Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids

Area of Science:

• Genomics
• Plant Biology
• Forestry

Background:

• Long-read DNA sequencing enables de novo phased (haplo)genome assembly, improving structural variant (SV) detection.
• Eucalyptus species and their interspecific hybrids are crucial for fast-growing pulpwood plantations.
• The extent of structural variation and its impact on interspecific hybridization in Eucalyptus is largely unknown.

Purpose of the Study:

• To elucidate the extent of structural variation between Eucalyptus grandis and E. urophylla genomes.
• To perform the first haplogenome assembly for an F1 hybrid of these two Eucalyptus species.

Main Methods:

• Utilized Nanopore sequencing and a trio-binning approach for haplogenome assembly.
• Employed high-density SNP genetic linkage maps for scaffolding contigs into pseudo-chromosomes.
• Analyzed structural variants (SVs) between the assembled haplogenomes.

Main Results:

• Assembled two separate haplogenomes (566.7 Mb and 544.5 Mb) with 98.0% BUSCO completion.
• Scaffolded 88.0% of contigs into 11 pseudo-chromosomes for each haplogenome.
• Identified 48,729 structural variants (SVs) between the E. grandis and E. urophylla haplogenomes, with 34.7% of genes affected by rearrangements.

Conclusions:

• This study provides the first detailed insight into genome structural rearrangements between E. grandis and E. urophylla.
• Understanding SV and haplotype diversity is foundational for investigating the genetic basis of hybrid superiority in Eucalyptus.
• The assembled haplogenomes and identified SVs will aid future research in Eucalyptus breeding and genetics.