Browse Articles

Article|13 Dec 2023|OPEN
A telomere-to-telomere reference genome of ficus (Ficus hispida) provides new insights into sex determination 
Zhenyang Liao1 , , Tianwen Zhang2,3 , Wenlong Lei1 , Yibin Wang1 , Jiaxin Yu1 , Yinghao Wang1 , Kun Chai1 , Gang Wang2 and Huahao Zhang4 , Xingtan Zhang,1 ,
1Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
2CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
3College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
4College of Pharmacy and Life Science, Jiujiang University, Jiujiang 332005, China
*Corresponding author. E-mail: zhenyangliao@126.com,zhangxingtan@caas.cn

Horticulture Research 11,
Article number: uhad257 (2024)
doi: https://doi.org/10.1093/hr/uhad257
Views: 29

Received: 10 May 2023
Accepted: 20 Nov 2023
Published online: 13 Dec 2023

Abstract

A high-quality reference genome is indispensable for resolving biologically essential traits. Ficus hispida is a dioecious plant. A complete Ficus reference genome will be crucial for understanding their sex evolution and important biological characteristics, such as aerial roots, mutualistic symbiosis with ficus-wasps, and fruiting from old stems. Here, we generated a telomere-to-telomere (T2T) genome for F. hispida using PacBio HiFi and Oxford Nanopore Ultra-long sequencing technologies. The genome contiguity and completeness has shown improvement compared with the previously released genome, with the annotation of six centromeres and 28 telomeres. We have refined our previously reported 2-Mb male-specific region into a 7.2-Mb genomic region containing 51 newly predicted genes and candidate sex-determination genes AG2 and AG3. Many of these genes showed extremely low expression, likely attributed to hypermethylation in the gene body and promoter regions. Gene regulatory networks (GRNs) revealed that AG2 and AG3 are related to the regulation of stamen development in male flowers, while the AG1 gene is responsible for regulating female flowers’ defense responses and secondary metabolite processes. Comparative analysis of GRNs showed that the NAC, WRKY, and MYB transcription factor families dominate the female GRN, whereas the MADS and MYB transcription factor families are prevalent in the male GRN.