Acta Physiol Plant 42:98. https://doi.org/10.1007/s11738-020-03089-x

    Article  CAS  Google Scholar 

  • Ganeshaiah KN, Sanjappa M, Rao R, Murugan C, Shivaprakash KN (2019) Spatial distribution pattern of taxonomic and phylogenetic diversity of woody flora in Andaman and Nicobar Islands. India for Ecosyst 6:38. https://doi.org/10.1186/s40663-019-0196-9

    Article  Google Scholar 

  • Hohmann N, Wolf EM, Rigault P, Zhou W, Kiefer M, Zhao Y, Fu C-X, Koch MA (2018) Ginkgo biloba’s footprint of dynamic Pleistocene history dates back only 390,000 years ago. BMC Genomics 19(1):299

    Article  Google Scholar 

  • Hong Z, Wu Z, Zhao K, Yang Z, Zhang N, Guo J, Tembrock LR, Xu D (2020) Comparative analyses of five complete chloroplast genomes from the genus Pterocarpus (Fabacaeae). Int J Mol Sci 21(11):3758. https://doi.org/10.3390/ijms21113758

    Article  CAS  Google Scholar 

  • Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol 395:348–384. https://doi.org/10.1016/S0076-6879(05)95020-9

    Article  CAS  Google Scholar 

  • Jansen PCM, Westphal E, Sosef MSM, Soerianegara I, Lemmens RHMJ (1993) Plant resources of South-East Asia 5–1. Timber Trees: Major Commercial Timbers. Bogor, Wageningen, The Netherlands.

  • Jiao L, Yu M, Wiedenhoeft AC, He T, Jiang X, Yin Y (2018) DNA barcode authentication of endangered and precious timber species of Pterocarpus: use of vouchered wood xylarium specimens for development of DNA reference library. Sci Rep 8:1945

    Article  Google Scholar 

  • Jiao L, Lu Y, He T, Li J, Yin Y (2019) A strategy for developing high-resolution DNA barcodes for species discrimination of wood specimens using the complete chloroplast genome of three Pterocarpus species. Planta 250(1):95–104

    Article  CAS  Google Scholar 

  • Jin JJ, Bin YuW, Yang JB, Song Y, dePamphilis CW, Yi T-S, Li D-Z (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21:241. https://doi.org/10.1186/s13059-020-02154-5

    Article  Google Scholar 

  • Katoh K, Rozewicki J, Yamada KD (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 20:1160–1166. https://doi.org/10.1093/bib/bbx108

    Article  CAS  Google Scholar 

  • Köhler M, Reginato M, Souza-Chies TT, Majure LC (2020) Insights into chloroplast genome evolution across Opuntioideae (Cactaceae) reveals robust yet sometimes conflicting phylogenetic topologies. Front Plant Sci 11:729. https://doi.org/10.3389/fpls.2020.00729

    Article  Google Scholar 

  • Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29(22):4633–4642

    Article  CAS  Google Scholar 

  • Li B, Zheng Y (2018) Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae. Sci Rep 8:9285. https://doi.org/10.1038/s41598-018-27453-7

    Article  CAS  Google Scholar 

  • Li W, Liu Y, Yang Y, Xie X, Lu Y, Yang Z, Jin X, Dong W, Suo Z (2018) Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros. BMC Plant Biol 8(1):210

    Article  Google Scholar 

  • Li B, Lin F, Huang P, Guo W, Zheng Y (2020) Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing. Biol Res 53:21. https://doi.org/10.1186/s40659-020-00289-0

    Article  CAS  Google Scholar 

  • Li C, Zheng Y, Huang P (2020) Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling. Sci Rep 10:12188. https://doi.org/10.1038/s41598-020-68092-1

    Article  CAS  Google Scholar 

  • Li S, Chang L, Zhang J (2021) Advancing organelle genome transformation and editing for crop improvement. Plant Commun 2:100–141

    Article  Google Scholar 

  • Magdy M, Ou L, Yu H, Chen R, Zhou Y, Hassan H, Feng B, Taitano N, van der Knaap E, Zou X, Li F, Ouyang B (2019) Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species. Horticult Res 6(1):108

