文献类型：期刊文献

英文题名：Chromosome-scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana

作者：Zhang, Yong[1] Wei, Yongcheng[1] Meng, Jingxiang[1] Wang, Yujiao[1] Nie, Sen[2] Zhang, Zeyu[3] Wang, Huiyuan[3] Yang, Yongkang[3] Gao, Yubang[3] Wu, Ji[3] Li, Tuhe[3] Liu, Xuqing[3] Zhang, Hangxiao[3] Gu, Lianfeng[3]

第一作者：张勇

通信作者：Gu, LF[1]

机构：[1]Chinese Acad Forestry, Res Inst Trop Forestry, Guangzhou 510520, Peoples R China;[2]Fujian Acad Forestry Sci, Fuzhou 350012, Fujian, Peoples R China;[3]Fujian Agr & Forestry Univ, Coll Forestry, Basic Forestry & Prote Res Ctr, Fuzhou 350002, Peoples R China

年份：0

外文期刊名：PLANT JOURNAL

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000964640500001)】；

基金：This work was supported by the National Natural Science Foundation of China (grant no. 31770716), the Fujian Forest Seedling Technology Project of Casuarina, and the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University (72202200205).

语种：英文

外文关键词：Casuarina; whole-genome assembly; chromosome conformation capture technology; PacBio single-molecular long-read technology (SMRT) sequencing; whole-genome bisulfite sequencing

摘要：Australian pine (Casuarina spp.) is extensively planted in tropical and subtropical regions for wood production, shelterbelts, environmental protection, and ecological restoration due to their superior biological characteristics, such as rapid growth, wind and salt tolerance, and nitrogen fixation. To analyze the genomic diversity of Casuarina, we sequenced the genomes and constructed de novo genome assemblies of the three most widely planted Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. We generated chromosome-scale genome sequences using both Pacific Biosciences (PacBio) Sequel sequencing and chromosome conformation capture technology (Hi-C). The total genome sizes for C. equisetifolia, C. glauca, and C. cunninghamiana are 268 942 579 bp, 296 631 783 bp, and 293 483 606 bp, respectively, of which 25.91, 27.15, and 27.74% were annotated as repetitive sequences. We annotated 23 162, 24 673, and 24 674 protein-coding genes in C. equisetifolia, C. glauca, and C. cunninghamiana, respectively. We then collected branchlets from male and female individuals for whole-genome bisulfite sequencing (BS-seq) to explore the epigenetic regulation of sex determination in these three species. Transcriptome sequencing (RNA-seq) revealed differential expression of phytohormone-related genes between male and female plants. In summary, we generated three chromosome-level genome assemblies and comprehensive DNA methylation and transcriptome datasets from both male and female material for three Casuarina species, providing a basis for the comprehensive investigation of genomic diversity and functional gene discovery of Casuarina in the future.