Abstract
Peony is a famous ornamental and medicinal plant in China, and peony hybrid breeding is an important means of germplasm innovation. However, research on the genome of this species is limited, thereby hindering the genetic and breeding research on peony. In the present study, simple sequence repeat (SSR) locus analysis was performed on expressed sequence tags obtained by the transcriptome sequencing of Paeonia using Microsatellite software. Primers with polymorphism were obtained via polymerase chain reaction amplification and electrophoresis. As a result, a total of 86,195 unigenes were obtained by assembling the transcriptome data of Paeonia. Functional annotations were obtained in seven functional databases including 49,172 (Non-Redundant Protein Sequence Database: 57.05%), 38,352 (Nucleotide Sequence Database: 44.49%), 36,477 (Swiss Prot: 42.32%), 38,905 (Clusters of Orthologous Groups for Eukaryotic Complete Genomes: 45.14%), 37,993 (Kyoto Encyclopedia of Genes and Genomes: 44.08%), 26,832 (Gene Ontology: 31.13%) and 37,758 (Pfam: 43.81%) unigenes. Meanwhile, 21,998 SSR loci were distributed in 17,567 unigenes containing SSR sequences, and the SSR distribution frequency was 25.52%, with an average of one SSR sequence per 4.66 kb. Mononucleotide, dinucleotide, and trinucleotide were the main repeat types, accounting for 55.74%, 25.58%, and 13.21% of the total repeat times, respectively. Forty-five pairs of the 100 pairs of primers selected randomly could amplify clear polymorphic bands. The polymorphic primers of these 45 pairs were used to cluster and analyze 16 species of peony. The new SSR molecular markers can be useful for the study of genetic diversity and marker-assisted breeding of peony.
Highlights
Peony, which is a deciduous woody plant that belongs to genus Paeonia, is one of the traditional famous flowers in China
A total of 92.02 Gb of data were measured on the BGISEQ-500 platform, and 86,195 unigenes were obtained by assembling clean reads with Trinity
All unigenes obtained by transcriptome sequencing were annotated into the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Non-Redundant Protein Sequence Database (NR), Nucleotide Sequence Database (NT), Swiss-Prot, Pfam, and KOG databases
Summary
Peony, which is a deciduous woody plant that belongs to genus Paeonia, is one of the traditional famous flowers in China. Paeonia is divided into three sections: Paeonia, Moutan, and Onaepia. In China, the distant hybridization of Paeonia is still in the primary stage. Most of the interspecific distant hybridization of Paeonia can complete fertilization, embryos in the developmental process often shrink or die, and even individual full hybrids cannot develop into normal seedlings [3]. Many studies on embryo abortion after hybridization among peony have been reported. Only limited research has been done on the molecular mechanism of embryo abortion, and relatively complete genomic studies are lacking at present
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