Tree Genetics & Genomes

, Volume 6, Issue 6, pp 931–939 | Cite as

Phylogenetic relationships of Citrus and its relatives based on rbcL gene sequences

  • Tshering Penjor
  • Toyoaki Anai
  • Yukio Nagano
  • Ryoji Matsumoto
  • Masashi Yamamoto
Original Paper


We sequenced the rbcL genes of 64 accessions from 24 genera of Citrus relatives and analyzed them by neighbor-joining and maximum parsimony methods. Both trees supported Swingle and Reece’s (1967) treatment of the subfamily Aurantioideae as monophyletic. However, the trees did not support Swingle and Reece’s treatment of tribes and subtribes. The subgenera Citrus and Papeda were not clustered clearly. The analysis associated the Fortunella group with mandarin, Poncirus with Citrus ichangensis, Severinia buxifolia with Atalantia ceylanica, Microcitrus with Eremocitrus and Citrus micrantha, and Hesperethusa crenulata with Citropsis. Furthermore, Atalantia species showed polytomy. The classification of Swingle and Reece should be reviewed.


Aurantioideae cpDNA Phylogeny Rutaceae Taxonomy 


  1. Aradhya MK, Potter D, Gao F, Simon CJ (2007) Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective. Tree Genetics & Genomes 3:363–378CrossRefGoogle Scholar
  2. Araújo EF, Queiroz LP, Machado MA (2003) What is Citrus? Taxonomic implications from a study of cp-DNA evolution in the tribe Citreae (Rutaceae subfamily Aurantioideae). Org Divers Evol 3:55–62CrossRefGoogle Scholar
  3. Asadi Abkenar A, Isshiki S, Tashiro Y (2004) Phylogenetic relationships in the “true citrus fruit trees” revealed by PCR-RFLP analysis of cpDNA. Sci Hort 102:233–242CrossRefGoogle Scholar
  4. 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 112:1519–1531CrossRefPubMedGoogle Scholar
  5. Barrett HC, Rhodes AM (1976) A numerical taxonomic study of affinity relationships in cultivated Citrus and its close relatives. Syst Bot 1:105–136CrossRefGoogle Scholar
  6. 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 96:668–685CrossRefGoogle Scholar
  7. Chase MW, Morton CM, Kallunki JA (1999) Phylogenetic relationships of Rutaceae: a cladistic analysis of the subfamilies using evidence from rbcL and atpB sequence variation. Am J Bot 86:1191–1199CrossRefPubMedGoogle Scholar
  8. Cheng Y, Vicente MR, Meng H, Guo W, Tao N, Deng X (2005) A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera. Tree Physiol 25:661–672PubMedGoogle Scholar
  9. Deng Z, La Malfa S, Xie Y, Xiong X, Gentile A (2007) Identification and evolution of chloroplast uni- and trinucleotide sequence repeats in citrus. Sci Hort 111:186–192CrossRefGoogle Scholar
  10. Eck RV, Dayhoff MO (1966) Evolution of the structure of ferredoxin based on living relics of primitive amino acid sequences. Science 152:363–366CrossRefPubMedGoogle Scholar
  11. Fang DQ, Roose ML (1997) Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet 95:408–417CrossRefGoogle Scholar
  12. 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 96:812–822CrossRefGoogle Scholar
  13. Fitch WN (1971) The nonidentity of invariable positions in the cytochromes c of different species. Biochem Genet 5:231–241CrossRefPubMedGoogle Scholar
  14. Gielly L, Taberlet P (1994) The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Mol Biol Evol 11:769–777PubMedGoogle Scholar
  15. Groppo MG, Pirani JR, Salatino MLF, Blanco SR, Kallunki JA (2008) Phylogeny of Rutaceae based on two noncoding regions from cpDNA. Am J Bot 95:985–1005CrossRefGoogle Scholar
  16. Guerra M, dos Santos KGB, e Silva AEB, Ehrendorfer F (2000) Heterochromatin banding patterns in Rutaceae–Aurantioideae. A case of parallel chromosomal evolution. Am J Bot 87:735–747CrossRefPubMedGoogle Scholar
  17. Hasebe M, Omori T, Kanazawa M, Sano T, Kato M, Iwatsuki K (1994) rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns. Proc Natl Acad Sci USA 91:5730–5734CrossRefPubMedGoogle Scholar
  18. 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 93:1327–1334CrossRefGoogle Scholar
