Department of Agriculture and Fisheries, Horticulture and Forestry Science, 28 Peters St, Mareeba, QLD, 4880, Australia.
Department of Bioscience, University of Milan, Via Celoria 26, 20133, Milan, Italy.
BMC Plant Biol. 2021 Feb 22;21(1):108. doi: 10.1186/s12870-021-02858-1.
Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency.
This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar 'Tommy Atkins'. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins', supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between 'Tommy Atkins' x 'Kensington Pride' was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the 'Tommy Atkins' x 'Kensington Pride' mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population.
The availability of the complete 'Tommy Atkins' mango genome will aid global initiatives to study mango genetics.
芒果（Mangifera indica L.）是一种重要的热带水果作物，因其香甜芳香的果实而种植。过去对该物种的改良主要依赖于来自印度次大陆的 1000 多个品种的偶然实生苗，这些实生苗在果实大小、产量、生物和非生物胁迫抗性以及果实品质等性状方面存在很大差异。历史上，芒果一直是一种孤儿作物，分子信息非常有限。直到最近，基于分子和基因组学的分析才使得构建连锁图谱、转录组和对大型集合的多样性分析成为可能。此外，基因组和表型信息的综合分析有望提高芒果的育种效率。
本研究对单核胚的芒果品种“Tommy Atkins”进行了测序、从头组装、分析和注释。使用 NRGene de-novo Magic 对“Tommy Atkins”的高分子量 DNA 进行测序，辅以 10X Genomics 长读测序来提高初始组装质量，生成了“Tommy Atkins”的草案基因组序列。利用“Tommy Atkins”x“Kensington Pride”的杂交群体生成了相染色体和高度解析的相 SNP 图谱。最终的“Tommy Atkins”基因组组装是一个共识序列，包括 20 个代表芒果 20 条染色体的拟基因组，包含约 439 Mb 单倍体芒果基因组的~86%。Skim 测序利用“Tommy Atkins”x“Kensington Pride”作图群体鉴定了约 330 万个 SNPs。重复掩蔽鉴定了 26616 个基因，其平均长度为 3348 bp。全基因组复制分析显示，芒果与腰果（Anacardium occidentale）在 6500 万年前经历了一次祖先多倍化事件。LG4 和 LG7 上各有一个包含 28 个候选基因的区域与作图群体中重要的果实大小性状相关。
完整的“Tommy Atkins”芒果基因组的可用性将有助于全球研究芒果遗传学的计划。
