ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae.

Leslie R Goertzen; Jamie J Cannone; Robin R Gutell; Robert K Jansen

doi:10.1016/s1055-7903(03)00094-0

Home/Archive/PubMed

PubMed · 13678678

ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae.

Leslie R Goertzen·Jamie J Cannone·Robin R Gutell·Robert K Jansen

View original source ↗Export metadata ↓

Abstract

An RNA secondary structure model is presented for the nuclear ribosomal internal transcribed spacers (ITS) based on comparative analysis of 340 sequences from the angiosperm family Asteraceae. The model based on covariation analysis agrees with structural features proposed in previous studies using mainly thermodynamic criteria and provides evidence for additional structural motifs within ITS1 and ITS2. The minimum structure model suggests that at least 20% of ITS1 and 38% of ITS2 nucleotide positions are involved in base pairing to form helices. The sequence alignment enabled by conserved structural features provides a framework for broadscale molecular evolutionary studies and the first family-level phylogeny of the Asteraceae based on nuclear DNA data. The phylogeny based on ITS sequence data is very well resolved and shows considerable congruence with relationships among major lineages of the family suggested by chloroplast DNA studies, including a monophyletic subfamily Asteroideae and a paraphyletic subfamily Cichorioideae. Combined analyses of ndhF and ITS sequences provide additional resolution and support for relationships in the family.

Explore related subjects

Asteraceae Base Sequence Cell Nucleus DNA DNA, Ribosomal DNA, Ribosomal Spacer Genes, Plant Molecular Sequence Data NADH Dehydrogenase Nucleic Acid Conformation Phylogeny Plant Proteins Sequence Homology, Nucleic Acid Thermodynamics Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Leslie R Goertzen, Jamie J Cannone, Robin R Gutell, Robert K Jansen. 2003. ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae.. https://doi.org/10.1016/s1055-7903(03)00094-0

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Performance Profiles of Short DNA Barcode Segments for Family Level Detection of Asteraceae Within Asterales.

Short DNA barcodes may facilitate sequence recovery from degraded material, but their ability to retain target-family identity while excluding related taxa varies among genomic regions. We computationally evaluated 16 nuclear, plastid, and mitochondrial marker regions from 11 Asterales families using 279,956 NCBI locus-record matches and an accession-disjoint discovery/test design. Thirty-one candidate segments of 50-200 bp (mean, 98.55 bp) were screened in discovery data and evaluated for within-Asteraceae sequence recall, differentiation from non-Asteraceae Asterales, in silico primer behavior, phylogenetic placement, and exploratory matching across 808 metadata-defined metagenomic samples. Conserved regions such as matR and rbcL showed high within-Asteraceae identity, whereas ITS1, ITS, and trnH-psbA showed larger differences from related-family backgrounds; ITS2 and ycf1 showed intermediate profiles. Candidate segments were placed within or immediately adjacent to Asteraceae reference branches in segment-specific maximum-likelihood analyses, although support and topology varied among regions. Metadata-defined target-containing groups had higher mean query coverage and identity than background groups; because target presence was not independently verified and no classifier was fitted, these comparisons were descriptive and did not estimate diagnostic accuracy. Definitionally linked sequence statistics were interpreted as structural associations rather than evidence of causal evolutionary mechanisms. These results provide a family-level computational comparison of candidate short segments for Asteraceae detection within Asterales. Species identification, operational marker combinations, threshold robustness, and laboratory performance require validation using taxonomically dense, voucher-linked, and experimentally characterized datasets.

Asteraceae↗

PubMed2026

The complete sequence of chloroplast genome of an important medicinal plant, Chamaemelum nobile Linaeus 1785 (Asteraceae).

Chamaemelum nobile L. (Asteraceae), commonly known as Roman chamomile, is a perennial herb with branched rhizomes and multiple leafy stems. The length of the complete cp genome is 149,827 bp, and it comprises 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. By conducting phylogenetic analyses based on chloroplast genomes, we found that C. nobile was more closely related to Matricaria chamomilla var. recutita within the chamomile species. This finding contributes to a better understanding of the phylogenetic relationship between C. nobile and other species.

Asteraceae↗

PubMed2007

Phylogenetic origins of the Himalayan endemic Dolomiaea, Diplazoptilon and Xanthopappus (Asteraceae: Cardueae) based on three DNA regions.

BACKGROUND AND AIMS: It is an enduring question as to the mechanisms leading to the high diversity and the processes producing endemics with unusual morphologies in the Himalayan alpine region. In the present study, the phylogenetic relationships and origins of three such endemic genera were analysed, Dolomiaea, Diplazoptilon and Xanthopappus, all in the tribe Cardueae of Asteraceae. METHODS: The nuclear rDNA internal transcribed spacer (ITS) and plastid trnL-F and psbA-trnH regions of these three genera were sequenced. The same regions for other related genera in Cardueae were also sequenced or downloaded from GenBank. Phylogenetic trees were constructed from individual and combined data sets of the three types of sequences using maximum parsimony, maximum likelihood and Bayesian analyses. KEY RESULTS: The phylogenetic tree obtained allowed earlier hypotheses concerning the relationships of these three endemic genera based on gross morphology to be rejected. Frolovia and Saussurea costus were deeply nested within Dolomiaea, and the strong statistical support for the Dolomiaea-Frolovia clade suggested that circumscription of Dolomiaea should be more broadly redefined. Diplazoptilon was resolved as sister to Himalaiella, and these two together are sister to Lipschitziella. The clade comprising these three genera is sister to Jurinea, and together these four genera are sister to the Dolomiaea-Frolovia clade. Xanthopappus, previously hypothesized to be closely related to Carduus, was found to be nested within a well-supported but not fully resolved Onopordum group with Alfredia, Ancathia, Lamyropappus, Olgaea, Synurus and Syreitschikovia, rather than the Carduus group. The crude dating based on ITS sequence divergence revealed that the divergence time of Dolomiaea-Frolovia from its sister group probably occurred 13.6-12.2 million years ago (Ma), and the divergence times of the other two genera, Xanthopappus and Diplazoptilon, from their close relatives around 5.7-4.7 Ma and 2.0-1.6 Ma, respectively. CONCLUSIONS: The findings provide an improved understanding of the intergeneric relationships in Cardueae. The crude calibration of lineages indicates that the uplifts of the Qiinghai-Tibetan Plateau since the Miocene might have served as a continuous stimulus for the production of these morphologically aberrant endemic elements of the Himalayan flora.

Asteraceae↗