De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China

Sci China Life Sci. 2019 May;62(5):609-618. doi: 10.1007/s11427-018-9455-2. Epub 2019 Jan 17.

Abstract

The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred ~5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (~ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy (0.271±0.051) and Hungary (0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.

Keywords: Populus alba; de novo assembly; genetic diversity; population expansion.

MeSH terms

  • China
  • DNA, Plant
  • Genetic Variation
  • Genome, Plant
  • Geography
  • Polymorphism, Single Nucleotide
  • Populus / classification*
  • Populus / genetics*
  • Rivers
  • Sequence Analysis, DNA

Substances

  • DNA, Plant