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Molecular Phylogeny of Citrus species in the Eastern Himalayan Region of Northeast India Based on Chloroplast and Nuclear DNA Sequence Data

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Molecular Genetics and Genomics Tools in Biodiversity Conservation

Abstract

Northeast India is home to natural and domestic populations of many Citrus L. (Rutaceae) species, suggesting this area is a centre of origin for the genus Citrus, which includes widely cultivated commercial fruit plants such as orange, lemon, and lime. To gain insights into the evolutionary history of Citrus species in the region, we reconstructed the phylogeny of 24 species of Citrus using nucleotide sequences of three chloroplast (trnL-trnF, trnS-trnG, and rps16) and one nuclear (ITS2) genomic region. Phylogenetic relationships inferred through maximum parsimony, maximum likelihood, and Bayesian analyses grouped the 24 morphologically distinct Citrus species into five phylogenetically defined groups. C. indica (Indian wild orange) and C. medica (Citron), both native to eastern Himalayan region of northeast India, clustered together and formed a basal clade, suggesting northeast India may be the ancestral region of Citrus. C. assamensis was a sister taxon to the remaining three Citrus clades, and we found evidence that morphologically based Citrus groups – including acid, papeda, and pomelo – were polyphyletic. Our results provide genetic clarification for Citrus evolution, a group that had a previously unclear in its phylogenetic history.

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References

  • Asadi Abkenar A, Matsumoto R, Yamamoto M (2019) Relatedness among Mandarins (Citrus spp.) and their close relatives revealed by cpDNA polymorphism summary. Bull Fac Agr Saga Univ 104:1–11

    CAS  Google Scholar 

  • Asadi-Abkenar A, Isshiki S, Tashiro Y (2004) Phylogenetic relationships in the ‘true citrus fruit trees’ revealed by PCR-RFLP analysis of cpDNA. Sci Hortic 102:233–242

    Article  Google Scholar 

  • Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing genetic diversity and population structure in a Citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531

    Article  CAS  PubMed  Google Scholar 

  • Barrett HC, Rhodes AM (1976) A numerical taxonomic study of affinity relationships in cultivated Citrus and its close relatives. Syst Bot 1:105–136

    Article  Google Scholar 

  • Bayer RJ, Mabberley DJ, Morton C, Miller CH, Sharma IK, Pfeil BE, Rich S, Hitchcock R, Sykes S (2009) A molecular phylogeny of the orange subfamily (Rutaceae: Aurantioideae) using nine cpDNA sequences. Am J Bot 96:668–685

    Article  CAS  PubMed  Google Scholar 

  • Bhattacharya SC, Dutta S (1956) Classifications of Citrus fruits of Assam. ICAR Sci Mono 20:1–110

    Google Scholar 

  • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dayanandan S, Bawa KS, Kesseli RV (1997) Conservation of microsatellite among tropical trees (Leguminosae). Am J Bot 84:1658–1663

    Article  CAS  PubMed  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Drummond A, Ashton B, Cheung M, Heled J, Kearse M, Moir R, Stones-Havas S, Thierer T, Wilson A (2009) Geneious v4.7. http:www.geneious.com [accessed 25 July 2016]

  • Farris JS, Kallersjo M, Kluge AG, Bult C (1994) Testing significance of congruence. Cladistics 10:315–320

    Article  Google Scholar 

  • Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 96:812–822

    Article  CAS  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Lor A, Curk F, Snoussi-Trifa H, Morill R, Ancillo G, Luro F, Navarro L, Ollitrault P (2013) A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true Citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species. Ann Bot 111:1–19

    Article  CAS  PubMed  Google Scholar 

  • Ghada B, Amel O, Aymen M, Aymen A, Amel SH (2019) Phylogenetic patterns and molecular evolution among ‘true citrus fruit trees’ group (Rutaceae family and Aurantioideae subfamily). Sci Hort 253(27):87–98

    Article  CAS  Google Scholar 

  • Hamilton MB (1999) Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol Ecol 8:513–525

    Google Scholar 

  • Herrero R, Asins MJ, Pina JA, Carbonell EA, Navarro L (1996) Genetic diversity in the orange subfamily Aurantioideae. II. Genetic relationships among genera and species. Theor Appl Genet 93:1327–1334

    Article  CAS  PubMed  Google Scholar 

  • Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66:411–453

    Article  CAS  PubMed  Google Scholar 

  • Hooker JD (1875) Rutaceae. The Flora of British India, volume 1. Reeve and Company, London, pp 484–517

