Email updates

Keep up to date with the latest news and content from BMC Plant Biology and BioMed Central.

Open Access Research article

Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size

Juliana Stival Sena1*, Isabelle Giguère1, Brian Boyle1, Philippe Rigault2, Inanc Birol3, Andrea Zuccolo45, Kermit Ritland6, Carol Ritland6, Joerg Bohlmann3, Steven Jones3, Jean Bousquet17 and John Mackay1

Author Affiliations

1 Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada

2 Gydle Inc., Québec, QC, Canada

3 Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

4 Applied Genomics Institute, Udine 33100, Italy

5 Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa 56127, Italy

6 Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

7 Canada Research Chair in Forest Genomics, Université Laval, Québec, QC G1V 0A6, Canada

For all author emails, please log on.

BMC Plant Biology 2014, 14:95  doi:10.1186/1471-2229-14-95

Published: 16 April 2014

Abstract

Background

A positive relationship between genome size and intron length is observed across eukaryotes including Angiosperms plants, indicating a co-evolution of genome size and gene structure. Conifers have very large genomes and longer introns on average than most plants, but impacts of their large genome and longer introns on gene structure has not be described.

Results

Gene structure was analyzed for 35 genes of Picea glauca obtained from BAC sequencing and genome assembly, including comparisons with A. thaliana, P. trichocarpa and Z. mays. We aimed to develop an understanding of impact of long introns on the structure of individual genes. The number and length of exons was well conserved among the species compared but on average, P. glauca introns were longer and genes had four times more intronic sequence than Arabidopsis, and 2 times more than poplar and maize. However, pairwise comparisons of individual genes gave variable results and not all contrasts were statistically significant. Genes generally accumulated one or a few longer introns in species with larger genomes but the position of long introns was variable between plant lineages. In P. glauca, highly expressed genes generally had more intronic sequence than tissue preferential genes. Comparisons with the Pinus taeda BACs and genome scaffolds showed a high conservation for position of long introns and for sequence of short introns. A survey of 1836 P. glauca genes obtained by sequence capture mostly containing introns <1 Kbp showed that repeated sequences were 10× more abundant in introns than in exons.

Conclusion

Conifers have large amounts of intronic sequence per gene for seed plants due to the presence of few long introns and repetitive element sequences are ubiquitous in their introns. Results indicate a complex landscape of intron sizes and distribution across taxa and between genes with different expression profiles.

Keywords:
Genome size; Pinus taeda; BAC; Repeat elements; Gymnosperms; Gene expression