Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.)

Shuigen Li; Jiaying Zhang; Liqing Zhang; Xianping Fang; Jun Luo; Haishan An; Xueying Zhang

doi:10.3389/fpls.2022.1078085

Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.)

Front Plant Sci. 2022 Dec 13:13:1078085. doi: 10.3389/fpls.2022.1078085. eCollection 2022.

Authors

Shuigen Li^{1

2}, Jiaying Zhang^{1

2}, Liqing Zhang^{1

2}, Xianping Fang^{1

2}, Jun Luo^{1

2}, Haishan An^{1

2}, Xueying Zhang^{1

2}

Affiliations

¹ Forest and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
² Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China.

Abstract

Introduction: Blueberries have a high antioxidant content and are produced as healthy food worldwide. Long non-coding RNAs (lncRNAs) are a type of regulatory RNAs that play a variety of roles in plants. Nonetheless, information on lncRNAs and their functions during blueberry fruit development is scarce in public databases.

Methods: In the present study, we performed genome-wide identification of lncRNAs in a southern highbush blueberry using strand-specific RNA sequencing (ssRNA-Seq). Differentially expressed lncRNAs (DE-lncRNAs) and their potential target genes were analyzed at four stages of fruit development. Cis-regulatory DE-lncRNAs were predicted using co-localization analysis.

Results: These findings included a total of 25,036 lncRNAs from 17,801 loci. Blueberry lncRNAs had shorter transcript lengths, smaller open reading frame (ORF) sizes, fewer exons, and fewer isoforms than protein-coding RNAs, as well as lower expression levels and higher stage-specificity during fruit development. A total of 105 DE-lncRNAs were identified among the comparison group of PAD vs. CUP, 443 DE-lncRNAs were detected when comparing CUP with PINK fruits, and 285 DE-lncRNAs were revealed when comparing PINK and BLUE fruits. According to Kyoto Encyclopedia of Genes and Genomes annotation, target genes of DE-lncRNAs were primarily enriched in the "Autophagy-other", "DNA replication", "Endocytosis", 'photosynthesis' and 'chlorophyll metabolism' pathways, suggesting that lncRNAs may pay potential roles in fruit expansion and ripening. Moreover, several lncRNAs have been proposed as cis-regulators of the key genes involved in flavonoid biosynthesis. MSTRG.107242.6, and its putative target gene, BTB/POZ and TAZ domain-containing protein, might play critical roles in anthocyanin accumulation in blueberries.

Discussion: These findings highlight the regulatory function of lncRNAs and aid in elucidating the molecular mechanism underlying blueberry fruit growth.

Keywords: RNA-seq; anthocyanin biosynthesis; blueberry; flavonoid biosynthesis; fruit development; lncRNA.