Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes

Honghe Sun; Shan Wu; Guoyu Zhang; Chen Jiao; Shaogui Guo; Yi Ren; Jie Zhang; Haiying Zhang; Guoyi Gong; Zhangcai Jia; Fan Zhang; Jiaxing Tian; William J Lucas; Jeff J Doyle; Haizhen Li; Zhangjun Fei; Yong Xu

doi:10.1016/j.molp.2017.09.003

Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes

Mol Plant. 2017 Oct 9;10(10):1293-1306. doi: 10.1016/j.molp.2017.09.003. Epub 2017 Sep 14.

Authors

Honghe Sun¹, Shan Wu², Guoyu Zhang³, Chen Jiao⁴, Shaogui Guo³, Yi Ren³, Jie Zhang³, Haiying Zhang³, Guoyi Gong³, Zhangcai Jia³, Fan Zhang³, Jiaxing Tian³, William J Lucas⁵, Jeff J Doyle⁶, Haizhen Li³, Zhangjun Fei⁷, Yong Xu⁸

Affiliations

¹ National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China; Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.
² Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA. Electronic address: sw728@cornell.edu.
³ National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.
⁴ Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.
⁵ Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
⁶ Section of Plant Breeding & Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
⁷ Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA; USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA. Electronic address: zf25@cornell.edu.
⁸ National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China. Electronic address: xuyong@nercv.org.

PMID: 28917590
DOI: 10.1016/j.molp.2017.09.003

Abstract

The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima × C. moschata interspecific F₁ hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops.

Keywords: Cucurbita maxima; Cucurbita moschata; allele-specific expression; karyotype stability; paleo-allotetraploid; unbiased fractionation.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosomal Instability*
Chromosomes, Plant*
Cucurbita / genetics*
Evolution, Molecular*
Genome, Plant*
Karyotype*
Sequence Analysis, DNA
Tetraploidy*