The pineapple reference genome:Telomere-to-telomere assembly, manually curated annotation, and comparative analysis  

作　　者：Junting Feng Wei Zhang Chengjie Chen Yinlong Liang Tangxiu Li Ya Wu Hui Liu Jing Wu Wenqiu Lin Jiawei Li Yehua He Junhu He Aiping Luan 

机构地区：[1]National Key Laboratory for Tropical Crop Breeding,Laboratory of Crop Gene Resources and Germplasm Enhancement in South China,Ministry of Agriculture and Rural Affairs,Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province,Tropical Crops Genetic Resources Institute,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,China [2]National Key Laboratory for Tropical Crop Breeding,Sanya Research Institute,Institute of Tropical Bioscience and Biotechnology,Chinese Academy of Tropical Agricultural Sciences,Haikou 572024,China [3]State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources,Guangdong Laboratory for Lingnan Modern Agriculture,Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China,Ministry of Agriculture and Rural Affairs,College of Horticulture,South China Agricultural University,Guangzhou 510642,China [4]Nanfan Research Institute of Hainan University,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource,Tropical Agriculture and Forestry,Hainan University,Sanya 572025,China [5]Environment and Plant Protection Institute,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,China [6]South Subtropical Crop Research Institute,Chinese Academy of Tropical Agricultural Sciences,Zhanjiang 524091,China

出　　处：《Journal of Integrative Plant Biology》2024年第10期2208-2225,共18页植物学报（英文版）

基　　金：supported by National Natural Science Foundation of China(32272677);National Key R&D Program of China(2019YFD1001104);Central Publicinterest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences(1630032024026,1630032024001,1630052023011);Hainan Provincial Natural Science Foundation of China(323QN279)。

摘　　要：Pineapple is the third most crucial tropical fruit worldwide and available in five varieties.Genomes of different pineapple varieties have been released to date;however,none of them are complete,with all exhibiting substantial gaps and representing only two of the five pineapple varieties.This significantly hinders the advancement of pineapple breeding efforts.In this study,we sequenced the genomes of three varieties:a wild pineapple variety,a fiber pineapple variety,and a globally cultivated edible pineapple variety.We constructed the first gap-free reference genome(Ref)for pineapple.By consolidating multiple sources of evidence and manually revising each gene structure annotation,we identified 26,656 proteincoding genes.The BUSCO evaluation indicated a completeness of 99.2%,demonstrating the high quality of the gene structure annotations in this genome.Utilizing these resources,we identified 7,209 structural variations across the three varieties.Approximately 30.8%of pineapple genes were located within±5 kb of structural variations,including 30 genes associated with anthocyanin synthesis.Further analysis and functional experiments demonstrated that the high expression of AcMYB528 aligns with the accumulation of anthocyanins in the leaves,both of which may be affected by a 1.9-kb insertion fragment.In addition,we developed the Ananas Genome Database,which offers data browsing,retrieval,analysis,and download functions.The construction of this database addresses the lack of pineapple genome resource databases.In summary,we acquired a seamless pineapple reference genome with highquality gene structure annotations,providing a solid foundation for pineapple genomics and a valuable reference for pineapple breeding.

关 键 词：PINEAPPLE reference genome MYB transcription factor genome database 

分 类 号：S668.3[农业科学—果树学]