Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendronsimsii (Ericaceae).

Qunlu Liu,Fiza Liaquat,Chunying Zhang,Yefeng He,Muhammad Farooq Hussain Munis

doi:10.3390/plants10040649

Abstract

Rhododendronsimsii is one of the top ten famous flowers in China. Due to its historical value and high aesthetic, it is widely popular among Chinese people. Various colors are important breeding objectives in Rhododendron L. The understanding of the molecular mechanism of flower color formation can provide a theoretical basis for the improvement of flower color in Rhododendron L. To generate the R. simsii transcriptome, PacBio sequencing technology has been used. A total of 833,137 full-length non-chimeric reads were obtained and 726,846 high-quality full-length transcripts were found. Moreover, 40,556 total open reading frames were obtained; of which 36,018 were complete. In gene annotation analyses, 39,411, 18,565, 16,102 and 17,450 transcriptions were allocated to GO, Nr, KEGG and COG databases, correspondingly. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with Protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT) and Coding Non Coding Index (CNCI) databases and observed 6170, 2265, 4084 and 1240 lncRNAs, respectively. Based on the results, most genes were enriched in the flavonoid biosynthetic pathway. The eight key genes on the anthocyanin biosynthetic pathway were further selected and analyzed by qRT-PCR. The F3′H and ANS showed an upward trend in the developmental stages of R. simsii. The highest expression of F3′5′H and FLS in the petal color formation of R. simsii was observed. This research provided a huge number of full-length transcripts, which will help to proceed genetic analyses of R. simsii. native, which is a semi-deciduous shrub.

Highlights

Rhododendron is one of the largest genera in the Ericaceae family, with several species having high horticultural value and being grown as ornamental plants all over the world.The genus contains 580 species in six subgenera in China, with approximately 420 being endemic, including several species described after the publication of the Flora of China [1].Numerous varieties of Rhododendron have been cultured, and it has become one of the most popular flowering shrubs in the world
Total 40G clean data were obtained from the qualified polymerase reads after the adapter sequences were removed
Among the total circular consensus (CCS) reads, 87.24% (726,846) of reads were identified as the full length non-chimeric (FLNC) reads

Summary

Introduction

Numerous varieties of Rhododendron have been cultured, and it has become one of the most popular flowering shrubs in the world. Their colorful flowers are the most attractive traits. Plant flower color is the result of the synergistic effect of many factors, but it is fundamentally due to the presence of specific pigments in petal cells [2]. Flavonoids are the main pigments, most of which exist in plant vacuoles, so that the petals show red, purple red and other colors [3]. Thin-layer chromatography was previously used to explore the flavonoid pigments that contribute to petal coloration in azalea cultivars and contain the anthocyanins cyanidin 3-O-galactoside, cyanidin 3-O-glucoside, cyanidin

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