Double the Genome, Double the Fun: Genome Duplications in Angiosperms

Abstract

Ancient whole-genome duplication (WGD), or polyploidy, dramatically changed the size, content, and complexity of the genome (Figure 1). Preferential gene retention, functional divergence, and regulatory network complexity after expansion of genetic material potentially result in key innovations, phenotypic novelty, and thereafter may serve as a catalyst for speciation and diversification (Soltis and Soltis, 2016). Furthermore, WGD has been identified in many lineages, including ciliates, fungi, vertebrates, and plants, and often seems to be accompanied by species rich groups, especially in angiosperms. Angiosperms, with more than 300 000 extant species, have been recognized as the largest group of land plants by far. An abrupt origin and highly accelerated rate of diversification of flowering plants in the mid-Cretaceous was described as an ''abominable mystery'' by Charles Darwin (Friedman, 2009). Even though the mystery is not about angiosperm per se, the origin of flower and diversification of angiosperms have been attracting great interest in the field of evolutionary biology.

Genome-Wide Identification and Characterization of Aquaporins and Their Role in the Flower Opening Processes in Carnation (Dianthus caryophyllus)

“…Furthermore, NIPs’ selection pressure was calculated. The number of AQPs in carnation was lesser than that in higher plants, such as A. thaliana , G. max , B. rapa , Z. mays L., O. sativa L, and P. trichocarpa , which may be attributed to the fact that higher plants have experienced more than once time gene repeat events [ 27 , 28 ], including whole genome duplication (WGD), fragment duplication (FD), and tandem duplication (TD) [ 29 , 30 , 31 ]. Interestingly, carnation was found to have more AQPs than basal plants such as P. patens and S. moellendorffii , but both MCScanx and blastP results showed no gene duplication events in carnation.…”

Genome-Wide Duplication of Allotetraploid Brassica napus Produces Novel Characteristics and Extensive Ploidy Variation in Self-Pollinated Progeny

“…Polyploidy or whole genome duplication (WGD) has long been considered a prominent force driving evolution of angiosperm species (Casacuberta et al 2016;Leitch and Leitch 2008;Soltis et al 2009;Jiao et al 2011). Advances in sequencing have revealed a series of ancient WGDs throughout the evolutionary history of angiosperms (Jiao 2018;Wendel et al 2016;Jiao et al 2011;Ren et al 2018). All extant seed plants have experienced at least one cycle of WGD in their evolutionary history (Jiao et al 2011).…”

“…More than a third of present angiosperm plants are polyploids ( Wood et al 2009 ), and approximately 13% of diploid plant species populations may harbor unnamed polyploid cytotypes ( Barker et al 2016 ). Accumulating evidence suggests that polyploidy has played a significant role in phenotypic innovation, species diversification, facilitation of biodiversity, and adaptation to broader ecological environments ( Soltis et al 2009 ; Schranz et al 2012 ; Ramsey and Schemske 1998 ; Hohmann et al 2015 ; Van de Peer et al 2017 ; Mandáková et al 2017 ; Jiao 2018 ; Soltis and Soltis 2016 ; Edger et al 2015 ; Tank et al 2015 ). Polyploidy may also facilitate species survival and radiation during periods of rapid ecological change ( Vanneste et al 2014 ; Jiao 2018 ; Cai et al 2019 ; Chao et al 2013 ).…”

“…B. napus is a classic example of the importance of WGD in plant evolution, and is considered an ideal system for investigation of the consequences and mechanisms of de novo and recurrent polyploidization ( Jenczewski and Alix 2004 ; Chalhoub et al 2014 ; Szadkowski et al 2010 ; Ferreira de Carvalho et al 2019 ; Mason and Snowdon 2016 ). Recent analysis suggests that recurrent WGDs may cyclically provide novel genetic resources for evolution and diversification, because duplicated sequences from ancient WGD tend to be lost in species that experienced additional recent WGD ( Jiao 2018 ; Ren et al 2018 ). However, although polyploidization remains a highly dynamic, active and ongoing process in nature ( Leitch and Leitch 2008 ; Comai 2005 ; Alix et al 2017 ), it is largely unclear whether recent allopolyploid species can benefit from an additional round of WGD, or if novel traits will be derived in such a scenario.…”

GenoDup Pipeline: a tool to detect genome duplication using the dS-based method

“…Therefore, identification of WGD is the first step to understanding the impacts of WGD and the fates of duplicated genes. WGD is now known to be a common event in plants, since the availability of genomic data generated by next generation sequencing (NGS) (Jiao, 2018; Jiao & Paterson, 2014; Soltis et al, 2009; Soltis et al, 2015). Meanwhile, recent studies also suggest that WGD is a common evolutionary force in animals (Li et al, 2018; Van De Peer, Mizrachi & Marchal, 2017).…”