Genome Survey Analysis in Ixora chinensis

doi:10.3969/j.issn.1009-7791.2024.03.004

Subtropical Plant Science ›› 2024, Vol. 53 ›› Issue (3): 214-219.DOI: 10.3969/j.issn.1009-7791.2024.03.004

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Genome Survey Analysis in Ixora chinensis

TU Shao-qiang, KE Ling-jun, CAI Yue-qin, LU Luan-mei, YU Hui-wen^*

(School of Biological Science and Biotechnology / Key Laboratory of Landscape Plants with Fujian and Taiwan Characteristics of Fujian Colleges, Minnan Normal University, Zhangzhou 363000, Fujian China)

Received:2024-05-05 Accepted:2024-05-25 Online:2024-06-30 Published:2024-08-23
Contact: YU Hui-wen

中国龙船花基因组Survey分析

涂绍强，柯玲俊，蔡月琴，陆銮眉，余惠文^*

(闽南师范大学生物科学与技术学院 / 闽台特色园林植物福建省高校重点实验室，福建漳州 363000)

通讯作者: 余惠文
基金资助:
福建省高校产学合作项目(2022N5019)；福建省林业科技推广项目(2023TG19)

Abstract

Abstract: Ixora chinensis is a traditional Chinese medicinal herb with both medicinal and ornamental values. The analysis of the genomic characteristics of I. chinensis can lay a theoretical basis for sequencing the whole genome and elucidating the molecular mechanism of biosynthesis of medicinal components. The genomic information of I. chinensis was evaluated by using Survey genome sequencing technology and K-mer analysis to obtain information on genomic duplications, heterozygosity and GC content. Results were as follows. Survey high-throughput sequencing obtained Raw Data 47.63 Gb, filtered Clean data 45.62 Gb. K-mer analysis showed that the genome size was 588.35 Mb, heterozygosity was 1.5598%, repeatability was 64.49%, GC content was 35.71%. The genome of I. chinensis presents high heterozygosity, high repetition, and genome bulky features.

Key words: Ixora chinensis, high-throughput sequencing, genome Survey, K-mer analysis, heterozygosity, repetitive sequences

摘要： 中国龙船花Ixora chinensis是一种兼备药用与观赏价值的传统中药材，解析中国龙船花的基因组特征信息，可为其全基因组测序和药效成分生物合成的分子机制研究奠定理论基础。本研究利用Survey基因组测序技术，使用K-mer分析方法对中国龙船花基因组特征信息展开评估，获得基因组重复度、杂合度以及GC含量等信息。Survey高通量测序获得Raw Data 47.63 Gb，过滤后Clean data 45.62 Gb。K-mer分析表明，基因组大小588.35 Mb，杂合度1.5598%，重复度64.49%，GC含量35.71%，中国龙船花基因组呈现高杂合度、高重复度、基因组庞大的特征。

关键词: 中国龙船花, 高通量测序, 基因组Survey, K-mer分析, 杂合度, 重复序列

CLC Number:

Q943

TU Shao-qiang, KE Ling-jun, CAI Yue-qin, LU Luan-mei, YU Hui-wen. Genome Survey Analysis in Ixora chinensis[J]. Subtropical Plant Science, 2024, 53(3): 214-219.

涂绍强, 柯玲俊, 蔡月琴, 陆銮眉, 余惠文. 中国龙船花基因组Survey分析[J]. 亚热带植物科学, 2024, 53(3): 214-219.

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Genome Survey Analysis in Ixora chinensis

中国龙船花基因组Survey分析

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