title: Evolution and alignment of the hypervariable arm 1 of Aeschynanthus (Gesneriaceae) ITS2 nuclear ribosomal DNA.
abstract: Comparative ITS2 sequencing in the plant genus Aeschynanthus(Gesneriaceae) reveals an insertion/deletion (indel) hot spot in the ITS2 sequences that is difficult to align. Examination of other Gesneriaceae sequences shows that this is a widespread phenomenon in this plant family. Minimum free-energy secondary structure analyses localize the hot spot to the terminal part of arm 1. Arm 1 is twice as long in Gesneriaceae than in other asterids. In addition, the pattern of indels is consistent with this secondary structure model. The high variability of the extended terminal part of arm 1 in Gesneriaceae and the fact that it can be deleted altogether imply that it is functionally superfluous. In contrast, the base of arm 1 is relatively conserved and may function as an exonuclease recognition site. This study illustrates how comparative secondary structure analyses can be helpful in fine-scale alignment. Alignment based on secondary structure conflicts with our initial manual alignment and, to a lesser extent, with a CLUSTAL X alignment with default parameters.
authors.affiliation: Institute of Cell and Molecular Biology, The University of Edinburgh, Edinburgh, EH9 3JH, United Kingdom.
authors.forename: J
authors.initials: J
authors.lastname: Denduangboripant
authors.forename: Q C
authors.initials: QC
authors.lastname: Cronk
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010944:Plants / Q000235:genetics*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018744:DNA, Plant; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D012335:RNA, Ribosomal