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Exploring the Causes of the Formation of Melon Genome GAPs

Mengwen WANG, Xianlei WANG(), Yuan PENG, Zeyu LI
School of Life Science and Technology, Xinjiang University, Urumqi Xinjiang 830017, China
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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 150 bp 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.

Keywords

melongenomerepetitive sequenceSSRGAPs
CLC number: S652 Document code: A Article ID: 2096-7675(2025)01-0066-07

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Journal of Xinjiang University(Natural Science Edition in Chinese and English)
Volume 42 Issue 1,
January 2025
Pages 66-72
DOI: 10.13568/j.cnki.651094.651316.2023.07.27.0002
Cite this article:
WANG M, WANG X, PENG Y, et al. Exploring the Causes of the Formation of Melon Genome GAPs. Journal of Xinjiang University(Natural Science Edition in Chinese and English), 2025, 42(1): 66-72. https://doi.org/10.13568/j.cnki.651094.651316.2023.07.27.0002
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