Abstract
Whole-genome duplications (WGDs) are widespread in plants and frequently coincide with global climatic change events, such as the Cretaceous–Tertiary (KT) extinction event approximately 65 million years ago (mya). Ferns have larger genomes and higher chromosome numbers than seed plants, which likely resulted from multiple rounds of polyploidy. Here, we use diploid and triploid material from a model fern species, Ceratopteris thalictroides, for the detection of WGDs. High-quality RNA-seq data was used to infer the number of synonymous substitutions per synonymous site (Ks) between paralogs; Ks age distribution and absolute dating approach were used to determine the age of WGD events. Evidence of an ancient WGD event with a Ks peak value of approximately 1.2 was obtained for both samples; however, the Ks frequency distributions varied significantly. Importantly, we dated the WGD event at 51–53 mya, which coincides with the Paleocene-Eocene Thermal Maximum (PETM), when the Earth became warmer and wetter than any other period during the Cenozoic. Duplicate genes were preferentially retained for specific functions, such as environment response, further support that the duplicates may have promoted quick adaption to environmental changes and potentially resulted in evolutionary success, especially for pantropical species, such as C. thalictroides, which exhibits higher temperature tolerance.
Highlights
Whole-genome duplication (WGD), or polyploidy, has long been considered as an important evolutionary force and often drives plant speciation [1,2,3,4,5]
WGDs are common in plants and are considered major factors driving plant diversity [3,5]
Several methods for the detection of WGDs have been reported, including synteny and gene-family trees with a reference species tree, and are widely used in plants with complete genome information. Another commonly applied method uses transcriptome data with a partial expressed sequence tag (EST), which is typically used in determining WGD features on the basis of Ks age distribution [3,6,9,12]
Summary
Whole-genome duplication (WGD), or polyploidy, has long been considered as an important evolutionary force and often drives plant speciation [1,2,3,4,5]. Gene retention after WGDs is not random; a general pattern has been observed indicating that regulators and signal transducers are preferentially retained in vertebrates and flowering plants [3,14,15]. Another type of biased retention following WGDs are involved in response to biotic and abiotic stress in flowering plants and are important for local adaptation [5,15]. Little is known about the occurrence of WGDs for nonflowering plants
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