The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A & F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Sci Rep. 2020 Mar 13;10(1):4698. doi: 10.1038/s41598-020-61611-0.
Chinese fir (Cunninghamia lanceolata) is an important coniferous species that accounts for 20-30% of the total commercial timber production in China. Though traditional breeding of Chinese fir has achieved remarkable success, molecular-assisted breeding has made little progress due to limited availability of genomic information. In this study, a survey of Chinese fir genome was performed using the Illumina HiSeq Xten sequencing platform. K-mer analysis indicated that Chinese fir has a large genome of approximately 11.6 Gb with 74.89% repetitive elements and is highly heterozygous. Meanwhile, its genome size was estimated to be 13.2 Gb using flow cytometry. A total of 778.02 Gb clean reads were assembled into 10,982,272 scaffolds with an N50 of 1.57 kb. In total, 362,193 SSR loci were detected with a frequency of 13.18 kb. Dinucleotide repeats were the most abundant (up to 73.6% of the total SSRs), followed by trinucleotide and tetranucleotide repeats. Forty-six polymorphic pairs were developed, and 298 alleles were successfully amplified from 199 Chinese fir clones. The average PIC value was 0.53, indicating that the identified genomic SSR (gSSR) markers have a high degree of polymorphism. In addition, these breeding resources were divided into three groups, and a limited gene flow existed among these inferred groups.
杉木（Cunninghamia lanceolata）是一种重要的针叶树种，约占中国商业木材总产量的 20-30%。尽管传统的杉木育种已经取得了显著的成功，但由于基因组信息有限，分子辅助育种进展甚微。本研究采用 Illumina HiSeq Xten 测序平台对杉木基因组进行了调查。K-mer 分析表明，杉木基因组约为 11.6Gb，其中 74.89%为重复序列，高度杂合。同时，利用流式细胞术估计其基因组大小为 13.2Gb。共组装了 778.02Gb 的清洁读取序列，形成了 10,982,272 个 N50 为 1.57kb 的支架。共检测到 362,193 个 SSR 位点，其分布频率为 13.18kb。二核苷酸重复序列最为丰富（占总 SSR 的 73.6%），其次是三核苷酸和四核苷酸重复序列。开发了 46 对多态性引物，从 199 个杉木无性系中成功扩增出 298 个等位基因。平均 PIC 值为 0.53，表明鉴定的基因组 SSR（gSSR）标记具有高度多态性。此外，这些育种资源被分为三组，推断的这些组之间存在有限的基因流。
