subtelomeric region of the Arabidopsis thaliana chromosome IIIR contains potential genes and duplicated fragments from other chromosomes

• Published in: Plant molecular biology Vol. 74; no. 1-2; pp. 155 - 166
• Main Authors: Wang, Chi-Ting, Ho, Chia-Hsing, Hseu, Ming-Jhy, Chen, Chung-Mong
• Format: Journal Article
• Language: English
• Published: Dordrecht Dordrecht : Springer Netherlands 01.09.2010; Springer Netherlands; Springer Nature B.V
• Subjects: Alternative Splicing; Amino Acid Sequence; Arabidopsis - classification; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis thaliana; Base Sequence; Biochemistry; Biomedical and Life Sciences; Chromosomes; Chromosomes, Plant - genetics; DNA Repair - genetics; DNA, Plant - genetics; Ecotypes; Flowers & plants; Gene Duplication; Gene identification; Genes, Plant; Genome structure; Genomics; Life Sciences; Molecular biology; Molecular Sequence Data; Plant biology; Plant Pathology; Plant Sciences; Proteins; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Single-telomere length analysis; Species Specificity; Subtelomere; Telomere - genetics; Telomere-associated sequence; Genome structure; Gene identification; Single-telomere length analysis; Telomere-associated sequence; Subtelomere
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1007/s11103-010-9664-x

The subtelomere and a portion of the associated telomeric region (together named 3RTAS) of chromosome IIIR from the Arabidopsis thaliana ecotypes Columbia (Col) and Wassilewskija (Ws) were specifically amplified by polymerase chain reaction and subsequently cloned and sequenced. The centromere-proximal portion of 3RTAS from both ecotypes contained two newly identified potential genes, one encoding the chloroplast luminal 19-kDa protein precursor and the other encoding three potential alternatively spliced CCCH-type zinc finger proteins. The telomere-proximal portion of 3RTAS from the Col ecotype contained short duplicated fragments derived from chromosomes I, II, and III, and that from the Ws ecotype contained a duplicated fragment derived from chromosome V. Each duplicated fragment has diverged somewhat in sequence from that of the ectopic template. Small patches of homologous nucleotides were found within the flanking sequences of both the duplicated fragments and the corresponding ectopic template sequences. The structural characteristics of these duplicated fragments suggest that they are filler DNAs captured by non-homologous end joining during double-strand break repair. Our characterization of 3RTAS not only filled up a gap in the chromosome IIIR sequence of A. thaliana but also identified new genes with unknown functions.