High-throughput sequencing of highbush blueberry transcriptome and analysis of basic helix-loop-helix transcription factors

• Main Authors: Yang SONG, Hong-di LIU, Qiang ZHOU, Hong-jun ZHANG, Zhi-dong ZHANG, Ya-dong LI, Hai-bo WANG, Feng-zhi LIU
• Format: Article
• Language: English
• Published: Elsevier 2017-03-01
• Series: Journal of Integrative Agriculture
• Subjects: blueberry; bioinformatics; transcriptome sequencing; basic helix-loop-helix; transcription factor
• Online Access: http://www.sciencedirect.com/science/article/pii/S2095311916614612

The highbush blueberry (Vaccinium corymbosum) Duke, was used to construct a de novo transcriptome sequence library and to perform data statistical analysis. Mega 4, CLC Sequence Viewer 6 software, and quantitative PCR were employed for bioinformatics and expression analyses of the basic helix-loop-helix (BHLH) transcription factors of the sequencing library. The results showed that 28.38 gigabytes of valid data were obtained from transcriptome sequencing and were assembled into 108 033 unigenes. Functional annotation showed that 32 244 unigenes were annotated into Clusters of Orthologous Groups (COG) and Gene Ontology (GO) databases, whereas the rest of the 75 789 unigenes had no matching information. By using COG and GO classification tools, sequences with annotation information were divided into 25 and 52 categories, respectively, which involved transport and metabolism, transcriptional regulation, and signal transduction. Analysis of the transcriptome library identified a total of 59 BHLH genes. Sequence analysis revealed that 55 genes of that contained a complete BHLH domain. Furthermore, phylogenetic analysis showed that BHLH genes of blueberry (Duke) could be divided into 13 sub-groups. PCR results showed that 45 genes were expressed at various developmental stages of buds, stems, leaves, flowers, and fruits, suggesting that the function of BHLH was associated with the development of different tissues and organs of blueberry, Duke. The present study would provided a foundation for further investigations on the classification and functions of the blueberry BHLH family.