Skip to main content
SpringerLink
Log in

Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences

  • Regular Paper
  • Published:
Journal of Plant Research Aims and scope Submit manuscript

Abstract

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Alvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417–434

    Article  PubMed  CAS  Google Scholar 

  • Bentham G (1880) Laurineae. In: Bentham G, Hooker JD (eds) Genera plantarum, vol 3. Reeve, London, pp 146–168

    Google Scholar 

  • Blattner F (1999) Direct amplification of the entire ITS region from poorly preserved plant material using recombinant PCR. Biotechniques 29:1180–1186

    Google Scholar 

  • Bracho MA, Moya A, Barrio E (1998) Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol 79:2921–2928

    PubMed  CAS  Google Scholar 

  • Chanderbali AS, van der Werff H, Renner SS (2001) Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes. Ann Mo Bot Gard 88:104–134

    Article  Google Scholar 

  • Darlu P, Lecointre G (2002) When does the congruence length different test fail? Mol Biol Evol 19:432–437

    PubMed  CAS  Google Scholar 

  • Denton AL, McConaughy BL, Hall BD (1998) Usefulness of RNA polymerase II coding sequences for estimation of green plant phylogeny. Mol Biol Evol 15:1082–1085

    PubMed  CAS  Google Scholar 

  • Farris JS, Kallersjo M, Kluge AG, Bult C (1994) Testing significance of incongruence. Cladistics 10:315–319

    Article  Google Scholar 

  • Felsentein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Fijridiyanto IA, Murakami N (2009) Molecular systematics of Malesian Litsea Lam. and putative related genera (Lauraceae). Acta Phytotax Geobot (in press)

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acid Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hutchinson J (1964) The genera of flowering plants, vol 1. Clarendon, Oxford

    Google Scholar 

  • Hyland BPM (1989) A revision of Lauraceae in Australia (excluding Cassytha). Aust Syst Bot 2:135–367

    Article  Google Scholar 

  • Johnson LA, Soltis DE (1995) Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences. Ann Mo Bot Gard 82:149–175

    Article  Google Scholar 

  • Kawahara T, Murakami N, Setoguchi H, Tsumura Y (1995) Procedure of plant DNA extraction for phylogenetic analysis (in Japanese with English abstract). Proc Jpn Soc Plant Taxon 11:13–32

    Google Scholar 

  • Kelchner SA (2000) The evolution of noncoding chloroplast DNA and its application in plant systematics. Ann Mo Bot Gard 87:482–498

    Article  Google Scholar 

  • Kostermans AJGH (1957) Lauraceae. Reinwardtia 4:193–256

    Google Scholar 

  • Li HW (1995) The origin and evolution of Litsea genera group (Laureae) in Lauraceae (in Chinese with English abstract). Acta Bot Yunnan 17:251–254

    CAS  Google Scholar 

  • Li J, Christophel DC (2000) Systematic relationships within Litsea complex (Lauraceae): a cladistic analysis based on morphological and leaf cuticle data. Aust Syst Bot 13:1–13

    Article  Google Scholar 

  • Li HW, Li J (1991) Notes on the taxonomy and distribution of the genus Caryodaphnopsis of Lauraceae and to discuss the characteristics of its area-type (in Chinese with English abstract). Acta Bot Yunnan 13:1–13

    Google Scholar 

  • Li HW, Pai PY, Lee SK, Wei FN, Wei YT, Yang YC, Huang PH, Tsui HP, Shia ZD, Li JL (1982) Lauraceae (in Chinese). In: Li H-W (ed) Flora of Republicae Popularis Sinicae, vol 31. Science, Beijing, pp 1–463

    Google Scholar 

  • Li J, Christophel DC, Conran JG, Li H-W (2004) Phylogenetic relationships within the ‘core’ Laureae (Litsea complex, Lauraceae) inferred from sequences of the chloroplast gene matK and nuclear ribosomal DNA ITS regions. Plant Syst Evol 246:19–34

    Article  CAS  Google Scholar 

  • Li Z-M, Li J, Li X-W (2006) Polyphyly of the genus Actinodaphne (Lauraceae) inferred from the analyses of nrDNA ITS and ETS sequences. Acta Phytotaxon Sin 44:272–285

