Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions.

Whole-genome duplication (WGD) has occurred repeatedly during plant evolution and diversification, providing genetic layers for evolving new functions and phenotypes. Advances in long-read sequencing technologies have enabled sequencing and assembly of over 1000 plant genomes spanning nearly 800 species, in which a large set of ancient WGDs has been uncovered. Here, we review the recently reported WGDs that occurred in major plant lineages and key evolutionary positions, and highlight their contributions to morphological innovation and adaptive evolution. Current gaps and challenges in integrating enormous volumes of sequenced plant genomes, accurately inferring WGDs, and developing web-based analysis tools are emphasized. Looking to the future, ambitious genome sequencing projects and global efforts may substantially recapitulate the plant tree of life based on broader sampling of phylogenetic diversity, reveal much of the timetable of ancient WGDs, and address the biological significance of WGDs in plant adaptation and radiation.

Introduction

The evolution of green plants to become the world’s dominant flora has been marked by prevalent whole-genome duplication (WGD) events [[1], [2], [3], [4], [5], [6], [7], [8]]. WGD can abruptly double the entire set of chromosomes in the nucleus, conferring polyploidy [9]. Occurring by fusion of unreduced gametes or doubling of chromosomes in zygote [[10], [11]], WGD has long been considered to provide ‘layers’ of redundant genetic information that can be co-opted for the evolution of genome complexity, phenotypic innovation and adaptability [[12], [13], [14], [15], [16], [17], [18], [19], [20]].

Genome sequencing propelled the identification of ancient WGD (paleopolyploidy) events in a range of taxa. Analysis of the first plant genome–Arabidopsis thaliana–revealed the remnants of three ancient WGDs referred to as the alpha (α)–beta (β)–gamma (γ) series shared by Brassicaceae [21]. Interestingly, rice, sorghum and other monocot genome analyses also unraveled three rounds of ancient WGDs predating the divergence of Poaceae species, termed the rho (ρ)–sigma (σ)–tau (τ) series [[22], [23]]. Paleopolyploidy has not been limited to duplication, with cases of whole-genome triplication (WGT) and even penta-plication contributing to the astonishing genome complexity of plants [[24], [25], [26]]. About 24 %-35 % of extant vascular plants were inferred to be of recent polyploid origin, with 15 % of speciation events in angiosperms related to ploidy increase as well as 31 % in ferns [[27], [28], [29]]. Polyploidy has also been suggested to be associated with crop domestication, with domesticated crops (e.g. wheat, canola, cotton, peanut, coffee, oat) having experienced more polyploidy events than their wild relatives [30]. Understanding polyploid speciation and archival of its products may be of growing importance for maintaining plant diversity and global food security, given the expectation that plant extinction will exceed plant speciation in the near future [31].

Considerable progress in long-read sequencing technologies has propelled the global wave of genome sequencing with over 1000 plant genomes representing ∼ 800 species available now [[32], [33]]. Remarkably, the quality of genome assembly has been elevated from ‘draft’ level to ‘chromosome-level’, and even to ‘telomere-to-telomere’ or ‘gap-free’ or ‘complete’ for many plants [[34], [35], [36], [37], [38], [39], [40]]. The large set of sequenced plant genomes provides valuable resources for deeply resolving ancient WGDs and tracing genome changes linked to major evolutionary transitions and variable adaptations [7].

Here, we detail WGDs identified in early-diverging seed-free plants and other major plant lineages. Ancient WGDs inferred at important phylogenetic positions were also highlighted, and their roles in phenotypic innovations, adaptive transitions, and species richness were addressed. The increasing challenges in processing and integrating plant genome data, and accurately identifying ancient WGDs are discussed. Collaborative research projects and global efforts remain required to fill current gaps in phylogenetic sampling, in inferring and positioning ancient WGDs across plant phylogeny and in deeply resolving the consequences of WGDs in plant adaptation and rapid expansion.

