Introduction
The genomics revolution has spurred unprecedented growth in the
sequencing and assembly of whole genomes in a wide variety of model and
non-model organisms (Ellegren, 2014).
While this has fueled the development of large genomic diversity panels
for studies into the genetic basis of adaptive traits, reliance on a
single well-assembled reference genome within a species or across a set
of closely related congeners poses significant limitations on genetic
and evolutionary inferences (Sherman &
Salzberg, 2020). The challenge is particularly acute when working with
large, structurally diverse, hybrid or heterozygous genomes, for which
low coverage and biases in variant calling may result when mapping short
read sequences against a divergent reference genome.
The genus Populus (poplars, cottonwoods, and aspens) has emerged
as the leading model in tree ecological genomics and biotechnology,
including development of the reference genome assembly for Populus
trichocarpa –the first tree to undergo whole genome sequencing
(Tuskan et al., 2006). In recent years,
the whole genomes of Populus euphratica , Populus tremulaand tremuloides , Populus alba var. pyramidalis andPopulus alba have also been published
(Lin et al., 2018;
Y. J. Liu, Wang, & Zeng, 2019;
J. Ma et al., 2019;
T. Ma et al., 2013). However, high
genetic heterozygosity and limited application of 3rd generation
sequencing technology has limited the quality of many of these genome
assemblies, which often remain highly fragmented into thousands of
scaffolds (Ambardar, Gupta, Trakroo, Lal,
& Vakhlu, 2016).
The availability of multiple highly contiguous, well-assembledPopulus reference genomes would greatly facilitate accurate
inferences of synteny, recombination, and chromosomal origins
(Lin et al., 2018). Diverse
well-assembled reference genomes would also provide a fundamental tool
for functional genomics, genetic engineering, and molecular breeding in
this economically important genus (L.
Zhang et al., 2019). It would also improve phylogenomic analyses of thePopulus pan-genome (Pinosio et al.,
2016; L. Zhang et al., 2019), without
the need for reliance on reference-guided mapping and variant calling
based solely on the P. trichocarpa reference. Recent advances in
approaches to whole genome sequencing, including chromosome conformation
capture (Hi-C) (van Berkum et al., 2010)
and long-read sequencing offer a means to go beyond fragmented draft
genomes and generate nearly comprehensive de novo assemblies
(El-Metwally, Ouda, & Helmy, 2014).
Populus tomentosa , also known as Chinese white poplar, is
indigenous and widely distributed across large areas of
China(An et al., 2011). Moreover, it is
also the first tree species planted in large-scale artificial
plantations in China. Like other white poplars, P. tomentosa has
become an important model for genetic research on trees
(An et al., 2011), but at present no
genome sequence is available and the origin, evolution and genetic
architecture of the P. tomentosa genome are unclear. It has been
proposed that P. tomentosa is a distinct species in thePopulus section (Dickmann &
Isebrands, 2001). However, the origin of P. tomentosa has been
remained controversial. Although P. tomentosa was proposed to
contain two genetic types with different maternal
parents(D. Wang, Wang, Kang, & Zhang,
2019), suggestions of a hybrid origin were based on a limited set of
molecular markers and an incomplete collection of provenance materials.
Thus, its ancestry and genome structure remains unclear. Our study adds
to knowledge of the species by providing a much greater understanding of
genomic architecture and structural composition following inferred
interspecies hybridization.
Here, we present de novo assembles for P. tomentosa (clone
GM15) by the combined application of PacBio, Illumina and Hi-C
sequencing technologies. We herein provide two high-quality
haplotype-resolved assemblies for all chromosomes whose phylogenetic
affinities demonstrate the hybrid origin of this species. Combining
phylogenetic analyses of chloroplast genomes in this study, we deduced
that the ancestors of P. tomentosa are P. adenopoda(female parent) and P. alba var. pyramidalis (male
parent). Furthermore, we uncovered extensive structural variations
across the genome. These findings help to elucidate the mechanisms of
speciation in Populus , and expand our understanding of the
genomic biology of Populus .