Features of Arabidopsis genes and genome discovered using full-length cDNAs

Nickolai N. Alexandrov, Maxim E. Troukhan, Vyacheslav V. Brover, Tatiana Tatarinova, Richard B. Flavell, Kenneth A Feldmann

Research output: Contribution to journalArticle

118 Citations (Scopus)

Abstract

Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including intron and exon lengths, intergenic distances, features of promoters, and variant 5′-ends of mRNAs transcribed from the same transcription unit. We also provide a statistical characterization of Arabidopsis transcripts in terms of their size, UTR lengths, 3′-end cleavage sites, splicing variants, and coding potential. These analyses were facilitated by scrutiny of our collection of sequenced full-length cDNAs and much larger collection of 5′-ESTs, together with another set of full-length cDNAs from Salk/Stanford/Plant Gene Expression Center/RIKEN. Examples of alternative splicing are observed for transcripts from 7% of the genes and many of these genes display multiple spliced isoforms. Most splicing variants lie in non-coding regions of the transcripts. Non-canonical splice sites constitute less than 1% of all splice sites. Genes with fewer than four introns display reduced average mRNA levels. Putative alternative transcription start sites were observed in 30% of highly expressed genes and in more than 50% of the genes with low expression. Transcription start sites correlate remarkably well with a CG skew peak in the DNA sequences. The intergenic distances vary considerably, those where genes are transcribed towards one another being significantly shorter. New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, including those antisense to known genes, are derived and cataloged in the Supplementary Material. They identify 148 new loci in the Arabidopsis genome. The conclusions drawn provide a better understanding of the Arabidopsis genome and how the gene transcripts are processed. The results also allow better predictions to be made for, as yet, poorly defined genes and provide a reference for comparisons with other plant genomes whose complete sequences are currently being determined. Some comparisons with rice are included in this paper.

Original languageEnglish (US)
Pages (from-to)69-85
Number of pages17
JournalPlant Molecular Biology
Volume60
Issue number1
DOIs
StatePublished - Jan 2006
Externally publishedYes

Fingerprint

Arabidopsis
Complementary DNA
Genes
Genome
genome
genes
Plant Genome
Transcription Initiation Site
Expressed Sequence Tags
transcription (genetics)
Introns
introns
Plant Genes
Messenger RNA
Pseudogenes
Alternative Splicing
3' Untranslated Regions
alternative splicing
Exons
Protein Isoforms

Keywords

  • Alternative splicing
  • Arabidopsis genome
  • Full-length cDNA
  • Gene prediction
  • Genome statistics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry

Cite this

Alexandrov, N. N., Troukhan, M. E., Brover, V. V., Tatarinova, T., Flavell, R. B., & Feldmann, K. A. (2006). Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Molecular Biology, 60(1), 69-85. https://doi.org/10.1007/s11103-005-2564-9

Features of Arabidopsis genes and genome discovered using full-length cDNAs. / Alexandrov, Nickolai N.; Troukhan, Maxim E.; Brover, Vyacheslav V.; Tatarinova, Tatiana; Flavell, Richard B.; Feldmann, Kenneth A.

In: Plant Molecular Biology, Vol. 60, No. 1, 01.2006, p. 69-85.

Research output: Contribution to journalArticle

Alexandrov, NN, Troukhan, ME, Brover, VV, Tatarinova, T, Flavell, RB & Feldmann, KA 2006, 'Features of Arabidopsis genes and genome discovered using full-length cDNAs', Plant Molecular Biology, vol. 60, no. 1, pp. 69-85. https://doi.org/10.1007/s11103-005-2564-9
Alexandrov, Nickolai N. ; Troukhan, Maxim E. ; Brover, Vyacheslav V. ; Tatarinova, Tatiana ; Flavell, Richard B. ; Feldmann, Kenneth A. / Features of Arabidopsis genes and genome discovered using full-length cDNAs. In: Plant Molecular Biology. 2006 ; Vol. 60, No. 1. pp. 69-85.
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