Paleopolyploidy events discovered across major plant lineages and their links to evolutionary innovations

Streptophyte algae–the closest sister lineage to land plants

Terrestrialization is a landmark of plant evolution and radiation, which had a profound influence on Earth’s ecosystems [[41], [42], [43], [44], [45], [46], [47]]. The genome sequencing of streptophyte algae–the sister lineage to land plants (Embryophyta)–has reinforced our understanding of genome and gene changes of early plants during the evolutionary transition from water to land [[48], [49], [50], [51], [52], [53]]. The WGD or polyploidy event is prevalent in land plant evolution, but is rare in green (chlorophyte and streptophyte) algae lineages (Fig. 1). Genome analysis of the earliest-diverging unicellular streptophyte algae, Mesostigma viride, showed evidence of WGD which contributed to relatively large genome size (442 Mb) and expansion of specific gene families involved in multicellularity and terrestrial pre-adaptation [53]. However, in a parallel study, evidence of WGD was not found in M. viride, perhaps due to fragmented and incomplete genome assembly with N50 = 113 Kb [52]. The occurrence of WGD or large-scale segmental duplications in basal streptophyte alga may be linked to the evolutionary transition from salt water to freshwater.

Fig. 1

The distribution of reported ancient WGDs across major lineages of green plants. WGDs (circle) and WGTs (square) were placed on the different branches of phylogenetic tree based on previous studies. The branch length is not proportional to the timescale. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Intriguingly, a whole-genome triplication (WGT) event was deciphered in the unicellular algae Spirogloea muscicola with subaerial habitat, belonging to another lineage of streptophyte algae–Zygnematophyceae, and representing a closer living relative to land plants [49]. This WGT event increased the gene sets in S. muscicola, conferring genetic redundancy useful to adapt to subaerial stress and symbiotic interaction. Intragenomic synteny analysis also suggested that S. muscicola may have undergone a more ancient WGD (4dTv peak ∼ 0.85). Although WGD was not detected in Penium margaritaceum (1C = 4.7 Gb), the closest relative to land plants sequenced so far, a large number of segmental duplications was discovered within its genome [50]. The roles of WGD or WGT events in the molecular changes and evolution from freshwater to terrestrial environment remain to be deeply resolved.

Bryophytes–the pioneer of land plants

As the representative of early land plants, bryophytes including hornworts, liverworts and mosses, emerged about 460–506 Mya [[54], [55]], and have aroused great interest to reveal key genome features involved in adaptation to terrestrial habitat [[56], [57], [58], [59], [60], [61], [62], [63], [64]]. Multiple ancient WGD events has been uncovered in the model moss Physcomitrium patens [[60], [65]]. The remnants of ancient WGDs were also unraveled in other moss species including those from Sphagnales order, and three subclasses of Bryopsida (Timmiidae, Dicranidae, and Bryidae) [[7], [66]]. The timing of WGD identified in moss Calohypnum plumiforme has been dated to 8 Mya (Ks ∼ 0.13–0.18) regardless of evolutionary rate correction [61]. The preferred retention of regulation- and stress-related genes after WGD in some moss genomes may have conferred the capability to survive adverse conditions such as cold, UV-B radiation, desiccation and heat [[64], [65], [67]]. In contrast, the currently sequenced species belonging to hornworts and liverworts lack evidence of WGD. The consequences of higher frequencies of WGDs in relation to the adaptation and diversification of mosses still need to be elucidated.

Lycophytes and Ferns–the early-diverging vascular plants

Lycophytes are thought to be representative of primitive vascular plants, and their origination has been dated to 392–451 Mya [68]. Strikingly, the evolution of a model lycophyte, Selaginella moellendorffii, has been influenced by at least two WGD events [69]. However, the contributions of repeated WGDs to genome changes and origin of the vascular system remain largely unclear. In contrast to desiccation sensitive S. moellendorffii, some Selaginella species showed extreme desiccation tolerance [[70], [71]]. The roles of WGDs and subsequent species-specific diploidization in the divergent evolution of desiccation tolerance need to be investigated. In addition, an ancient WGD (Ks = 1.8) was revealed in the aquatic lycophyte Isoetes taiwanensis, implying its potential roles in the evolution of aquatic adaptation and CAM [72].

