Pineapple Genome: Complete Assembly, Detailed Annotation, and Comparative Study

Jenn Hoskins
8th August, 2024

Pineapple Genome: Complete Assembly, Detailed Annotation, and Comparative Study

Image Source: Natural Science News, 2024

Key Findings

  • Researchers sequenced the genomes of three pineapple varieties, creating the first complete reference genome for pineapple
  • They identified 26,656 protein-coding genes with a high-quality annotation of 99.2%
  • The study found 7,209 structural variations, impacting traits like anthocyanin pigment accumulation in pineapple leaves
Pineapple is the third most crucial tropical fruit worldwide, yet the incomplete genomes of its varieties have hindered advancements in breeding efforts. The Chinese Academy of Tropical Agricultural Sciences has addressed this limitation by sequencing the genomes of three pineapple varieties: a wild variety, a fiber variety, and a globally cultivated edible variety, resulting in the first gap-free reference genome for pineapple[1]. This study identified 26,656 protein-coding genes and achieved a completeness of 99.2% through BUSCO evaluation, indicating the high quality of the gene structure annotations. The research identified 7,209 structural variations (SVs) across the three pineapple varieties. SVs are large-scale changes in the genome, such as deletions, duplications, or insertions, that can significantly impact gene function and expression. Approximately 30.8% of pineapple genes were located within ±5 kb of these SVs, including 30 genes associated with anthocyanin synthesis. Anthocyanins are pigments responsible for red, purple, and blue colors in plants, and their accumulation in pineapple leaves was linked to a high expression of the AcMYB528 gene, which may be influenced by a 1.9-kb insertion fragment. This study builds on previous research that highlighted the importance of SVs in crop improvement. For instance, a study on tomatoes using long-read nanopore sequencing identified 238,490 SVs in 100 diverse tomato lines, revealing their role in modifying traits such as fruit flavor, size, and production[2]. Similarly, the current pineapple study underscores the significance of SVs in influencing important traits, such as anthocyanin accumulation. The researchers also developed the Ananas Genome Database, a comprehensive resource for data browsing, retrieval, analysis, and download. This database addresses the previous lack of pineapple genome resource databases, providing a valuable tool for further research and breeding efforts. By constructing a seamless reference genome and identifying key SVs, this study provides a solid foundation for pineapple genomics and breeding. The high-quality gene structure annotations and the new database will facilitate more targeted and efficient breeding strategies, ultimately improving pineapple varieties for global cultivation.

GeneticsBiochemPlant Science

References

Main Study

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

Published 7th August, 2024

https://doi.org/10.1111/jipb.13748

Related Studies

2) Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.

https://doi.org/10.1016/j.cell.2020.05.021


Related Articles

An unhandled error has occurred. Reload 🗙