Genome projects

Because of our unique and long-standing expertise in gene prediction and genome annotation, as well as our expertise in documenting ancient whole genome duplication events, our lab has been (and still is) involved in many international genome projects. For instance, some of the genome projects we has been heavily involved in were those of the poplar tree Populus trichocarpa (published in Science), the grape Vitis vinifera (PLoS One), Arabidopsis lyrata (Nature Genetics), the apple tree Malus domestica (Nature Genetics), Eucalyptus grandis (Nature), Solanum lycopersicum (Nature), the orchid Phalaenopsis equestris (Nature Genetics), the orchid Apostasia shenzhenica (Nature), the seagrass Zostera marina (Nature), the olive tree Olea europaea var. sylvestris (PNAS), Nymphaea colorata (Nature), the moss Physcomitrella patens (Science), the fungi Laccaria bicolor (Nature) and Pichia pastoris (Nature Biotechnology), the unicellular algae Ostreococcus spp. (PNAS) and Micromonas spp. (Science), the multicellular sea lettuce Ulva mutabilis (Current Biology), the diatom Phaeodactylum tricornutum (Nature), the brown alga Ectocarpus siliculosus (Nature), and the spider mite Tetranychus urticae (Nature). Currently, we are involved in analyzing the genomes of many more plant species, amongst which several orchids, but also other ornamental plants. We are also currently involved in the annotation of several of the African Orphan Crop genomes.

Selected Publications:

Tao, Wan, Zhiming, Liu, Ilia J. Leitch, Haiping, Xin, Gillian Maggs-Kölling, Yanbing, Gong, Zhen Li, et al. 2021. “The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts.” Nature Communications, July.

You-Long, Cao, Yan-long, Li, Yun-Fang, Fan, Zhen, Li, et al. 2021. “Wolfberry genomes and the evolution of Lycium (Solanaceae).” Communications Biology, June.

Xuewen, Wang, Shiyu, Chen, Xiao, Ma, Anna E J Yssel, et al. 2021. “Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis).” GigaScience , March.

Fu-Sheng, Yang, Shuai, Nie, Hui, Liu, Tian-Le, Shi, Xue-Chan, Tian, Shan-Shan, Zhou, et al. 2020. “Chromosome-level genome assembly of a parent species of widely cultivated azaleas.” Nature Communications, October.

Linzhou, Li, Sibo, Wang, Hongli, Wang, Sunil Kumar Sahu, Birger Marin, Haoyuan, Li, Yan, Xu, Hongping, Liang, Zhen, Li, et al. 2020. “The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.” Nature Ecology & Evolution, June.

Zhang, Jian, Xin-Xing Fu, Rui-Qi Li, Xiang Zhao, Yang Liu, Ming-He Li, Arthur Zwaenepoel, et al. 2020. “The Hornwort Genome and Early Land Plant Evolution.” Nature Plants, February.

Zhang, Liangsheng, Fei Chen, Xingtan Zhang, Zhen Li, Yiyong Zhao, Rolf Lohaus, Xiaojun Chang, et al. 2020. “The Water Lily Genome and the Early Evolution of Flowering Plants.” Nature 577 (7788): 79–84.

Wan, Tao, Zhi-Ming Liu, Ling-Fei Li, Andrew R. Leitch, Ilia J. Leitch, Rolf Lohaus, Zhong-Jian Liu, et al. 2018. “A Genome for Gnetophytes and Early Evolution of Seed Plants.” Nature Plants 4 (2): 82–89.

Zhang, Guo-Qiang, Ke-Wei Liu, Zhen Li, Rolf Lohaus, Yu-Yun Hsiao, Shan-Ce Niu, Jie-Yu Wang, et al. 2017. “The Apostasia Genome and the Evolution of Orchids.” Nature 549 (7672): 379–83.

Unver, Turgay, Zhangyan Wu, Lieven Sterck, Mine Turktas, Rolf Lohaus, Zhen Li, Ming Yang, et al. 2017. “Genome of Wild Olive and the Evolution of Oil Biosynthesis.” Proceedings of the National Academy of Sciences 114 (44): E9413–22.