Gapless genome assembly and population genomics highlights diversity of mango germplasms

作者：Cui‐Xian Zhang, Huaifeng Yi, Xiuxu Ye, Jingye Fu, Dehong Xie, Tianqi Bai, Xinyue Gong, Zhangguang Ni, Xinping Luo, Yusuf Chong Yu Lok, Qiong Luo, Peng Wang · 发表于：Horticulture Research · 年份：2025 · DOI：10.1093/hr/uhaf007 · 被引用次数：4 · 研究领域：Cocoa and Sweet Potato Agronomy、Phytoplasmas and Hemiptera pathogens、Plant biochemistry and biosynthesis

Dear Editor Mango (Mangifera indica) is grown in many tropical and subtropical regions worldwide, and is renowned for its rich flavor and nutritional value. Over recent years, several mango genome assemblies have been released, providing foundational information for genomics-based mango breeding [1–4]. However, only genomes for commercial accessions are reported in these studies, and publications are lacking on genome assembly of mango landraces , whose value in breeding has been demonstrated in many other crops [5]. Recent advances in sequencing technology have made it possible to construct gapless genome assemblies, offering insights into genome evolution and gene functioning [6]. As gaps are left in each of the publicly available mango genomes, construction of a gapless assembly would facilitate the utility of mango genomics data for genetics and breeding. Here we present the gapless genome assembly of a mango landrace, San Nian Mang (hereafter, SNM). Deep sequencing harnessed 31.4 Gb Oxford Nanopore Technologies (ONT) ultra-long reads (80×), 13.7 Gb PacBio Sequel II HiFi reads (40×), 29.3 Gb Illumina short reads (80×), and 81.1 Gb Hi-C sequencing data (200×). Hybrid genome assembly was performed using HiFi reads and ONT ultra-long reads, yielding a draft assembly of 380.8 Mb [7]. The assembly was scaffolded and further corrected, generating 20 pseudomolecules. After filling all the gaps, a gapless genome containing 20 chromosomes with a total length of 377.6 Mb was genera...