    Article  Google Scholar 

  • McKain, M Wilson (2017) Fast-Plast: rapid de novo assembly and finishing for whole chloroplast genomes. https://github.com/mrmckain/Fast-Plast

  • Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O’Leary MA (2015) A restful API for access to phylogenetic tools via the CIPRES science gateway. Evol Bioinform Online 11:43–48. https://doi.org/10.4137/EBO.S21501

    Article  CAS  Google Scholar 

  • Morris GP, Grabowski PP, Borevitz JO (2011) Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. Mol Ecol 20(23):4938–4952. https://doi.org/10.1111/j.1365-294X.2011.05335.x

    Article  Google Scholar 

  • Mower JP, Vickrey TL (2018) Structural diversity among plastid genomes of land plants. In: Chaw S-M, Jansen RK (eds) Advances in botanical research, vol 85. Academic Press, Cambridge, pp 263–292

    Google Scholar 

  • Nagabhatla N, Roy PS (2006) Modelling the distribution of Pterocarpus dalbergioides (Padauk) at landscape level using a geospatial approach, in Andaman- Bay Islands South Asia. In: Dayawansa, NDK (ed) Geoinformatics for Environmental Conservation and Management: Third National Symposium on Geoinformatics, Sri Lanka, 25 August 2006, Peradeniya, Sri Lanka, 35–43

  • Nagarajan B, Kala N (2010) The reproductive biology of Andaman padauk (Pterocarpus dalbergioides roxb.) In: Ramakrishna, Raghunathan C, Sivaperuman C (eds) Recent Trends in Biodiversity of Andaman and Nicobar Islands, Zoological Survey of India, Kolkata, 231–237

  • Nguyen HQ, Nguyen T, Doan TN, Nguyen T, Phạm MH, Le TL, Sy DT, Chu HH, Chu HM (2021) Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis. Sci Rep 11(1):11731. https://doi.org/10.1038/s41598-021-91071-z

    Article  CAS  Google Scholar 

  • Osuna-Mascaró C, Rubio de Casas R, Perfectti F (2018) Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq. Sci Rep 8:17404. https://doi.org/10.1038/s41598-018-35654-3

    Article  CAS  Google Scholar 

  • Prasad RCP, Reddy CS, Raza SH, Dutt CBS (2008) Population structure, age gradations, and regeneration status of Pterocarpus dalbergioides Roxb., an endemic species of Andaman Islands, India. Pac J Sci Technol 9(2):658–664.

  • Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol 67(5):901.

  • Rambaut A (2018) FigTree version 1.4.4. http://tree.bio.ed.ac.uk/software/figtree.

  • Rao PSN (2000) The andaman red wood tree Pterocarpus dalbergioides Roxb. – an economic timber plant. Bull Bot Surv. India 42(4):149–154

    Google Scholar 

  • Sekhsaria P (2001) Deforestation in Andaman and nicobar: its impact on onge. Econ Pol Wkly 36:3643–3648

    Google Scholar 

  • Senthilkumar S, Ulaganathan K, Ghosh Dasgupta M (2021) Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus. 3 Biotech 11:393

    Article  Google Scholar 

  • Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94(3):275–288. https://doi.org/10.3732/ajb.94.3.275

    Article  CAS  Google Scholar 

  • Shi C, Wang S, Xia EH, JiangJ-J Z-C, Gao L-Z (2016) Full transcription of the chloroplast genome in photosynthetic eukaryotes. Sci Rep 6:30135. https://doi.org/10.1038/srep30135

    Article  CAS  Google Scholar 

  • Skuza L, Filip E, Szućko I (2013) Use of organelle markers to study genetic diversity in soybean. In: Board JE (ed) A comprehensive survey of international soybean research - genetics, physiology, agronomy and nitrogen relationships, IntechOpen. https://doi.org/10.5772/52028

  • Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S (2017) GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45:6–11. https://doi.org/10.1093/nar/gkx391