    Google Scholar 

  • Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinf 17:754–755

    Article  CAS  Google Scholar 

  • Hynniewta M, Malik SK, Rao SR (2014) Genetic diversity and phylogenetic analysis of citrus (L) from north-East India as revealed by meiosis, and molecular analysis of internal transcribed spacer region of rDNA. Meta Gene 2:237–251

    Article  PubMed  PubMed Central  Google Scholar 

  • Jena SN, Kumar S, Nair KN (2009) Molecular phylogeny in Indian Citrus L. (Rutaceae) inferred through PCR-RFLP and trnL-trnF sequence data of chloroplast DNA. Sci Hortic 199:403–416

    Article  Google Scholar 

  • Kumar K, Nair KN (2013) Genetic variation and phylogenetic relationships among Indian Citrus taxa revealed by DAMD-PCR markers. Genet Resour Crop Evol 60:777–1800

    Article  Google Scholar 

  • Kumar S, Nair KN, Jena SN (2013) Molecular differentiation in Indian citrus L. (Rutaceae) inferred from nrDNA- ITS sequence analysis. Genet Resour Crop Evol 60:59–75

    Article  CAS  Google Scholar 

  • Langgut D (2017) The Citrus route revealed: from Southeast Asia into the Mediterranean. Sci Hortic 52:814–822

    Google Scholar 

  • Linnaeus C (1753) Species Plantarum. Stockholm

    Google Scholar 

  • Lushington AW (1910) The genus citrus. Ind Forester 36:323–353

    Google Scholar 

  • Mabberley DJ (2004) Citrus (Rutaceae): a review of recent advances in etymology, systematics and medical applications. Blumea 49:481–498

    Article  Google Scholar 

  • Maddi T, Perez-Roman E, Maiza-Benabdesselam F et al (2018) New citrus chloroplast haplotypes revealed by molecular markers using Algerian and Spanish accessions. Genet Resour Crop Evol 65(8):2199–2214

    Article  Google Scholar 

  • Maddison DR, Maddison WP (2001) MacClade 4. Sinauer, Sunderland, MA

    Google Scholar 

  • Malik SK, Kumar S, Singh IP, Dhariwal OP, Chaudhury R (2013) Socio-economic importance, domestication trends and in situ conservation of wild citrus species of Northeast India. Genet Resour Crop Evol 60(5):1655–1671

    Article  Google Scholar 

  • Nair KN, Nayar MP (1997) Rutaceae. Flora of India. In: Hajra PK, Nair VJ, Daniel P (eds) Botanical survey of India, volume IV, Calcutta, India, pp 229–407

    Google Scholar 

  • Nicolosi E, Deng ZN, Genetile A, La Malfa S, Ciontinella G, Tribulata E (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100:1155–1166

    Article  CAS  Google Scholar 

  • Ollitrault P, Curk F, Krueger R (2020) Citrus taxonomy. In: Talon M, Caruso M, Gmitter GF (eds) The genus citrus. Woodhead Publishing, Elsivier, UK, pp 57–81

    Chapter  Google Scholar 

  • Oxelman B, Liden M, Berglund D (1997) Chloroplast rpsl6 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Syst Evol 206:393–410

    Article  Google Scholar 

  • Pang XM, Hu CG, Deng XX (2007) Phylogenetic relationships within citrus and its related genera as inferred from AFLP markers. Genet Resour Crop Evol 54:429–436

    Article  CAS  Google Scholar 

  • Pessina D, Gentili R, Barcaccia G, Nicole BS, Rossi G, Barbesti S, Sgorbatia S (2011) DNA content, morphometric and molecular marker analyses of C.limonimedica, C. limon and C. medica for the determination of their variability and genetic relationships within the genus citrus. Sci Hortic 129:663–673

    Article  CAS  Google Scholar 

  • Pridgeon MA, Solano R, Chase MW (2001) Phylogenetic relationships in Pleurothallidinae (Orchidaceae): combined evidence from nuclear and plastid DNA sequences. Am J Bot 88(12):2286–2308

    Article  CAS  PubMed  Google Scholar 

  • Richardson JE, Fay MF, Cronk QCB, Bowman D, Chase MW (2000) A phylogenetic analysis of Rhamnaceae using RBCL and TRNL-F plastid DNA sequences. Am J Bot 87(9):1309–1324

    Article  CAS  PubMed  Google Scholar 

  • Sagawa CHD, Cristofani-Yaly M, Novelli VM, Bastianel M, Machado MA (2018) Assessing genetic diversity of citrus by DArTseq™ genotyping. Plant Biosyst 152(4):593–598

