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

Area of Science:

• Genomics
• Plant Science
• Agricultural Science

Background:

• Pineapple is a globally significant tropical fruit with limited genomic resources.
• Existing pineapple genome assemblies are incomplete and cover only two varieties, hindering breeding efforts.

Purpose of the Study:

• To sequence and assemble the first gap-free reference genome for pineapple.
• To identify genetic variations and improve gene annotations across multiple pineapple varieties.
• To establish a comprehensive pineapple genome database.

Main Methods:

• Whole-genome sequencing of three distinct pineapple varieties (wild, fiber, edible).
• De novo genome assembly and gap-filling strategies.
• Manual gene structure annotation and BUSCO analysis for quality assessment.
• Identification and analysis of structural variations.

Main Results:

• Construction of the first gap-free pineapple reference genome (Ref) with 99.2% completeness.
• Identification of 26,656 protein-coding genes and 7,209 structural variations.
• Discovery of structural variations impacting genes related to anthocyanin synthesis, potentially linked to a 1.9-kb insertion.
• Development of the Ananas Genome Database for data accessibility.

Conclusions:

• The seamless pineapple reference genome provides a high-quality foundation for future genomic studies.
• This resource is invaluable for advancing pineapple breeding programs and understanding genetic diversity.
• The Ananas Genome Database enhances accessibility to crucial pineapple genomic data.