A haplotype-resolved reference genome for Eucalyptus grandis.

Area of Science:

• Genomics
• Plant Science
• Forestry

Background:

• Eucalyptus grandis is a key hardwood species for timber and biomass production.
• The v2.0 genome reference has been instrumental in developing molecular breeding tools for eucalypts.
• Advancements in sequencing technology enable more comprehensive genome analysis.

Purpose of the Study:

• To produce an improved, haplotype-phased genome assembly (v4.0) for Eucalyptus grandis.
• To enhance the accuracy and completeness of the E. grandis genome reference.
• To facilitate further research in molecular breeding and population genetics of E. grandis.

Main Methods:

• Utilized PacBio HiFi long reads and Omni-C proximity ligation sequencing.
• Generated a haplotype-phased assembly (v4.0) for an E. grandis selection (TAG0014).
• Analyzed assembly size, contiguity, telomere capture, gene models, and repeat content.

Main Results:

• Produced a haplotype-phased assembly (v4.0) with two haplotypes (HAP1: 571 Mbp, HAP2: 552 Mbp).
• Assembly size is smaller than v2.0, with improved contiguity (N50s of 28.9 and 16.7 Mbp) and telomere capture.
• Increased gene annotation completeness to 99.4%, identified numerous genes in tandem arrays, and characterized repeat elements.

Conclusions:

• The v4.0 E. grandis genome assembly represents a significant improvement over v2.0.
• This enhanced assembly provides a more accurate resource for understanding genome structure and variation.
• The findings will accelerate the development of elite Eucalyptus breeding programs for sustainable forestry.