Hengchi Chen

Hengchi Chen — PhD student
Joined the group in 2020

My research interests focus on the ecological and evolutionary significance of polyploid (as well as Whole Genome Duplicaiton, WGD). There is a large body of literatures depicting the funtional and evolutionary innovation&potential conferred by WGD, while some report that WGD could be detrimental and deadly. The debate of the ecological and evolutionary significance of polyploid suggests that the consequence of being a polyploid is largely depending on the ecological condition where the polyploid is inhabiting and coping with. Recent studies show that there is a nonrandom pattern of WGD occurance across the evolutionary timeline of diverse species, for example a recent research elucidates that a wave of successful genome duplications is associated with the Cretaceous–Paleogene boundary in the analysis of 41 plant genomes. The association between WGD and massive extinction events (glaciation events etc, as well) provides strong evidence that WGD is an important evolutionary force for survival and success especially in extreme environment. For now, the confirmed association reported in literatures is quite limited in taxa sampling and reliability. I'm trying to build a reliable WGD dating system to explore connections between WGD and massive extinction events in more lineages(mainly angiosperms). The commonness of WGD accumulating around the boundary of massive extinction events across the tree of life would be a powerful argument for the selective advantage of WGD in harsh environment.

Ghent Unversity
Sep. 2020 - present PhD student, Bioinformatics & Evolutionary Genomics, Department of Plant Systems Biology, VIB, Gent, Belgium
Fudan University
Sep. 2016 - Jun. 2020 B.S. of Ecology, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, China

Publications

  1. Chen, H., Zwaenepoel, A., & Van de Peer, Y. (2024). wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication. Bioinformatics. https://doi.org/10.1093/bioinformatics/btae272
    Motivation Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant. Results Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to a) construct KS age distributions for the whole-paranome (collection of all duplicated genes in a genome), b) unravel intra- and inter- genomic collinearity resulting from WGDs, c) fit mixture models to age distributions of gene duplicates, d) correct substitution rate variation for phylogenetic placement of WGDs, and e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes.
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  2. Chen, H., Fang, Y., Zwaenepoel, A., Huang, S., Van de Peer, Y., & Li, Z. (2023). Revisiting ancient polyploidy in leptosporangiate ferns. NEW PHYTOLOGIST, 237(4), 1405–1417. https://doi.org/10.1111/nph.18607
    Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building KS-age distributions and applying substitution rate corrections, and by conducting statistical gene tree – species tree reconciliation analyses. Our integrative analyses confidently identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree – species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.
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  3. Chen, H., & Zwaenepoel, A. (2023). Inference of ancient polyploidy from genomic data. In Y. Van de Peer (Ed.), Polyploidy : methods and protocols (Vol. 2545, pp. 3–18). https://doi.org/10.1007/978-1-0716-2561-3_1
    Whole-genome sequence data have revealed that numerous eukaryotic organisms derive from distant polyploid ancestors, even when these same organisms are genetically and karyotypically diploid. Such ancient whole-genome duplications (WGDs) have been important for long-term genome evolution and are often speculatively associated with important evolutionary events such as key innovations, adaptive radiations, or survival after mass extinctions. Clearly, reliable methods for unveiling ancient WGDs are key toward furthering understanding of the long-term evolutionary significance of polyploidy. In this chapter, we describe a set of basic established comparative genomics approaches for the inference of ancient WGDs from genomic data based on empirical age distributions and collinearity analyses, explain the principles on which they are based, and illustrate a basic workflow using the software “wgd,” geared toward a typical exploratory analysis of a newly obtained genome sequence.
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  4. Fang, Y., Qin, X., Liao, Q., Du, R., Luo, X., Zhou, Q., … Yan, J. (2022). The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences. NATURE PLANTS, 8(9), 1024–1037. https://doi.org/10.1038/s41477-022-01222-x
    Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.
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