    Article  Google Scholar 

  • Li L, Li J, Conran JG, Li X-W (2007) Phylogeny of Neolitsea (Lauraceae) inferred from Bayesian analysis of nrDNA ITS and ETS sequences. Plant Syst Evol 269:203–221

    Article  CAS  Google Scholar 

  • Loo AH, Dransfield J, Chase MW, Baker WJ (2006) Low-copy nuclear DNA, phylogeny and the evolution of dichogamy in the betel nut palms and their relatives (Arecinae; Arecaceae). Mol Phylogenet Evol 39:598–618

    Article  PubMed  CAS  Google Scholar 

  • Luo J, Yoshikawa N, Hodson MC, Hall BD (2007) Duplication and paralog sorting of RPB2 and RPB1 genes in core eudicots. Mol Phylogenet Evol 44:850–862

    Article  PubMed  CAS  Google Scholar 

  • Mickevich MF, Farris JS (1981) The implications of congruence in Menidia. Syst Zool 30:351–370

    Article  Google Scholar 

  • Mort ME, Crawford DJ (2004) The continuing search: low-copy nuclear sequences for lower-level plant molecular phylogenetic studies. Taxon 53:257–261

    Article  Google Scholar 

  • Nylander JAA (2004) MrModeltest2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. Uppsala, Sweden. Available at: http://www.abc.se/~nylander/

  • Olmstead RG, Sweere JA (1994) Combining data in phylogenetic systematics: an empirical approach using three molecular data sets in the Solanaceae. Syst Biol 43:467–481

    Article  Google Scholar 

  • Ooi K, Endo Y, Yokoyama J, Murakami N (1995) Useful primer designs to amplify DNA fragments of the plastid gene matK from angiosperm plants. J Jpn Bot 70:328–331

    Google Scholar 

  • Oxelman B, Bremer B (2000) Discovery of paralogous nuclear gene sequences coding for the second-largest subunit of RNA polymerase II (RPB2) and their phylogenetic utility in Gentianales of the Asterids. Mol Biol Evol 17:1131–1145

    PubMed  CAS  Google Scholar 

  • Oxelman B, Yoshikawa N, McConaughy BL, Luo J, Denton AL, Hall BD (2004) RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids. Mol Phylogenet Evol 32:462–479

    Article  PubMed  CAS  Google Scholar 

  • Pax F (1891) Lauraceae. In: Engler A, Prantl K (eds) Die naturelichen Pflanzenfamilien Bd. III, 2. Engelmann, Leipzig, pp 106–126

    Google Scholar 

  • Pfeil BE, Brubaker CL, Craven LA, Crisp MD (2004) Paralogy and orthology in Malvaceae rpb2 gene family: investigation ofgene duplication in Hibiscus. Mol Biol Evol 21:1428–1437

    Article  PubMed  CAS  Google Scholar 

  • Popp M, Oxelman B (2001) Inferring the history of the polyploidy Silene aegaea (Caryophyllaceae) using plastid and homoeologous nuclear DNA sequences. Mol Phylogenet Evol 20:474–481

    Article  PubMed  CAS  Google Scholar 

  • Rohwer JG (1993) Lauraceae. In: Kubitzki K, Rohwer JG, Bittrich V (eds) The families and genera of vascular plants, vol 2. Springer, Berlin, pp 366–391

    Google Scholar 

  • Rohwer JG (2000) Toward a phylogenetic classification of the Lauraceae: evidence from matK sequences. Syst Bot 25:60–71

    Article  Google Scholar 

  • Rohwer JG, Richer HG, van der Werff H (1991) Two new genera of neotropical Lauraceae and critical remarks on the generic delimitation. Ann Mo Bot Gard 78:388–400

    Article  Google Scholar 

  • Roncal J, Francisco-Ortega J, Asmussen CB, Lewis CE (2005) Molecular phylogenetics of tribe Geonomeae (Arecaceae) using nuclear DNA sequences of phosphoribulokinase and RNA polymerase II. Syst Bot 30:275–283

