Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of Potentilla anserina

Abstract

Potentilla anserina is a perennial stoloniferous plant with edible tuberous roots in Rosaceae, served as important food and medicine sources for Tibetans in the Qinghai-Tibetan Plateau (QTP), China, over thousands of years. However, a lack of genome information hindered the genetic study. Here, we presented a chromosome-level genome assembly using single-molecule long-read sequencing, and the Hi-C technique. The assembled genome was 454.28 Mb, containing 14 chromosomes, with contig N50 of 2.14 Mb. A total of 46,495 protein-coding genes, 169.74 Mb repeat regions, and 31.76 Kb non-coding RNA were predicted. P. anserina diverged from Potentilla micrantha ∼28.52 million years ago (Mya). Furthermore, P. anserina underwent a recent tetraploidization ∼6.4 Mya. The species-specific genes were enriched in Starch and sucrose metabolism and Galactose metabolism pathways. We identified the sub-genome structures of P. anserina, with A sub-genome was larger than B sub-genome and closer to P. micrantha phylogenetically. Despite lacking significant genome-wide expression dominance, the A sub-genome had higher homoeologous gene expression in shoot apical meristem, flower and tuberous root. The resistance genes was contracted in P. anserina genome. Key genes involved in starch biosynthesis were expanded and highly expressed in tuberous roots, which probably drives the tuber formation. The genomics and transcriptomics data generated in this study advance our understanding of the genomic landscape of P. anserina, and will accelerate genetic studies and breeding programs.

The Identification of SQS/SQE/OSC Gene Families in Regulating the Biosynthesis of Triterpenes in Potentilla anserina

“…The genome of Pan contains 14 chromosomes, which underwent a tetraploidization in 6.4 Mya. The A sub-genome (A1–A7, from Chr1 to Chr13, odd numbers) and B sub-genome (B1–B7, from Chr2 to Chr14, even numbers) showed good collinearity [ 16 ]. SQSs were symmetrically distributed on two sub-genomes.…”

“…The divergence of Vitales and Rosales occurred at about 121.9 Mya, while the Rosoideae divergence from Amygdaloideae occurred at 84.4 Mya [ 19 ]. The Potentilla genus was separated from Fragaria genus at about 40.68 Mya, followed by the divergence between Pan and Pmi (28.52 Mya) [ 16 ]. Pmi and Fve diverged at about 34.5 Mya [ 19 ], and Fve diverged from Rru at about 52.3 Mya [ 19 ].…”

“…Rru has no additional genome-wide duplication after whole-genome triplication (WGT) [ 22 ]. The genome of Pan underwent a recent WGD event to form an allotetraploid after the divergence of Rosaceae, and the A sub-genome and the B sub-genome were found to have good collinearity [ 16 ].…”

“…The sub-genome structures of Pan are characterized with the A sub-genome, which is larger than the B sub-genome and phylogenetically closer to the genome of Pmi. In general, the A sub-genome had higher homoeologous gene expression in the tuberous root [ 16 ]. Fifty-one percent of genes of Pan and Pmi are in a ratio of 2:1, based on the collinearity analysis of 26,032 genes [ 16 ].…”

“…In general, the A sub-genome had higher homoeologous gene expression in the tuberous root [ 16 ]. Fifty-one percent of genes of Pan and Pmi are in a ratio of 2:1, based on the collinearity analysis of 26,032 genes [ 16 ]. In this study, we analyzed SQSs , SQEs , and OSCs involved in the biosynthesis of triterpenes in Pan and revealed function and evolutionary relationships via comparative genomic studies, which could facilitate research on bioactive triterpenes in Pan.…”