Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae: Insights into the polyploidization of Phlegmariurus

Xia, Zeng-Qiang; Wei, Zuo-Ying; Shen, Hui; Shu, Jiang-Ping; Wang, Ting; Gu, Yu‐Cheng; Jaisi, Amit; Yan, Yue‐Hong

doi:10.1016/j.pld.2021.08.004

Cited by 8 publications

(3 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The combination of high repetition and high heterozygosity reflects the extraordinary genome complexity and results in a fragmented genome assembly (Table 1), which hampers further exploration of the genome structure and the evolution in lycophytes and vascular plants. Using Ks-based and phylogenomic-based methods, we both identified two independent WGD events in the L. clavatum genome, which is consistent with previous studies using transcriptome data (One Thousand Plant Transcriptomes Initiative, 2019; Xia et al, 2022). Furthermore, the least loss and the least gain of gene families in the homosporous lycophyte genome (Figure 2c), are of great significance for studying the evolution of the common ancestor of lycophytes and euphyllophytes.…”

Section: Discussionsupporting

confidence: 88%

The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation

Tang

Wei

et al. 2022

Preprint

View full text Add to dashboard Cite

Lycophytes and euphyllophytes (ferns and seed plants) are the two surviving lineages of vascular plants. The modern lycophytes (clubmosses) are herbaceous found either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). The contrasting genome size between homosporous and heterosporous plants has long been an attractive topic. Most clubmosses are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimer's disease, but the evolutionary trajectory of which in land plants is unexplored. To better understand these fundamental questions, the genome data of a homosporous lycophyte is urgently required. We generated the Lycopodium clavatum L. genome by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is LTR. Two whole genome duplications (WGDs) are rigorously detected. The content of LTR-RTs was more than ten times higher in homosporous lycophytes than heterosporous ones, although most appeared within one Mya. Then, we find that the LTR-RTs' birth-death mode (a much greater birth and extremely slower death) contributes the accumulation of LTR-RTs resulting homosporous lycophyte genome expansion, while in heterosporous lycophytes, the mode is exactly the opposite. Furthermore, the five necessary enzymes of the HupA biosynthetic pathway were identified in the L. clavatum genome, but absent in the other land plants. This decoded genome data will be a key cornerstone to elucidating the fundamental aspects of lycophyte biology and land plant evolution.

show abstract

Section: Discussionsupporting

confidence: 88%

The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation

Tang

Wei

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…This coincides well with the previous estimate for the D event (20.6–24.2 Ma) based on whole-genome sequence data ( Feng et al 2020 ). WGDs in other plant families are reported to have occurred around the Oligocene–Miocene boundary, including in Asteraceae ( Huang et al 2016 ), Cucurbitaceae ( Guo et al 2020 ), Poaceae ( Guo et al 2019 ), Fabaceae ( Zhao et al 2021 ), and others ( Ren et al 2018 ; Cai et al 2019 ; Xia et al 2022 ). Together, these results suggest that the Oligocene–Miocene boundary was likely an important geological age associated with WGD events in plants.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation

et al. 2023

View full text Add to dashboard Cite

Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.

show abstract

“…Polyploidy, or whole genome duplication, is pervasive in eukaryotes ( Van De Peer et al., 2017 ). It is especially common in plants ( Wood et al., 2009 ), and ancient polyploidization has occurred in most lineages of land plants including mosses ( Gao et al., 2022 ), lycophytes ( Xia et al., 2022 ; Li et al., 2023 ), ferns ( Huang et al., 2020 ; Pelosi et al., 2022 ; Chen et al., 2023 ), gymnosperms ( Li et al., 2015 ), and angiosperms (e.g. Landis et al., 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales)

Katayama,

Yamamoto,

Aiuchi

et al. 2024

Front. Plant Sci.

View full text Add to dashboard Cite

Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern—Phegopteris decursivepinnata—and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.

show abstract

Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae: Insights into the polyploidization of Phlegmariurus

Cited by 8 publications

References 47 publications

The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation

The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation

Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation

Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales)

Contact Info

Product

Resources

About