    Article  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  PubMed  CAS  Google Scholar 

  • Sang T (2002) Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit Rev Biochem Mol 37:121–147

    Article  CAS  Google Scholar 

  • Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in recently diverged plant group. Am J Bot 85:1301–1315

    Article  CAS  Google Scholar 

  • Small RL, Cronn RC, Wendel JF (2004) Use of nuclear genes for phylogeny reconstruction in plants. Aust Syst Bot 17:145–170

    Article  CAS  Google Scholar 

  • Sun G, Daley T, Ni Y (2007) Molecular evolution and genome divergence at RPB2 gene of the St and H genome in Elmus species. Plant Mol Biol 64:645–665

    Article  PubMed  CAS  Google Scholar 

  • Swofford DL (2002) PAUP* Phylogenetic analysis using parsimony. Sinauer, Sunderland, MA

    Google Scholar 

  • Thomas MM, Garwood NC, Baker WJ, Henderson SA, Russell SJ, Hodel DR, Bateman RM (2006) Molecular phylogeny of the palm genus Chamaedorea, based on the low-copy nuclear genes PRK and RPB2. Mol Phylogenet Evol 38:398–415

    Article  PubMed  CAS  Google Scholar 

  • Tsui HP (1987) A study on the system of Lindera (in Chinese with English abstract). Acta Phytotaxon Sinica 25:161–171

    Google Scholar 

  • van der Werff H (2001) An annotated key to the genera of Lauraceae in the flora Malesiana region. Blumea 46:125–140

    Google Scholar 

  • van der Werff H, Richter HG (1996) Toward an improved classification of Lauraceae. Ann Mo Bot Gard 83:409–418

    Article  Google Scholar 

  • White TJ, Bruns TD, Lee SB, Taylor JW (1990) Amplification and direct sequencing of ribosomal RNA genes and the internal transcribed spacer in fungi. In: Inni MA, Gelfand GH, Sninsky JJ, White TJ (eds) PCR-protocols and applications—a laboratory manual. Academic, Orlando, pp 315–322

    Google Scholar 

  • Woychik NA, Young RA (1990) RNA polymerase II: subunit structure and function. Trends Biochem Sci 15:347–350

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We would like to thank Dr. Irawati, Director of Bogor Botanic Garden; Mr. Holif Imanuddin, Director of Cibodas Botanic Garden; and Prof. Jin Murata, Director of Koishikawa Botanical Garden, Graduate School of Science, University of Tokyo, for allowing us to use materials from their plant collections. We would also like to thank Ms. Lucy Chong, Sarawak Forest Research Center, for permitting us to conduct fieldwork in Lambir National Park as well as to use the Sarawak Herbarium facilities. We would like to express our sincere thanks to the staff of Lambir National Park and the Sarawak Herbarium for their hospitality. We greatly appreciate the assistance of Dr. Shoko Sakai, Center for Ecological Research, Kyoto University and the late Dr. Kuniyasu Momose, Faculty of Agriculture, Ehime University, for accompanying us during our fieldwork in Malaysia. We would like to acknowledge Prof. Hiroshi Tobe, Dr. Kyoko Aoki, Dr. Hidetsugu Miwa, Dr. Akihiro Seo, Dr. Wataru Shinohara, Dr. Hirotoshi Sato and Mr. Keigo Mori for their generous support and technical assistance, and Mr. Takaya Iwasaki for providing plant materials from Japan.

Author information

Authors and Affiliations

  1. Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-850, Japan

    Izu A. Fijridiyanto

  2. Center for Plant Conservation Bogor Botanical Gardens, Indonesian Institute of Sciences, Jl. Ir. H. Juanda 13, Bogor, West Java, 16003, Indonesia

    Izu A. Fijridiyanto

  3. Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan

    Noriaki Murakami

Authors
  1. Izu A. Fijridiyanto
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Noriaki Murakami
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Noriaki Murakami.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fijridiyanto, I.A., Murakami, N. Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences. J Plant Res 122, 283–298 (2009). https://doi.org/10.1007/s10265-009-0218-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10265-009-0218-8

Keywords

Search

Navigation