    Article  CAS  Google Scholar 

  • Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5(2):123–135. https://doi.org/10.1038/nrg1271 (PMID: 14735123)

    Article  CAS  Google Scholar 

  • Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D (2019) Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 47(21):10994–11006. https://doi.org/10.1093/nar/gkz841

    Article  CAS  Google Scholar 

  • Twyford AD, Ness RW (2017) Strategies for complete plastid genome sequencing. Mol Ecol Resour 17(5):858–868. https://doi.org/10.1111/1755-0998.12626

    Article  Google Scholar 

  • Vinga S, Carvalho AM, Francisco AP, Russo LM, Almeida JS (2012) Pattern matching through chaos game representation: bridging numerical and discrete data structures for biological sequence analysis. Algoritm Mol Biol AMB 7(1):10. https://doi.org/10.1186/1748-7188-7-10

    Article  Google Scholar 

  • Wang R, Park SY, Park SW, Puja AM, Kim Y-J (2021) Development of a molecular marker based on chloroplast gene for specific identification of Korean Hibiscus (Hibiscus syriacus ‘Simbaek’). Appl Biol Chem 64:96. https://doi.org/10.1186/s13765-021-00669-4

    Article  CAS  Google Scholar 

  • Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D (2011) The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol 76(3–5):273–297

    Article  CAS  Google Scholar 

  • Xu DH, Abe J, Gai JY, Shimamoto Y (2002) Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean. Theor Appl Genet 105(645):653

    Google Scholar 

  • Xu C, Dong W, Li W, Lu Y, Xie X, Jin X, Shi J, He K, Suo Z (2017) Comparative analysis of six lagerstroemia complete chloroplast genomes. Front Plant Sci 8(15):15

    Google Scholar 

  • Xue S, Shi T, Luo W, Ni X, Iqbal S, Ni Z, Huang X, Yao D, Shen Z, Gao Z (2019) Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina. Hortic Res 6: 89. https://doi.org/10.1038/s41438-019-0171-1

  • Yagi Y, Shiina T (2014) Recent advances in the study of chloroplast gene expression and its evolution. Front Plant Sci 5:61

    Article  Google Scholar 

  • Yang Q, Fu G-F, Wu Z-Q, Li L, Zhao J-L, Li Q-J (2022) Chloroplast genome evolution in four montane Zingiberaceae Taxa in China. Front Plant Sci 12:774482. https://doi.org/10.3389/fpls.2021.774482

    Article  Google Scholar 

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Funding

This study was funded by the National Biodiversity Authority of India, Government of India. The funding support as a research fellowship was provided to SS by the National Biodiversity Authority, Government of India.

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Authors and Affiliations

  1. Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Forest Campus, Pincode-641002, Tamil Nadu, India

    Shanmugavel Senthilkumar & Modhumita Ghosh Dasgupta

  2. Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi P. O, Thrissur, Kerala, 680653, India

    Paremmal Sarath & Suma Arun Dev

Authors
  1. Shanmugavel Senthilkumar
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  2. Paremmal Sarath
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  3. Suma Arun Dev
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  4. Modhumita Ghosh Dasgupta
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Contributions

Shanmugavel Senthilkumar carried out chloroplast genome assembly, annotation, and genome comparison and contributed to writing the manuscript. Paremmal Sarath and Suma Arun Dev carried out the phylogenetic analysis and contributed to writing the manuscript. Modhumita Ghosh Dasgupta conceptualized the study and proofread and finalized the manuscript.

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Correspondence to Modhumita Ghosh Dasgupta.

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Data archiving statement

The raw paired-end sequence data were deposited in NCBI's Short Read Archive with the accession number SRR15910684.

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Communicated by W. Ratnam.

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Senthilkumar, S., Sarath, P., Dev, S.A. et al. Chloroplast genome assembly and phylogenetic analysis of Pterocarpus dalbergioides Roxb., an endemic timber species. Tree Genetics & Genomes 18, 43 (2022). https://doi.org/10.1007/s11295-022-01574-7

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