甜瓜基因组GAPs特征及形成原因探究

王孟文; 王贤磊; 彭媛; 李泽玉

doi:10.13568/j.cnki.651094.651316.2023.07.27.0002

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甜瓜基因组GAPs特征及形成原因探究

更新时间：2026-01-21

- 甜瓜基因组GAPs特征及形成原因探究
- Journal of Xinjiang University (Natural Science Edition in Chinese and English) Vol. 42, Issue 1, Pages: 66-72(2025)
- 作者机构：
  
  新疆大学生命科学与技术学院
- 作者简介：
- 基金信息：
- DOI：10.13568/j.cnki.651094.651316.2023.07.27.0002
  CLC： S652
- Published：2025
- 稿件说明：
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[1]王孟文,王贤磊,彭媛,等.甜瓜基因组GAPs特征及形成原因探究[J].新疆大学学报(自然科学版中英文),2025,42(01):66-72.
[1]王孟文,王贤磊,彭媛,等.甜瓜基因组GAPs特征及形成原因探究[J].新疆大学学报(自然科学版中英文),2025,42(01):66-72. DOI： 10.13568/j.cnki.651094.651316.2023.07.27.0002.

DOI：10.13568/j.cnki.651094.651316.2023.07.27.0002.

摘要

未知区域（GAPs）是基因组中未被测序或组装的区域．经单分子三代测序，甜瓜基因组中GAPs由基因组V3.6.1中的79.68 Mb减少至基因组V4.0中的0.12 Mb．以甜瓜基因组V3.6.1和V4.0数据为研究对象，获取并分析基因组中GAPs内部及侧翼序列特征及规律，并探究GAPs形成原因，为组装高质量甜瓜基因组提供参考．结果表明：与基因组整体相比，GAPs内部两侧150 bp区域，简单重复序列（Simple Sequence Repeats

SSR）密度较高、非SSR区域GC含量较高，GAPs外侧150 bp含有较高的多拷贝序列．较高GC含量和微卫星密度会影响PCR扩增，多拷贝序列的存在会影响下游序列的拼接组装，且在GAPs两侧150 bp与GAPs全序列比较发现，越临近GAPs边界，其GC含量与微卫星密度越高．认为甜瓜基因组V3.6.1中GAPs形成的主要原因是含有较高GC含量、微卫星密度及较多的多拷贝序列；对V4.0基因组GAPs两侧序列比对分析发现，多拷贝序列占比为98.24%，多拷贝序列可能是V4.0中GAPs形成的重要原因．

Abstract

Unknown regions(GAPs) are regions of the genome that have not been sequenced or assembled.After single molecule real-time(SMRT) sequencing

the size of GAPs in melon genome was reduced from 79.68 Mb(genome V3.6.1) to 0.12 Mb(genome V4.0). Based on the genome V3.6.1 and V4.0 data

the internal and flanking sequence characteristics and rules of GAPs in the genome were obtained and analyzed

and the reasons for the formation of GAPs were explored

so as to provide a reference for assembling high-quality melon genomes. The results showed that the inner 150 bp region of GAPs had a higher density of simple sequence repeats(SSR)

a higher GC content in the non-SSR region

and the outer 150 bp of GAPs contained more multi-copy sequences compared to the whole genome. Higher GC content and microsatellite density will affect PCR amplification

and the presence of multi-copy sequences will affect the splicing and assembly of downstream sequences

and a comparison of the 150bp on both sides of the GAPs with the full sequence of the GAPs revealed that the closer to the GAPs boundary

the higher the GC content and the higher the microsatellite density. Therefore

the main reason for the formation of V3.6.1 GAPs in melon genome is that it contains higher GC content

microsatellite density and more multi-copy sequences. Sequence comparison analysis of both sides of GAPs in V4.0 genome revealed that the high ratio of multi-copy sequences(98.24%) may be the important reason for the formation of GAPs in V4.0.

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