日本雪松(Cryptomeria japonica D. Don.)模式针叶植物染色体级基因组组装。

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY BMC Genomics Pub Date : 2024-11-05 DOI:10.1186/s12864-024-10929-4
Takeshi Fujino, Katsushi Yamaguchi, Toshiyuki T Yokoyama, Toshiya Hamanaka, Yoritaka Harazono, Hiroaki Kamada, Wataru Kobayashi, Tokuko Ujino-Ihara, Kentaro Uchiyama, Asako Matsumoto, Ayako Izuno, Yoshihiko Tsumura, Atsushi Toyoda, Shuji Shigenobu, Yoshinari Moriguchi, Saneyoshi Ueno, Masahiro Kasahara
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引用次数: 0

摘要

背景:日本雪松(Cryptomeria japonica D. Don)是日本最重要的林木之一,约占人工林的 44%,种植于东亚、亚速尔群岛和印度洋的一些岛屿。虽然该物种基因组庞大(约 9 Gbp),重复元件丰富,可能会成为遗传分析的障碍,但该物种很容易通过切割繁殖、赤霉素催花、农杆菌转化和 CRISPR/Cas9 编辑。C. japonica 的这些特点建议将其作为需要参考基因组序列的针叶树模式物种:在此,我们报告了利用第三代自交后代(估计同源性为 0.96)进行的首次 C. japonica(2n = 22)染色体组组装。利用幼叶组织提取高分子量 DNA(> 50 kb)用于 HiFi PacBio 长读程测序,并构建 Hi-C/Omni-C 文库用于 Illumina 短读程测序。用于从头组装的 HiFi 和 Illumina 读数的基因组覆盖率分别为 29 倍和 26 倍,共产生 2,651 个等位基因(9.1 Gbp,N50 等位基因大小为 12.0 Mbp)。Hi-C 分析映射了 11 条染色体上 97% 的核苷酸。通过与由 7781 个标记组成的共识连接图进行比较,对组装结果进行了验证。BUSCO 分析确定了 91% 的保守基因:基因的注释以及与其他濯缨科和松科物种重复元素的比较为针叶树研究提供了基础资源。
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A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don.

Background: The Japanese cedar (Cryptomeria japonica D. Don) is one of the most important Japanese forest trees, occupying approximately 44% of artificial forests and planted in East Asia, the Azores Archipelago, and certain islands in the Indian Ocean. Although the huge genome of the species (ca. 9 Gbp) with abundant repeat elements may have represented an obstacle for genetic analysis, this species is easily propagated by cutting, flowered by gibberellic acid, transformed by Agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica recommend it as a model conifer species for which reference genome sequences are necessary.

Results: Herein, we report the first chromosome-level assembly of C. japonica (2n = 22) using third-generation selfed progeny (estimated homozygosity rate = 0.96). Young leaf tissue was used to extract high molecular weight DNA (> 50 kb) for HiFi PacBio long-read sequencing and to construct an Hi-C/Omni-C library for Illumina short-read sequencing. The 29× and 26× genome coverage of HiFi and Illumina reads, respectively, for de novo assembly yielded 2,651 contigs (9.1 Gbp, N50 contig size 12.0 Mbp). Hi-C analysis mapped 97% of the nucleotides on 11 chromosomes. The assembly was verified through comparison with a consensus linkage map comprising 7,781 markers. BUSCO analysis identified ∼ 91% conserved genes.

Conclusions: Annotations of genes and comparisons of repeat elements with other Cupressaceae and Pinaceae species provide a fundamental resource for conifer research.

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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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