Ribosomal ITS sequences and plant phylogenetic inference - PubMed (original) (raw)
Review
Ribosomal ITS sequences and plant phylogenetic inference
I Alvarez et al. Mol Phylogenet Evol. 2003 Dec.
Abstract
One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. The prominence of this source of nuclear DNA sequence data is underscored by a survey of phylogenetic publications involving comparisons at the genus level or below, which reveals that of 244 papers published over the last five years, 66% included ITS sequence data. Perhaps even more striking is the fact that 34% of all published phylogenetic hypothesis have been based exclusively on ITS sequences. Notwithstanding the many important contributions of ITS sequence data to phylogenetic understanding and knowledge of genome relationships, a number of molecular genetic processes impact ITS sequences in ways that may mislead phylogenetic inference. These molecular genetic processes are reviewed here, drawing attention to both underlying mechanism and phylogenetic implications. Among the most prevalent complications for phylogenetic inference is the existence in many plant genomes of extensive sequence variation, arising from ancient or recent array duplication events, genomic harboring of pseudogenes in various states of decay, and/or incomplete intra- or inter-array homogenization. These phenomena separately and collectively create a network of paralogous sequence relationships potentially confounding accurate phylogenetic reconstruction. Homoplasy is shown to be higher in ITS than in other DNA sequence data sets, most likely because of orthology/paralogy conflation, compensatory base changes, problems in alignment due to indel accumulation, sequencing errors, or some combination of these phenomena. Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis. It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.
Similar articles
- Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: a case study from Naucleeae (Rubiaceae).
Razafimandimbison SG, Kellogg EA, Bremer B. Razafimandimbison SG, et al. Syst Biol. 2004 Apr;53(2):177-92. doi: 10.1080/10635150490423278. Syst Biol. 2004. PMID: 15205048 - Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus.
Hartmann S, Nason JD, Bhattacharya D. Hartmann S, et al. J Mol Evol. 2001 Aug;53(2):124-34. doi: 10.1007/s002390010200. J Mol Evol. 2001. PMID: 11479683 - Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants.
Nieto Feliner G, Rosselló JA. Nieto Feliner G, et al. Mol Phylogenet Evol. 2007 Aug;44(2):911-9. doi: 10.1016/j.ympev.2007.01.013. Epub 2007 Feb 15. Mol Phylogenet Evol. 2007. PMID: 17383902 Review. - Utility of low-copy nuclear gene sequences in plant phylogenetics.
Sang T. Sang T. Crit Rev Biochem Mol Biol. 2002;37(3):121-47. doi: 10.1080/10409230290771474. Crit Rev Biochem Mol Biol. 2002. PMID: 12139440 Review.
Cited by
- Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept.
Wolf M, Chen S, Song J, Ankenbrand M, Müller T. Wolf M, et al. PLoS One. 2013 Jun 24;8(6):e66726. doi: 10.1371/journal.pone.0066726. Print 2013. PLoS One. 2013. PMID: 23826120 Free PMC article. - Lack of ITS sequence homogenization in Erysimum species (Brassicaceae) with different ploidy levels.
Osuna-Mascaró C, de Casas RR, Berbel M, Gómez JM, Perfectti F. Osuna-Mascaró C, et al. Sci Rep. 2022 Oct 7;12(1):16907. doi: 10.1038/s41598-022-20194-8. Sci Rep. 2022. PMID: 36207443 Free PMC article. - Identification and validation of Aeluropus littoralis reference genes for Quantitative Real-Time PCR Normalization.
Hashemi SH, Nematzadeh G, Ahmadian G, Yamchi A, Kuhlmann M. Hashemi SH, et al. J Biol Res (Thessalon). 2016 Jul 19;23:18. doi: 10.1186/s40709-016-0053-8. eCollection 2016 Dec. J Biol Res (Thessalon). 2016. PMID: 27437194 Free PMC article. - Application of DNA barcoding for ensuring food safety and quality.
Dawan J, Ahn J. Dawan J, et al. Food Sci Biotechnol. 2022 Jul 27;31(11):1355-1364. doi: 10.1007/s10068-022-01143-7. eCollection 2022 Oct. Food Sci Biotechnol. 2022. PMID: 36060568 Free PMC article. Review. - Molecular phylogeny of Anaphalis (Asteraceae, Gnaphalieae) with biogeographic implications in the Northern Hemisphere.
Nie ZL, Funk V, Sun H, Deng T, Meng Y, Wen J. Nie ZL, et al. J Plant Res. 2013 Jan;126(1):17-32. doi: 10.1007/s10265-012-0506-6. Epub 2012 Jul 10. J Plant Res. 2013. PMID: 22776917