    Article  Google Scholar 

  • Scora RW (1975) On the history and origin of citrus. Bull Torr Bot Club 102:369–375

    Article  Google Scholar 

  • Shahsavar AR, Izadpanah K, Tafazoli E, Tabatabaei BES (2007) Characterization of citrus germplasm including unknown variants by inter-simple sequence repeat (ISSR) markers. Sci Hortic 112:310–314

    Article  CAS  Google Scholar 

  • Silvestro D, Michalak I (2012) RAxMLGUI: a graphical front-end for RAxML. Org Divers Evol 12:335–337

    Article  Google Scholar 

  • Singh IP, Singh S (2003) Exploration, collection and mapping of citrus genetic diversity in India. Technical Bulletin No. 7, National Research Centre for Citrus, Nagpur, India

    Google Scholar 

  • Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690

    Article  CAS  PubMed  Google Scholar 

  • Swingle WT (1943) The botany of Citrus and its wild relatives. In: Webber HJ, Batchelor DL (eds) The citrus industry, vol 1. University of California, Berkeley, pp 128–474

    Google Scholar 

  • Swingle WT, Reece PC (1967) The botany of citrus and its wild relatives. In: Reuther W, Batchelor LD, Webber HJ (eds) The citrus industry. University of California Press, Berkeley, pp 190–340

    Google Scholar 

  • Swofford DL (2001) PAUP*: phylogenetic analysis using parsimony. Version 4.0b8 for Macintosh. Sinauer, Sunderland, MA

    Google Scholar 

  • Talon M, Wu GA, Gmitter GF, Rokhsar SD (2020) The origin of citrus. In: Talon M, Caruso M, Gmitter GF (eds) The genus citrus. Woodhead Publishing, Elsivier, UK, pp 9–31

    Chapter  Google Scholar 

  • Tanaka T (1954) Species problem in citrus. Japanese Society for promotion of Science, Ueno

    Google Scholar 

  • Tanaka T (1958) The origin and dispersal of citrus fruits having their centre of origin in India. Indian J Horticult 15:101–115

    Google Scholar 

  • Tanaka T (1969) Taxonomic problem of Citrus fruits in the Orient. Bull.Univ. Osaka Prefecture, Series B 21:133–138

    Google Scholar 

  • Tanaka T (1977) Fundamental discussion of citrus classification. Studia Citrologica 14:1–6

    Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang X, Yuantao Xu Y, Zhang S et al (2017) Genomic analyses of primitive, wild and cultivated Citrus provide insights into asexual reproduction. Nat Genet 49:765–772

    Article  CAS  PubMed  Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand DJ, Sninsky J, White T (eds) PCR protocols: a guide to methods and applications. Academic Press, Orlando, Florida, pp 315–322

    Google Scholar 

  • Wu GA, Javier TJ, Ibanez V et al (2018) Genomics of the origin and evolution of citrus. Nature 554:311–316

    Article  CAS  PubMed  Google Scholar 

  • Yu F, Bi C, Wang X, Xin Qian X, Ye N (2018) The complete mitochondrial genome of Citrus sinensis. Mitochondrial DNA Part B 3(2):592–593

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhen-Hua L, Zhi-Qin Z, Rang-Jin X (2011) Molecular phylogeny of the “true citrus fruit trees” group (Aurantioideae, Rutaceae) as inferred from chloroplast DNA sequence. Agric Sci China 10(1):49–57

    Article  Google Scholar 

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Acknowledgments

We thank the Natural Sciences and Engineering Research Council of Canada and School of Graduate Studies, Faculty of Arts and Science, Concordia University for the financial support. Authors thank home gardeners of NEI for providing Citrus species leaf materials. We are also thankful to the Director and staff members of Botanical Survey of India, Northeast Circle, Shillong, and the Principal Scientist, Krishi Vigyan Kendra, Citrus Research Station, Tinsukia, Assam, in identifying species and providing leaf materials.

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Barbhuiya, A.R., Khan, M.L., Dayanandan, S. (2022). Molecular Phylogeny of Citrus species in the Eastern Himalayan Region of Northeast India Based on Chloroplast and Nuclear DNA Sequence Data. In: Kumar, A., Choudhury, B., Dayanandan, S., Khan, M.L. (eds) Molecular Genetics and Genomics Tools in Biodiversity Conservation. Springer, Singapore. https://doi.org/10.1007/978-981-16-6005-4_9

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