Differential lineage-specific amplification of transposable elements is responsible for genome size variation inGossypium
- 1Iowa State University, Department of Ecology, Evolution and Organismal Biology, Ames, Iowa 50011, USA;
- 2University of Arizona, Department of Plant Sciences, Arizona Genomics Institute, Tucson, Arizona 85721, USA
Abstract
The DNA content of eukaryotic nuclei (C-value) varies ∼200,000-fold, but there is only a ∼20-fold variation in the number of protein-coding genes. Hence, most C-value variation is ascribed to the repetitive fraction, although little is known about the evolutionary dynamics of the specific components that lead to genome size variation. To understand the modes and mechanisms that underlie variation in genome composition, we generated sequence data from whole genome shotgun (WGS) libraries for three representative diploid (n = 13) members ofGossypium that vary in genome size from 880 to 2460 Mb (1C) and from a phylogenetic outgroup,Gossypioides kirkii, with an estimated genome size of 588 Mb. Copy number estimates including all dispersed repetitive sequences indicate that 40%–65% of each genome is composed of transposable elements. Inspection of individual sequence types revealed differential, lineage-specific expansion of various families of transposable elements among the different plant lineages.Copia-like retrotransposable element sequences have differentially accumulated in theGossypium species with the smallest genome,G. raimondii, whilegypsy-like sequences have proliferated in the lineages with larger genomes. Phylogenetic analyses demonstrated a pattern of lineage-specific amplification of particular subfamilies of retrotransposons within each species studied. One particular group ofgypsy-like retrotransposon sequences,Gorge3 (Gossypium retrotransposablegypsy-like element), appears to have undergone a massive proliferation in two plant lineages, accounting for a major fraction of genome-size change. Like maize,Gossypium has undergone a threefold increase in genome size due to the accumulation of LTR retrotransposons over the 5–10 Myr since its origin.
Footnotes
↵1 Corresponding author.
↵1 E-mailjfw{at}iastate.edu; fax (515) 294-1337.
The sequence data described in this paper have been submitted to the GSS Division of GenBank under accessions DX390732–DX406528.
Article published online before print. Article and publication date are athttp://www.genome.org/cgi/doi/10.1101/gr.5282906.
- Received March 3, 2006.
- Accepted May 22, 2006.
- Copyright © 2006, Cold Spring Harbor Laboratory Press