Ferns present great diversity with over 10,000 species, and generally possess large genome size and high chromosome number [[73], [74], [75]]. The mean genome size of ferns is estimated to be 14 Gb [76], and the most common chromosome number (n) is 41, compared to 9 in eudicots and 7 in monocots [74]. It has been hypothesized that recurrent WGD events have led to an unusual increase of chromosome number, genome size, and fern species richness [[5], [27], [74], [77], [78]]. Indeed, a high-frequency WGD events were unraveled across the fern phylogeny, with 66 %–97 % of extant ferns inferred to be derived from ancient polyploids [[5], [66]]. Chromosome number analysis also suggested that over 30 % of speciation events occurring in ferns are related to polyploidy events [27]. In contrast to their high species richness, only four fern genomes are available now, of which one is chromosomal-scale (Alsophila spinulosa) [79], two (Azolla filiculoides and Salvinia cucullata) are draft [80] and one is fragmented and incomplete (Ceratopteris richardii) [81]. The tree fern A. spinulosa was found to have experienced two ancient WGDs, the more recent one shared by Cyatheaceae species (termed ‘Cyatheaceae WGD’, Ks = 0.3), and the ancient one in the common ancestor of Cyatheales (termed ‘Cyatheales WGD’, Ks = 1.5) [79]. The large proportion of syntenic blocks are well preserved in genome of A. spinulosa following ‘Cyatheaceae WGD’ (∼100 Mya), which was considered to be due to slow genome reshuffling and diploidization but responsible for the large genome size (6.2 Gb) and high chromosome number (n = 69). However, the associations between successive WGD events and the evolution of xylem and vascular tissues remain elusive. Genome analysis of A. filiculoides and S. cucullata revealed an ancient WGD occurring in the common ancestor of core leptosporangiates, and a more recent Azolla-specific WGD [80]. Analysis of the model fern C. richardii also revealed a lineage-specific WGD [81]. Future efforts are highly desired to improve the current fern genomes and sequence more fern species in poorly represented lineages, accelerating the investigation of genome changes related to the evolutionary switch between homospory and heterospory which is regarded to be important for the evolution of seed [82].

Gymnosperms–the appearance of seed

Gymnosperms are the pioneers of seed plants, and appeared around 300 Mya [68]. The genome size of gymnosperms is commonly large with average 18 Gb [76]. Gymnosperms also show longevity, and are prone to occur in harsh environments such as cold, mountainous areas at high altitudes [[83], [84]]. Contradicting prior hypothesis that WGD is largely absent in gymnosperm lineages, important roles of WGDs in the evolution and radiation of gymnosperms have recently been suggested. Based on phylogenomic analysis of 24 transcriptomes, three ancient WGD events were revealed during the radiation of gymnosperms, with one in the common ancestor of Pinaceae, one in the common ancestor of Cupressaceae and Taxaceae (cupressophytes), and one in Welwitschia mirabilis [85]. The ancient WGD event (denoted as zeta, ζ) [1] inferred to have occurred in the common ancestor of seed plants was not shared with ferns [85]. However, analysis of chromosome-level genomes of three species from Taxaceae showed no evidence of recent WGD [[86], [87], [88]], countering the inference from [85]. The deeper investigation of WGDs in the chromosome-scale genome of Sequoiadendron giganteum (Cupressaceae) is required to verify the cupressophytes-specific WGD [89]. A broader sampling of gymnosperm transcriptomes uncovered a more ancient WGD occurring in the common ancestor of all extant gymnosperms and corroborated the Pinaceae-specific and Welwitschia-specific WGD event, but the contribution of WGDs to the diversification of gymnosperms was found to be limited [90]. Welwitschia-specific WGD was further confirmed and dated to ∼ 86 Mya (Ks = ∼1) based on genome analysis of W. mirabilis [91], but not discovered in assembling and analyzing a genome of the same species in another parallel study [92]. The chromosome-level genome assembly for Cycas panzhihuaensis (cycads) enables deep investigation of occurrence of ancient WGDs during gymnosperm evolution [93].

An ancient ‘gymnosperm-wide WGD’ (denoted as ω, Ks = ∼0.85) was revealed based on a combination of phylogenomic and syntenic analysis of C. panzhihuaensis and other plant genomes, which contributed to the evolution of lineage-specific genes in gymnosperms. In addition, a Pinaceae-specific WGD (Ks = ∼0.6) [90] was reconfirmed based on genome analysis of high-quality assembly of Pinus tabuliformis [94]. It has been suggested that duplicated genes provide important layers of redundancy for convergent evolution of conifer adaptation to cold tolerance [95] and morphological innovation [90]. Some questions remain to be resolved regarding potential links between polyploidy or small-scale gene duplication and stress tolerance adaptation of gymnosperms [84], the origin of protective layers surrounding seeds [96], and extreme longevity of some gymnosperm species [[91], [97]].

