First high-quality genome assembly data of sago palm (Metroxylon sagu Rottboll)

Area of Science:

• Genomics
• Plant Science
• Bioinformatics

Background:

• The sago palm (Metroxylon sagu) is an economically important tropical crop, primarily cultivated for starch production in Southeast Asia.
• Previous genome surveys using Illumina sequencing yielded low completeness (21.5% BUSCO score), with most gene sequences fragmented or missing.
• A more complete genome assembly is essential for understanding sago palm's genetic makeup and improving crop traits.

Purpose of the Study:

• To enhance the completeness and contiguity of the sago palm genome assembly.
• To provide a high-quality genome resource for future molecular and evolutionary studies.
• To investigate the genetic basis of starch synthesis in sago palm.

Main Methods:

• Utilized Nanopore sequencing technology to generate long reads, overcoming limitations of previous short-read sequencing.
• Performed a hybrid genome assembly strategy, combining Nanopore and potentially existing Illumina data.
• Employed Benchmarking Universal Single-Copy Orthologs (BUSCO) to assess genome completeness and gene integrity.

Main Results:

• Achieved a significantly improved BUSCO completeness score of 97.9%, with only approximately 2% of genes fragmented or missing.
• Estimated the sago palm genome size at 509,812,790 base pairs.
• Identified 33,242 protein-coding genes, with 96.39% functionally annotated, revealing starch synthesis as a key metabolic pathway.

Conclusions:

• The Nanopore-based hybrid assembly provides a highly complete and contiguous sago palm genome.
• This improved genome resource is vital for advancing research in sago palm molecular evolution and crop improvement.
• The findings facilitate future genome-wide association studies and the genetic enhancement of starch production in sago palm.