Abstract
Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq) technology have provided an effective means to obtain genomic information from non-model species. Here, we applied RNA-seq for sequencing S. pohuashanensis leaves and obtained a total of 137,506 clean reads. After assembly, 96,213 unigenes with an average length of 770 bp were obtained. We found that 64.5% of the unigenes could be annotated using bioinformatics tools to analyze gene function and alignment with the NCBI database. Overall, 59,089 unigenes were annotated using the Nr database(non-redundant protein database), 35,225 unigenes were annotated using the GO (Gene Ontology categories) database, and 33,168 unigenes were annotated using COG (Cluster of Orthologous Groups). Analysis of the unigenes using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database indicated that 13,953 unigenes were involved in 322 metabolic pathways. Finally, simple sequence repeat (SSR) site detection identified 6,604 unigenes that included EST-SSRs and a total of 7,473 EST-SSRs in the unigene sequences. Fifteen polymorphic SSRs were screened and found to be of use for future genetic research. These unigene sequences will provide important genetic resources for genetic improvement and investigation of biochemical processes in S. pohuashanensis.
Highlights
Sorbus pohuashanensis (Hance) Hedl. is a species of small deciduous tree in the genus Sorbus that is native to China [1]
The primary unigenes were assembled using CAP3 expressed sequence tags (ESTs) software to produce a final unigene set of 96,213 unigenes with an average length of 700 bp and N50 value of 894
The final unigene set was searched against the Nr, Uniprot, Gene Ontology (GO), COG and KEGG databases and a total of 62,053 unigenes were annotated (Table 2)
Summary
Sorbus pohuashanensis (Hance) Hedl. is a species of small deciduous tree in the genus Sorbus (subfamily Maloideae, family Rosaceae) that is native to China [1]. Is a species of small deciduous tree in the genus Sorbus (subfamily Maloideae, family Rosaceae) that is native to China [1]. It has a high ornamental value due to the appearance of its leaves, flowers, and fruit in different seasons (S1 Fig). Can de novo sequencing of the transcriptome provide genetic information of a species without the aid of a reference genome, and can forecast probable non-coding RNAs [9]. We used RNA-seq to construct a transcriptome database for S. pohuashanensis This information will be of value for future development and genetic modification of the germplasm of this species
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