Basal angiosperms–the starting point towards the largest plant group

Flowering plants (termed angiosperms), the crown-group of plants, have experienced an extraordinarily high-frequency of WGD events which shaped their genomes and morphological complexity [[1], [4], [12], [16], [98], [99]]. WGDs has long been regarded as an important driving force to render the first appearance of flowering plants and subsequent rapid expansion during an incredibly short period of time, a phenomenon referred to as the “abominable mystery” by Darwin [[100], [101]]. Over recent years, understanding of the early evolution of angiosperms has been enhanced owing to the genome sequencing of the earliest-diverging angiosperm lineages including Amborellales, Nymphaeales and Austrobaileyales, collectively referred to as ANA-grade angiosperms. The decoding of the Amborella genome showed no evidence of recent lineage-specific WGD but revealed an ancient polyploidy event (denoted as epsilon, ɛ) preceding the diversification of angiosperms [102]. Genome analysis of water lily (Nymphaea colorata) unveiled a lineage-specific WGD (denoted π, Ks = 0.9) shared by Nymphaeaceae, which has been linked to the evolution of key genes underpinning flower development and attractive features [103]. The roles of genome and gene duplication in the evolutionary retrogressions of water lily from terrestrial to aquatic environment and from woody to herbaceous habit are worthy of being explored [[104], [105]]. Interestingly, prickly waterlily (Euryale ferox, Nymphaeaceae) experienced an additional WGT event after divergence with water lily [106], which was correlated to evolution of specific leaf development and aquatic adaptation [107].

Monocots

Monocots (termed monocotyledons) were estimated to have over 70,000 species [[108], [109]], including economically important food crops and fruits such as wheat, rice, maize, barley, banana, pineapple, sugarcane. The major source of human nutrients and calories come from monocots. The genome sequencing and assembly of basal monocots open new door for studying the early evolution of monocots. The Lemnaceae family (known as duckweed) belonging to the Alismatales has a basal phylogenetic position relative to other monocot families, and evolved to readapt to aquatic habitat [110]. The high-quality genomes of several Lemnaceae species have been published including Spirodela polyrhiza [[111], [112]], Spirodela intermedia [113], Lemna minuta [114], Wolffia australiana [[115], [116]]. The S. polyrhiza has undergone two ancient WGDs (∼95 Mya) but showed considerable reduction in genome size (∼158 Mb) and gene number (∼19,000) which may be associated with the simplification of its plant body (lacking stem) [[117], [118]]. Wolffia australiana has a smaller and simpler plant body lacking roots, and has further reduced gene number (∼15,000) but a larger genome (∼400 Mb) with signature of an ancient WGD (Ks peak = ∼1.6). An ancient WGD was also found in L. minuta, presenting a close Ks peak (∼1.7) to that found in the sister species-W. australiana, implying that the tau (τ) WGD may have occurred before the divergence of Lemnaceae and other major monocot lineages [114]. The ancient WGDs and subsequent extensive gene loss and genome readjustment may have contributed to the evolution of specialized gene sets underpinning fast growth rate, specific body plan, and aquatic lifestyle of these tiny and basal monocots. Seagrass (Alismatales) is sister to Lemnaceae with basal position in monocot lineage, and is the only marine flowering plants. The genome sequencing of Zostera marina [[119], [120]] and Zostera muelleri [121] has laid a solid foundation for better understanding of angiosperm adaption to the sea. The remnants of a lineage-specific WGD (64–72 Mya) were detected in Zostera genomes. The gene gain and loss have been linked to the degeneration and acquisition of specific traits of seagrasses to readapt from freshwater to marine environment [122].

The evolution and diversification of major monocot groups has been influenced by recurrence of lineage-specific and species-specific WGDs [[123], [124], [125], [126], [127]]. Intragenomic and intergenomic synteny analysis of rice (Oryza sativa) and sorghum (Sorghum bicolor) genome revealed two ancient WGD events in the common ancestor of grass lineage (Poaceae), denoted as ρ and σ respectively [[22], [128]]. A combination of phylogenomic and syntenic analysis further uncovered a more ancient WGD (denoted τ) common to commelinid monocots including Arecales, Poales, Zingiberales and Commelinales, terming as a WGD series of rho (ρ)-sigma (σ)-tau (τ) [23]. The ρ WGD was positioned before the divergence of the Pharoideae and the core grasses based on evolutionary analysis of Pharus latifolius genome [129]. The assembly of pineapple (Ananas comosus), and detailed synteny and phylogenetic analysis of pineapple and other monocot plants placed the σ WGD (100–120 Mya) before the divergence of Poales, and placed τ WGD (110–135 Mya) after the split of Alismatales and commelinids but before the split of commelinids and Asparagales [[124], [130]]. The Orchidaceae (commonly called orchids) is one of the largest families of flowering plants and the largest family of monocots, with more than 20,000 species. The genome analysis of Apostasia shenzhenica [130] and Vanilla planifolia [127] jointly provided evidence for a ‘Orchidaceae-wide’ WGD (or pan-orchid αO WGD), which was inferred to occur shortly before orchid radiation and to be associated with the great diversity of extant orchids.

