Whole genome duplication in coast redwood (<i>Sequoia sempervirens</i>) and its implications for explaining the rarity of polyploidy in conifers

Scott, Alison Dawn; Stenz, Noah; Ingvarsson, Pär K.; Baum, David A.

doi:10.1111/nph.13930

Cited by 52 publications

(63 citation statements)

References 65 publications

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“…Our evidence supports two WGDs in ginkgo, with an ancient WGD occurring 515 to 735 mya, consistent with previous reports [46–48, 60, 61], and a more recent event reported for the first time in this study and not yet observed in other seed plants [46]. This recent WGD may have uniquely contributed to the morphological and biological diversity of the gingko lineage.…”

Section: Discussionsupporting

confidence: 91%

Draft genome of the living fossil Ginkgo biloba

Guan

Zhao

Zhang

et al. 2016

GigaSci

234

222

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Background Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution.FindingsThe 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways.ConclusionsThe ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-016-0154-1) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 91%

Draft genome of the living fossil Ginkgo biloba

Guan

Zhao

Zhang

et al. 2016

GigaSci

234

222

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“…For example, Adansonia digitata is a recent tetraploid (Baum and Oginuma ), but no recent peak is observed. One possibility is that this was an autotetraploidy event that occurred recently enough that tetrasomic inheritance is still in effect, which could prevent paralogs diverging enough to result in two separate gene models during transcriptome assembly (Scott et al ).…”

Section: Discussionmentioning

confidence: 99%

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Conover

Karimi

Stenz

et al. 2019

JIPB

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Previous research suggests that Gossypium has undergone a 5‐ to 6‐fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae‐Bombacoideae and Sterculioideae‐Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae‐Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

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“…Therefore, the absence of biased fractionation should not be considered informative when attempting to differentiate ancient allopolyploidy from ancient autopolyploidy. Autopolyploidy has also been inferred through coalescent modeling in Capsella bursa‐pastoris (St. Onge et al, ) and through phylogenetic analysis of orthologous transcripts in the conifer Sequoia sempervirens (Scott et al, ). Unfortunately, extensive genomic rearrangements after WGD, as well as more recent WGDs, can obscure the nature of an ancient WGD to a point where multiple lines of evidence either cannot resolve an auto‐ or allopolyploid origin or produce conflicting results (e.g., Chaintreuil et al, ).…”

Section: Ancient Autopolyploidymentioning

confidence: 99%

Pure polyploidy: Closing the gaps in autopolyploid research

Spoelhof

Soltis

2017

J of Sytematics Evolution

156

129

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Polyploidy (whole-genome duplication, WGD) is an integral feature of eukaryotic evolution with two main forms typically recognized, autopolyploidy and allopolyploidy. In plants, a growing body of research contradicts historical assumptions that autopolyploidy is both infrequent and inconsequential in comparison to allopolyploidy. However, the legacy of these assumptions still persists through a lack of research on central facets of autopolyploid evolution. This review highlights recent research that has significantly increased scientific understanding of autopolyploidy. Key advances include: 1) unreduced female gametes contribute disproportionally to polyploidization through the formation of triploids, 2) niche divergence in autopolyploids can occur immediately or gradually after WGD through a diverse set of mechanisms, but broad niche overlap is also common between diploids and autopolyploids, and 3) the degree of genomic and transcriptomic changes following WGD is lower in autopolyploids than allopolyploids, but is highly variable both within and between species in both types of polyploids. We discuss the implications of these and other recent findings, present promising systems for future research, and advocate for expanded research in diverse areas of autopolyploid evolution.

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Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers

Cited by 52 publications

References 65 publications

Draft genome of the living fossil Ginkgo biloba

Draft genome of the living fossil Ginkgo biloba

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Pure polyploidy: Closing the gaps in autopolyploid research

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