Haplotype-resolved genome assembly of poplar line NL895 provides a valuable tree genomic resource

Abstract

Poplar line NL895 can potentially become a model plant for poplar study as it is a widely cultivated elite line. However, the lack of genome resources hindered the use of NL895 as the major plant material in poplar. In this study, we provided a high-quality genome assembly for poplar line NL895 with PacBio single molecule real-time (SMRT) sequencing and High-throughput chromosome conformation capture (Hi-C) technology. The raw assembly of NL895 for the diploid genome included 606 contigs with a total size of ~815 Mb, and the monoploid genome included 246 contigs with a total size of ~412 Mb. The haplotype-resolved chromosomes in the diploid genomes were also generated. All the monoploid, diploid, and haplotype-resolved genomes showed more than 97% completeness and they can largely improve the mapping efficiency in RNA-Seq analysis. By comprehensively comparing the two haplotype genomes we found the heterozygosity of NL895 is much higher than other poplar lines. We also found that NL895 harbors more genomic variants and more gene diversity. The haplotype-specific genes showed higher variable gene expression patterns. These characters would be attributed to the high heterosis of poplar line NL895. The allele-specific expression (ASE) was also investigated and lots of alleles showed biased expressions in different tissues or environmental conditions. Taken together, the genome sequence for NL895 is a valuable tree genomic resource and it would greatly facilitate studies in poplar.

Keywords

• poplar
• nl895
• genome assembly
• haplotype-resolved genome
• heterozygosity
• allele specific expression (ase)