Chloranthales and magnoliids

Genome and phylogenomic analysis of two Chloranthales species (Chloranthus spicatus and C. sessilifolius) provides evidence for an ancient WGD in the common ancestor of Chloranthales (denoted as kappa, κ), and supported Chloranthales as the sister lineage to magnoliids [[131], [132]]. This Chloranthales-specific WGD was also resolved to have a large role in the evolution of high volatile content. Magnoliids, comprised of four orders (Laurales, Magnoliales, Piperales, and Canellales) and containing over 9,000 species, has attracted interest for genome sequencing due to its uncertain phylogenetic relationships to eudicots and monocots [[133], [134], [135]]. Interestingly, magnoliid evolution has been influenced by frequent WGD events. An ancient WGD event preceding the divergence of Laurales and Magnoliales [[3], [136]] was termed lambda (λ) [2] although this symbol had been used to indicate the Nelumbo-specific WGD in a prior study [137]. Two Laurales families, Lauraceae and Calycanthaceae, each experienced an additional lineage-specific WGD event [[136], [138]]. In addition, Cassytha filiformis (Lauranceae) underwent a more recent species-specific WGD [136]. A WGD was also suggested to take place in the common ancestor of Gomortegaceae and Atherospermataceae (Laurales) [136]. Remarkably, genome comparison with Aristolochia fimbriata indicated that Piper nigrum (black pepper, Piperales) has experienced three successive WGDs [3], contradicting a previous report of only one WGD [139]. Their high-frequency of WGDs has been recognized as an important driving force for the evolution of unique features of magnoliids species such as rich volatile compounds and specific floral morphology.

Ceratophyllales and eudicots

Ceratophyllales has been inferred as the sister lineage to all extant eudicots [[106], [131]]. The relics of three WGD events were discovered in an aquatic Ceratophyllales species–rigid hornwort (Ceratophyllum demersum) [106]. Recently, genome sequences of a number of species from early-branching eudicot lineages or basal eudicots (Ranunculales, Proteales, Trochodendrales and Buxales) shed light on the early evolution of eudicots [140]. Aquilegia (Ranunculaceae, Ranunculales) possesses a basal phylogenetic position relative to other eudicots, and has been corroborated to experience a paleo-tetraploidy event shared with Coptis chinensis (Ranunculaceae) [141], although incongruent views about the placement of this event have been proposed [[142], [143], [144], [145]]. Papaveraceae (Ranunculales) is the closest sister lineage to Ranunculaceae. Genome analysis of three Papaver (Papaveraceae) species showed that P. setigerum shared a WGD with P. somniferum (opium poppy) (∼7.2 Mya), and experienced an additional more recent WGD (∼4 Mya) after its split with opium poppy [146]. These WGD events play important roles in evolution of the biosynthetic pathway of benzylisoquinoline alkaloids (BIAs) which are the medically important constituents of opium poppy. Akebia trifoliata (Lardizabalaceae, Ranunculales), a successor lineage to Aquilegia, showed evidence of a lineage-specific WGD, but whether this event is shared with Aquilegia remains unclear [147]. Another Ranunculales species Kingdonia uniflora (Circaeasteraceae) likewise presented evidence of WGD but with phylogenetic placement remaining to be determined [148]. Genome sequencing of sacred lotus (Nelumbo nucifera) [137] and Macadamia integrifolia [149], belonging to Proteales, indicated that they have experienced independent lineage-specific WGDs. As the closest and successive lineages to core eudicots, Trochodendrales (Tetracentron sinense) and Buxales (Buxus sinica) genomes analysis revealed that they each underwent one or more lineage-specific WGDs [[140], [150], [151]]. More WGDs discovered in core eudicots have been well documented [[2], [3], [4], [8], [18], [19]].

