Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing

Yanxia Sun; Aidi Zhang; Xu Zhang; Jacob B Landis; Huajie Zhang; Xiujun Zhang; Hang Sun; Hengchang Wang

doi:10.1016/j.isci.2023.106159

Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing

iScience. 2023 Feb 8;26(3):106159. doi: 10.1016/j.isci.2023.106159. eCollection 2023 Mar 17.

Authors

Yanxia Sun^{1

2}, Aidi Zhang^{1

3}, Xu Zhang^{1

2}, Jacob B Landis^{4

5}, Huajie Zhang^{1

2}, Xiujun Zhang^{1

3}, Hang Sun⁶, Hengchang Wang^{1

2}

Affiliations

¹ CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
² Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
³ Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
⁴ School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA.
⁵ BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, USA.
⁶ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.

Abstract

Circaeaster agrestis and Kingdonia uniflora are sister species that reproduce sexually and mainly asexually respectively, providing a good system for comparative genome evolution between taxa with different reproductive models. Comparative genome analyses revealed the two species have similar genome size, but C. agrestis encodes many more genes. The gene families specific to C. agrestis show significant enrichment of genes associated with defense response, while those gene families specific to K. uniflora are enriched in genes regulating root system development. Collinearity analyses revealed C. agrestis experienced two rounds of whole-genome duplication. Fst outlier test across 25 C. agrestis populations uncovered a close inter-relationship between abiotic stress and genetic variability. Genetic feature comparisons showed K. uniflora presents much higher genome heterozygosity, transposable element load, linkage disequilibrium degree, and π_N/π_S ratio. This study provides new insights into understanding the genetic differentiation and adaptation within ancient lineages characterized by multiple reproductive models.

Keywords: Plant biology; Plant evolution; Plant genetics.