<i>De Novo</i> Genome Assembly of <i>Populus simonii</i> Further Supports That <i>Populus simonii</i> and <i>Populus trichocarpa</i> Belong to Different Sections

Abstract

<i>Populus simonii</i> is an important tree in the genus <i>Populus</i>, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of <i>P. simonii</i> using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the <i>P. simonii</i> assembly. Genomic repeat analysis revealed that 41.47% of the <i>P. simonii</i> genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the <i>P. simonii</i> genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that <i>P. simonii</i> and <i>Populus trichocarpa</i> should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different <i>Populus</i> species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F₁ hybrid population derived by crossing <i>P. simonii</i> with other <i>Populus</i> species.