Links between paleopolyploidy and plant survival in extreme environments

Ancient WGDs have been found in some extremophytes such as halophytes [152], resurrection plants [[60], [153]], alpine plants [[154], [155], [156]], desert plants [[64], [157], [158]], and invasive plants [[159], [160], [161]], suggesting important roles of WGD in the evolution of plant adaptation to extreme environments [[64], [162]]. Interestingly, the occurrence of paleopolyploidy events has been suggested to coincide with periods of environmental upheaval, such as mass extinction events or extreme climate change [[4], [17]]. Several ‘waves’ of WGD have been suggested to be associated with different epochs or geologic time periods, including the Cretaceous–Paleogene (K–Pg) extinction event (∼66 Mya) [[4], [163]], early Aptian epoch within the Cretaceous period (∼120 Mya), and Neogene period (23.0–2.6 Mya) [[2], [18]]. Moreover, some genetic evidence supports significant contributions of ancient WGDs to plant adaptation and survival under abrupt climate changes [18]. Duplicated genes involved in resistance to cold, heat, darkness, and other adverse conditions were preferentially retained after independent WGDs near period of dramatic climate change [[18], [164], [165]]. In addition, polyploidy has been found with higher frequency in colder and higher latitude regions, consistent with the notion that polyploids have a propensity to survive in and inhabit extreme and fluctuating environments [166].

Summary and outlook

Over 1000 genomes representing 798 plant species have been sequenced and assembled in the past twenty years [[32], [33]]. A large number of ancient WGD events have been deciphered among diverse lineages [[4], [18], [19]], with 244 inferred and placed across plant phylogeny based on analysis of 1000 plant transcriptomes [[7], [8]]. Nonetheless, resolving dates and phylogenetic placements of ancient WGDs remains challenging due to plant genome complexity. For instance, reanalysis of available genomes of Cucurbitaceae species revealed a paleo-tetraploidy predating the divergence of Cucurbitaceae that was overlooked in previous studies [167]. Reinvestigation confirmed that the WGD found in durian (Durio zibethinus) is lineage-specific [168] rather than shared with cotton [169]. Moreover, new WGD events were uncovered based on reanalysis of Selaginella moellendorffii [69] and Aquilaria sinensis [170] genomes respectively. More effort remains necessary to reconfirm reported WGDs and rediscover overlooked WGDs based on high-quality and chromosome-level genomes.

Driven by the rapid development of long-read sequencing technologies (e.g. PacBio HiFi, Nanopore), telomere-to-telomere and gap-free genome assemblies have been produced for some model plants and important crops such as Arabidopsis [[37], [39]], tomato [40], maize [34], rice [[36], [38]] and banana [35]. These highly contiguous genome assemblies provide a valuable opportunity to perform more accurate genome comparisons and synteny analysis, refine the resolution of evolutionary analysis, and recheck ancient WGDs reported in previous studies. Moreover, growing software resources have been developed to infer date and place ancient WGDs across plant phylogeny such as MAPS [85], Whale [171], Beluga [172], wgd [173], WGDI [145], in which synteny-based or phylogenomic-based strategies are implemented. A combination of synteny- and phylogenomic-based methods to correctly identify and verify ancient polyploidy events has an important role in ongoing and upcoming genome sequencing projects.

Several ambitious projects including the Earth BioGenome Project [174], Darwin Tree of Life Project [175], and 10KP [176] have been launched to sequence the genomes of all eukaryotic species on earth, and eventually to document the biodiversity on our planet. Such efforts pose considerable challenges for integrating enormous plant genome data and developing interactive web tools for performing genome comparison and synteny analysis, identifying genome and gene duplications, and visualizing results. Some pioneering databases including Phytozome [177], Ensembl Plants [178], PLAZA [179], CoGe [180], PGDD [181] incorporating genome integration, synteny analysis, WGD inference and comparative genomic analysis tools, have facilitated research in plant genome evolution. Nonetheless, the capacity of current computational tools and storage systems remain limited toward dealing with the huge volumes of 400,000 plant genomes [109]. Apart from well-known databases such as NCBI, EMBL-EBI and DDBJ, some new platforms have been built to provide prompt and convenient access to sequenced plant genomes such as Genome Warehouse [182], CNGBdb (https://db.cngb.org) and Plant GARDEN (https://plantgarden.jp/en/index).

Moving forward, global efforts by the plant science community may substantially reconstruct the genome-level green plant phylogeny based on broader sampling and sequencing of plant diversity, and anchor/position WGDs on different branches along the evolutionary timeline.

CRediT authorship contribution statement

Xin Qiao: Conceptualization, Writing – original draft, Writing – review & editing, Funding acquisition. Shaoling Zhang: Writing – review & editing, Supervision, Funding acquisition. Andrew H. Paterson: Conceptualization, Writing – review & editing, Supervision, Funding acquisition.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.