Jiyang Chang

Jiyang Chang — PhD student
Joined the group in 2020

The expanding world population poses a great challenge on sustainable global food supply and nutrition demands. Out of an estimated 50,000 edible plant species, only a small portion has been selected as major crops for commercial cultivation. To diversify and stabilize the global food supply, minor crops (also known as orphan crops, as these crops are neglected or underutilized by the international research community) could be a partial solution. Furthermore, these minor crops not only play an important role in providing food and nutrition to a large number of people, but also are a treasure of genetic resources as well. With the advent of third generation sequencing technology, Thanks to the rapid development of sequencing technologies, many orphan crops have already been sequenced, such as Faidherbia albida, Moringa oleifera, Sclerocarya birrea, Lablab purpureus, Vigna radiate, Solanum aethiopicum, and others. However, there are still many important orphan crops waiting to get sequenced and studied. My research is focused on these valuable orphan crops and uses state-of-the-art technologies to get the assembly and annotation of these species’ genomes, trying to further broaden our understanding of the evolutionary history of these orphan crops and crop genomics.

Ghent Unversity
September 2020 - present: PhD student, Bioinformatics & Evolutionary Genomics, Department of Plant Systems Biology, VIB, Gent, Belgium.
Annoroad Gene Technology
July 2017 - May 2019: Bioinformatician, the key Responsibilities is genome assembly and annotation.
Institute of Botany, Chinese Academy of Sciences
September 2014 - July 2017: Master of Science in Developmental Biology, The Key Laboratory of Photobiology, CAS.

Publications

  1. Ma, X., Vanneste, S., Chang, J., Ambrosino, L., Barry, K., Bayer, T., … Van de Peer, Y. (2024). Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment. NATURE PLANTS, 10, 240–255. https://doi.org/10.1038/s41477-023-01608-5
    We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.
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  2. Kersten, S., Chang, J., Huber, C. D., Voichek, Y., Lanz, C., Hagmaier, T., … Rabanal, F. A. (2023). Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 120(16). https://doi.org/10.1073/pnas.2206808120
    Repeated herbicide applications in agricultural fields exert strong selection on weeds such as blackgrass (Alopecurus myosuroides), which is a major threat for temperate climate cereal crops. This inadvertent selection pressure provides an opportunity for investigating the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much target-site resistance (TSR) relies on de novo mutations vs. standing variation is important for developing strategies to manage herbicide resistance. We first generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Next, through empirical data in the form of highly accurate long-read amplicons of alleles encoding acetyl-CoA carboxylase (ACCase) and acetolactate synthase (ALS) variants, we showed that most populations with resistance due to TSR mutations-23 out of 27 and six out of nine populations for ACCase and ALS, respectively-contained at least two TSR haplotypes, indicating that soft sweeps are the norm. Finally, through forward-in-time simulations, we inferred that TSR is likely to mainly result from standing genetic variation, with only a minor role for de novo mutations.
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  3. Chang, J., Duong, T. A., Schoeman, C., Ma, X., Roodt, D., Barker, N., … Mizrachi, E. (2023). The genome of the king protea, Protea cynaroides. PLANT JOURNAL, 113(2), 262–276. https://doi.org/10.1111/tpj.16044
    The king protea (Protea cynaroides), an early-diverging eudicot, is the most iconic species from the Megadiverse Cape Floristic Region, and the national flower of South Africa. Perhaps best known for its iconic flower head, Protea is a key genus for the South African horticulture industry and cut-flower market. Ecologically, the genus and the family Proteaceae are important models for radiation and adaptation, particularly to soils with limited phosphorus bio-availability. Here, we present a high-quality chromosome-scale assembly of the P. cynaroides genome as the first representative of the Fynbos biome. We reveal an ancestral Whole-Genome Duplication (WGD) event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family and its extant diversity in all Southern continents. The relatively stable genome structure of P. cynaroides is invaluable for comparative studies and for unveiling paleopolyploidy in other groups, such as the distantly related sister group Ranunculales. Comparative genomics in sequenced genomes of the Proteales shows loss of key arbuscular mycorrhizal symbiosis genes likely ancestral to the Family, and possibly the Order. The P. cynaroides genome empowers new research in plant diversification, horticulture, and adaptation, particularly to nutrient-poor soils.
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  4. Catania, T., Li, Y., Winzer, T., Harvey, D., Meade, F., Caridi, A., … Graham, I. A. (2022). A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago. NATURE COMMUNICATIONS, 13(1). https://doi.org/10.1038/s41467-022-30856-w
    The STORR gene fusion event is considered essential for the evolution of the promorphinan/morphinan subclass of benzylisoquinoline alkaloids (BIAs) in opium poppy as the resulting bi-modular protein performs the isomerization of (S)- to (R)-reticuline essential for their biosynthesis. Here, we show that of the 12 Papaver species analysed those containing the STORR gene fusion also contain promorphinans/morphinans with one important exception. P. californicum encodes a functionally conserved STORR but does not produce promorphinans/morphinans. We also show that the gene fusion event occurred only once, between 16.8-24.1 million years ago before the separation of P. californicum from other Clade 2 Papaver species. The most abundant BIA in P. californicum is (R)-glaucine, a member of the aporphine subclass of BIAs, raising the possibility that STORR, once evolved, contributes to the biosynthesis of more than just the promorphinan/morphinan subclass of BIAs in the Papaveraceae. The STORR gene fusion event is a key step in the evolution of benzylisoquinoline alkaloid metabolism in opium poppy. Here, the authors combine phylogenetic, transcriptomic, metabolomic, biochemical and genomic analyses to show the STORR gene fusion occurred only once between 16.8-24.1 million years ago in Papaver species.
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  5. Chang, J., Marczuk‐Rojas, J. P., Waterman, C., Garcia‐Llanos, A., Chen, S., Ma, X., … Carretero‐Paulet, L. (2022). Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication. PLANT GENOME, 15(3). https://doi.org/10.1002/tpg2.20238
    The African Orphan Crops Consortium (AOCC) selected the highly nutritious, fast growing and drought tolerant tree crop moringa (Moringa oleifera Lam.) as one of the first of 101 plant species to have its genome sequenced and a first draft assembly was published in 2019. Given the extensive uses and culture of moringa, often referred to as the multipurpose tree, we generated a significantly improved new version of the genome based on long-read sequencing into 14 pseudochromosomes equivalent to n = 14 haploid chromosomes. We leveraged this nearly complete version of the moringa genome to investigate main drivers of gene family and genome evolution that may be at the origin of relevant biological innovations including agronomical favorable traits. Our results reveal that moringa has not undergone any additional whole-genome duplication (WGD) or polyploidy event beyond the gamma WGD shared by all core eudicots. Moringa duplicates retained following that ancient gamma events are also enriched for functions commonly considered as dosage balance sensitive. Furthermore, tandem duplications seem to have played a prominent role in the evolution of specific secondary metabolism pathways including those involved in the biosynthesis of bioactive glucosinolate, flavonoid, and alkaloid compounds as well as of defense response pathways and might, at least partially, explain the outstanding phenotypic plasticity attributed to this species. This study provides a genetic roadmap to guide future breeding programs in moringa, especially those aimed at improving secondary metabolism related traits.
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