Archaeogenomic Evidence of Punctuated Genome Evolution in Gossypium

Abstract

Transposable elements (TEs) are drivers of evolution resulting in episodic surges of genetic innovation and genomic reorganization (Oliver KR, Greene WK. 2009. TEs: powerful facilitators of evolution. Bioessays 31:703-714.), but there is little evidence of the timescale in which this process has occurred (Gingerich PD. 2009. Rates of evolution. Ann Rev Ecol Evol Syst. 40:657-675.). The paleontological and archaeological records provide direct evidence for how evolution has proceeded in the past, which can be accessed through ancient DNA to examine genomes using high-throughput sequencing technologies (Palmer SA, Smith O, Allaby RG. 2011. The blossoming of plant archaeogenetics. Ann Anat. 194:146-156.). In this study, we report shotgun sequencing of four archaeological samples of cotton using the GS 454 FLX platform, which enabled reconstruction of the TE composition of these past genomes and species identification. From this, a picture of lineage specific evolutionary patterns emerged, even over the relatively short timescale of a few thousand years. Genomic stability was observed between South American Gossypium barbadense samples separated by over 2,000 miles and 3,000 years. In contrast, the TE composition of ancient Nubian cotton, identified as G. herbaceum, differed dramatically from that of modern G. herbaceum and resembled closely the A genome of the New World tetraploids. Our analysis has directly shown that considerable genomic reorganization has occurred within the history of a domesticated plant species while genomic stability has occurred in closely related species. A pattern of episodes of rapid change and periods of stability is expected of punctuated evolution. This observation is important to understanding the process of evolution under domestication.

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene

“…Domesticated plants again fit this expectation with the vast majority of domestication syndrome traits for which the underlying genetic basis has been identified being regulatory in nature (Purugganan and Fuller, 2009). An important aspect of regulation is the action of RNA and epigenetic interactions such as the targeting of loci for methylation.…”

“…The dramatic change in the TE composition of the very young species G. herbaceum over a short period of time is evidence of large amounts of small change. In contrast, the very similar TE composition of the two G. barbadense samples indicates very little change despite the samples being separated by 2,000 miles and 3,000 years (fromPalmer et al, 2012). yBP ¼ years before present.…”

“…Comparison of archaeological and modern samples of cotton shows a startling amount of change in TE composition in Gossypium herbaceum over a short period of time ( Fig. 2; Palmer et al, 2012). Gossypium herbaceum, from the Old World, is thought to be a very young species, speculated to be little older than the Holocene (Fryxell, 1979).…”

“…However, while more labile than DNA, ancient RNA still occurs in useful quantities (Fordyce et al, 2013;Smith et al, 2014a). Furthermore, methylation can be detected in archaeological samples (Briggs et (Palmer et al, 2012) mapped to Arabidopsis thaliana metabolic pathways. Reads were mapped to the KEGG A. thaliana metabolic pathway.…”

Breeding Open-Pollinated, Hybrid and Transgenic Outcrossing Species

“…Shotgun sequencing of four archaeological samples of cotton enabled the reconstruction of the transposable composition of these past genomes and species identification (Palmer et al 2012). Genomic stability was observed between G. barbadense accessions separated by over 2000 miles and 3000 years while the transposable composition of ancient G. herbaceum, differed significantly from that of G. herbaceum but resembled closely the A genome of tetraploid cottons.…”