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Nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in Picea (Pinaceae): sequence divergence and structure
Christopher S Campbell1, Wesley A Wright, Margaret Cox
1Department of Biological Sciences, University of Maine, Orono, ME 04469, USA. campbell@maine.edu
Molecular Phylogenetics and Evolution
|March 2, 2005
Summary
The nuclear ribosomal DNA internal transcribed spacer 1 (nrDNA ITS1) in Picea species is exceptionally long. Sequence divergence within Picea species is higher than between them, potentially due to rDNA repeat separation on multiple chromosomes.
Area of Science:
- Molecular Biology
- Plant Genetics
- Evolutionary Biology
Background:
- The nuclear ribosomal DNA internal transcribed spacer 1 (nrDNA ITS1) in Picea species represents the longest known among all plants.
- Understanding the genetic variation and evolutionary mechanisms within Picea ITS1 is crucial for plant genomics.
Purpose of the Study:
- To analyze the nrDNA ITS1 sequences from six Picea species.
- To investigate sequence divergence, subrepeat structure, and secondary structure formation within Picea ITS1.
- To explore the evolutionary dynamics, including concerted evolution and sequence coalescence, in Picea ITS1.
Main Methods:
- Cloning and sequencing of 24 ITS1 regions from six Picea species (Picea glehnii, Picea mariana, Picea orientalis, Picea rubens).
- Sequence alignment and divergence analysis.
- Identification and comparison of subrepeat motifs and their conservation.
- Inference of secondary structures and analysis of subrepeat pairing.
Main Results:
- Picea ITS1 sequences range from 2747-3271 bp, exhibiting significant intra-individual sequence divergence (0.018+/-0.009) exceeding inter-specific divergence (0.031+/-0.011).
- Three conserved subrepeats with a specific motif (5'-GGCCACCCTAGTC) were identified across Pinaceae, with tandem subrepeats showing higher similarity.
- Inferred secondary structures revealed hairpin formations and pairing between tandem subrepeats, with sequence coalescence observed only in Picea orientalis.
Conclusions:
- Intra-individual divergence in Picea ITS1 may be maintained by the separation of rDNA repeats on multiple chromosomes, potentially counteracting concerted evolution.
- The conserved subrepeat motif and their structural organization suggest evolutionary processes like duplication or concerted evolution within rDNA repeats.
- Differential sequence coalescence in Picea orientalis indicates varying evolutionary trajectories among Picea species.