The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition

Authors: HUANG, YOUJUN - Zhejiang A & F University; XIAO, LIHONG - Zhejiang A & F University; ZHANG, ZHONGREN - Novogene Bioinformatics Institue; ZHANG, RUI - Zhejiang A & F University; WANG, ZHENGJIA - Zhejiang A & F University; HUANG, CHUNYING - Zhejiang A & F University; HUANG, REN - Zhejiang A & F University; LUAN, YUMENG - Zhejiang A & F University; FAN, TONGQIANG - Zhejiang A & F University; WANG, JIANHUA - Zhejiang A & F University; SHEN, CHEN - Zhejiang A & F University; ZHANG, SHENMEI - Zhejiang A & F University; Wang, Xinwang; RANDALL, JENNIFER - New Mexico State University; ZHENG, BINGSONG - Zhejiang A & F University; WU, JIASHENG - Zhejiang A & F University; ZHANG, QIXIANG - Zhejiang A & F University; XIA, GUOHUA - Zhejiang A & F University; XU, CHUANMEI - Zhejiang A & F University; CHEN, MING - Zhejiang University; ZHANG, LIANGSHENG - Fujian Agriculture And Forest University; JIANG, WENKAI - Novogene Bioinformatics Institue; GAO, LIZHI - Chinese Academy Of Sciences; CHEN, ZHIDUAN - Chinese Academy Of Sciences; LESLIE, CHARLES - University Of California, Davis; Grauke, Larry; HUANG, JIANQIN - Zhejiang A & F University

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2019
Publication Date: 5/1/2019
Citation: Huang, Y., Xiao, L., Zhang, Z., Zhang, R., Wang, Z., Huang, C., Huang, R., Luan, Y., Fan, T., Wang, J., Shen, C., Zhang, S., Wang, X., Randall, J., Zheng, B., Wu, J., Zhang, Q., Xia, G., Xu, C., Chen, M., Zhang, L., Jiang, W., Gao, L., Chen, Z., Leslie, C.A., Grauke, L.J., Huang, J. 2019. The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. Gigascience. 8(5):giz036. https://doi.org/10.1093/gigascience/giz036.
DOI: https://doi.org/10.1093/gigascience/giz036

Interpretive Summary: This work focused on two important commercial nut tree species in the walnut family (Juglandaceae): pecan (Carya illinoinensis) and Chinese hickory (Carya cathayensis). The family and genus have been the focus of recent publications addressing the development of these species in the distant past that have integrated interpretation of modern species distributions using fossil flora. This work provided information relevant to those perspectives, but adds value by providing a firm genomic foundation for continued crop improvement through breeding based on understanding adaptation and promoting improved nutrition. This research is grounded in the study of cooperatively developed germplasm collections being actively used in breeding. It will contribute motivation to conserve and maintain endangered species within this genus as it provides the tools for future crop improvement. Local adaptations promote local use and are the foundations of sustainability and food security.

Technical Abstract: Pecan (Carya illinoinensis) and Chinese hickory (C. cathayensis) are important commercially cultivated nut trees in Carya (Juglandaceae), with high nutritional value and significant health benefits. Here we obtained more than 178 Gb and 191 Gb sequences, ~248x and 288x genome coverage, to a pecan cultivar ('Pawnee') and a domesticated Chinese hickory landrace (ZAFU-1). The total assembly is 651.31 Mb for pecan and 706.43 for Chinese hickory, representing 97% or 101% of their estimated genome size. Two genome duplication events before divergence from walnut were found in these species. Gene family expansion analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids and B vitamins accumulation. Analysis of reduced-coverage genome sequences of 17 Carya and 2 Juglans species provides additional phylogenetic perspective on crop wild relatives. Cooperative characterization of these valuable resources provides a window to their evolutionary development, and a valuable foundation for future crop improvement.