  19. Jung YH, Kwon HM, Kang SH, Kang JH, Kim SC (2005) Investigation of the phylogenetic relationships within the genus Citrus (Rutaceae) and related species in Korea using plastid trnL-trnF sequences. Sci Hort 104:179–188CrossRefGoogle Scholar
  20. Kellogg E, Juliano ND (1997) The structure and function of RuBisCo and their implications for systematic studies. Am J Bot 84:413–428CrossRefGoogle Scholar
  21. Mabberley DJ (1998) Australian Citreae with notes on other Aurantioideae (Rutaceae). Telopea 7:333–344Google Scholar
  22. Mabberley DJ (2004) Citrus (Rutaceae): a review of recent advances in etymology, systematics and medical applications. Blumea 49:481–498Google Scholar
  23. Moore WS (1995) Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49:718–726CrossRefGoogle Scholar
  24. Morton CM, Grant M, Blackmore S (2003) Phylogenetic relationships of the Aurantioideae inferred from chloroplast DNA sequence data. Am J Bot 90:1463–1469CrossRefGoogle Scholar
  25. Murray GC, Thompson WF (1980) Rapid isolation of high molecular weight DNA. Nucleic Acid Res 8:4321–4325CrossRefPubMedGoogle Scholar
  26. Nicolosi E, Deng ZN, Gentile A, La Malfa Continella SG, Tribulato E (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100:1155–1166CrossRefGoogle Scholar
  27. Pang XM, Hu CG, Deng XX (2007) Phylogenic relationships within Citrus and its related genera as inferred from AFLP markers. Genet Res Crop Evol 54:429–436CrossRefGoogle Scholar
  28. Platt AR, Woodhall RW, George AL (2007) Improved DNA sequencing quality and efficiency using an optimized fast cycle sequencing protocol. Biotechniques 43:58–62CrossRefPubMedGoogle Scholar
  29. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  30. Samuel RF, Ehrendorfer MW, Chase GH (2001) Phylogenetic analyses of Aurantioideae (Rutaceae) based on non-coding plastid DNA sequences and phytochemical features. Plant Biol 3:77–87CrossRefGoogle Scholar
  31. Silva MFDGF, Gottlieb OR, Ehrendorfer F (1988) Chemosystematics of Rutaceae: suggestions for a more natural taxonomy and evolutionary interpretation of the family. Pl Syst Evol 161:97–124CrossRefGoogle Scholar
  32. Stace HM, Armstrong JA, James SH (1993) Cytoevolutionary patterns in Rutaceae. Pl Syst Evol 187:1–28CrossRefGoogle Scholar
  33. Suyama Y, Yoshimaru H, Tsumura Y (2000) Molecular phylogenetic position of Japanese Abies (Pinaceae) based on chloroplast sequences. Mol Phylogenet Evol 16:271–277CrossRefPubMedGoogle Scholar
  34. Swingle WT, Reece PC (1967) The botany of Citrus and its wild relatives. In: Reuther W, Webber HJ, Batchelor LD (eds) The citrus industry, vol 1. University of California, Berkeley, pp 190–430Google Scholar
  35. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  36. Tanaka T (1977) Fundamental discussion of citrus classification. Studia Citrologia 14:1–5Google Scholar
  37. Yamamoto M, Kobayashi S (1996) Polymorphism of chloroplast DNA in citrus. J Jpn Soc Hort Sci 65:291–296CrossRefGoogle Scholar
  38. Yamamoto M, Kobayashi S, Nakamura Y, Yamada Y (1993) Phylogenic relationships of citrus revealed by RFLP analysis of mitochondrial and chloroplast DNA. Jpn J Breed 43:355–365Google Scholar
  39. Yamamoto M, Asadi Abkenar A, Matsumoto R, Nesumi H, Yoshida T, Kuniga T, Kubo T, Tominaga S (2007) CMA banding patterns of chromosomes in major Citrus species. J Jpn Soc Hort Sci 76:36–40CrossRefGoogle Scholar
  40. Yamamoto M, Asadi Abkenar A, Matsumoto R, Kubo T, Tominaga S (2008) CMA staining analysis of chromosomes in several species of Aurantioideae. Genet Resour Crop Evol 55:1167–1173CrossRefGoogle Scholar
  41. Zhang D-X, Hartley TG, Mabberley DJ (2008) Rutaceae.

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Tshering Penjor
    • 1
    • 2
  • Toyoaki Anai
    • 1
  • Yukio Nagano
    • 3
  • Ryoji Matsumoto
    • 1
  • Masashi Yamamoto
    • 4
  1. 1.Faculty of AgricultureSaga UniversitySagaJapan
  2. 2.Renewable Natural Resources Research Centre WengkharMongarBhutan
  3. 3.Analytical Research Center for Experimental SciencesSaga UniversitySagaJapan
  4. 4.Faculty of AgricultureKagoshima UniversityKagoshimaJapan

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