Genome Size Estimation and Genome Survey Sequencing of Chicory (Cichorium intybus L.)

doi:10.11733/j.issn.1007-0435.2022.12.005

Acta Agrestia Sinica ›› 2022, Vol. 30 ›› Issue (12): 3207-3214.DOI: 10.11733/j.issn.1007-0435.2022.12.005

Genome Size Estimation and Genome Survey Sequencing of Chicory (Cichorium intybus L.)

FEI Xing-yu¹, ZHAO Hong², DU Yang¹, DUAN Meng-qi¹, WANG Chen-chen³, ZHANG Bin², LIU Xue², LI Da-yong², XU Li-xin¹

1. College of Grassland Science, Beijing Forestry University, Beijing 100083, China;
2. Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China;
3. College of Life Sciences, Shandong Normal University, Jinan, Shandong Province 250014, China

Received:2022-05-20 Revised:2022-09-13 Published:2023-01-04

菊苣的基因组大小估算及基因组调查测序

费星宇¹, 赵泓², 杜洋¹, 段梦琪¹, 王晨晨³, 张彬², 刘雪², 李大勇², 许立新¹

1. 北京林业大学草业与草原学院, 北京 100083;
2. 北京市农林科学院蔬菜研究所, 北京 100083;
3. 山东师范大学生命科学学院, 山东济南 250014

通讯作者: 许立新,E-mail:liberisa@163.com
作者简介:费星宇(1998-),女,汉族,山西吕梁人,硕士研究生,主要从事草地植物遗传育种研究,E-mail:2973086900@qq.com
基金资助:
中央高校基本科研业务费专项资金(2021ZY83)资助

Abstract

Abstract: Chicory (Cichorium intybus L.),a perennial plant,is known as a medicine food homology which can be used not only as vegetable,but also as high-quality forage. In this study,a chicory forage variety with elite forage value,‘general’ (K042),was selected to characterize the genome of chicory. Phylogenetic analysis showed that K042 was closely related to lettuce (Lactuca sativa L.). Chromosme counting revealed that the somatic cells of K042 had 18 chromosomes (2n = 18). Flow cytometry analysis estimated the genome size of K042 was 1 170.00 Mb. Genome survey sequencing based on the next-generation sequencing (Illumina HiSeq) showed its genome size was 1 424.00 Mb,with genome heterozygosity rate of 1.12% and the repeat sequence content of 73.56%. It indicated that the K042 genome had the complex characteristics of high duplication and high heterozygosity. Using the sequencing data of K042,a 823.36 Mb genome was de novo assembled,with contig N50 length of 1.03 Kb. This study would provide a valuable genomical resource for future molecular biological research and molecular breeding of chicory.

Key words: Chicory (Cichorium intybus L.), Whole genome survey sequencing, Flow cytometry, K-mer Analyses

摘要： 菊苣(Cichorium intybus L.)是一种多年生、药食同源的植物，既可作为蔬菜种植，也可作为优质牧草推广应用。本研究对‘将军’(K042)这一具有较高饲用价值的菊苣牧草品种展开物种鉴定、染色体计数、基因组大小估算、调查测序及初步组装研究。系统进化分析表明，K042跟生菜的亲缘关系较近。染色体计数结果显示，K042体细胞有18条染色体(2n=18)；流式细胞术实验结果显示，K042的基因组大小约为1170.00Mb；二代Illumina HiSeq测序分析进一步估算K042基因组大小约为1424.00Mb。K042基因组的杂合率为1.12%，重复序列含量为73.56%。K042基因组具有高重复、高杂合的复杂特征。根据基因组测序结果对K042展开基因组组装工作，组装后基因组大小为823.36Mb，重叠群N50长度约为1.03kb，本研究结果可为将来菊苣分子生物学和遗传育种研究提供重要的基因组学基础参考数据。

关键词: 菊苣(Cichorium intybus L.), 全基因组测序, 流式细胞术, K-mer分析

CLC Number:

S548

FEI Xing-yu, ZHAO Hong, DU Yang, DUAN Meng-qi, WANG Chen-chen, ZHANG Bin, LIU Xue, LI Da-yong, XU Li-xin. Genome Size Estimation and Genome Survey Sequencing of Chicory (Cichorium intybus L.)[J]. Acta Agrestia Sinica, 2022, 30(12): 3207-3214.

费星宇, 赵泓, 杜洋, 段梦琪, 王晨晨, 张彬, 刘雪, 李大勇, 许立新. 菊苣的基因组大小估算及基因组调查测序[J]. 草地学报, 2022, 30(12): 3207-3214.

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Genome Size Estimation and Genome Survey Sequencing of Chicory (Cichorium intybus L.)

菊苣的基因组大小估算及基因组调查测序

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