Screening of differentially expressed genes from transcriptomes in blooming female flower clusters of Vitis flexuosa

• Published in: Horticulture, environment and biotechnology Vol. 65; no. 6; pp. 1053 - 1067
• Main Authors: Ahn, Soon Young, Myint, Zar Le, Kim, Seon Ae, Kim, Seung Heui, Yun, Hae Keun
• Format: Journal Article
• Language: English
• Published: Singapore Springer Nature Singapore 01.12.2024; Springer Nature B.V; 한국원예학회
• Subjects: Agriculture; Biological activity; Biomedical and Life Sciences; biosynthesis; cations; Clusters; female flowers; Flowering; Flowers; Gene expression; gene expression regulation; Genes; Genetic resources; Genomic analysis; genomics; Life Sciences; Oxidation; Oxidation-reduction potential; Plant Breeding/Biotechnology; Plant Ecology; Plant Physiology; quantitative polymerase chain reaction; Research Report; sequence analysis; transcriptome; Transcriptomes; transcriptomics; Vitis; 농학; Flower development; Genetic resource; De novo assembly; Grapevine
• ISSN: 2211-3452; 2211-3460
• DOI: 10.1007/s13580-024-00631-5

To characterize genes expressed specifically at blooming stages in V. flexuosa , mRNA samples from flower clusters harvested at pre-bloom and full bloom stage were sequenced on a single lane of an Illumina HiSeq 2000. From total 65,765,120 and 36,613,180 paired-end reads of 101 bp in length, we obtained a total of 58,859,224 and 50,931,158 paired-end reads for samples of V. flexuosa at pre-blooming and full blooming stages, respectively. We obtained the assembly results with a total number of 174,844 contigs (≥ 200 bp in length) with a N50 length of 2,217 bp, an average contig length of 1,806 bp and a maximum contig length of 12,228 bp from both flowering staged samples of V. flexuosa . Differentially expressed genes (DEGs) were divided into 45, 10, and 13 main functional categories of biological process, cellular component, and molecular function, respectively, with different degrees at level 3. In the GO terms of biological process, single-organism biosynthetic process (22.8%) was the largest category followed by small molecule metabolic process (17.9%) and oxidation-reduction process (16.8%). The largest proportions of molecular function were annotated as cation binding (25%) and substrate-specific transmembrane transporter (9.2%). Real-time PCR results validated that top 20 up- and down-expressed genes selected in transcriptome analysis showed the differential expression profile at full bloom flower stages. RNA-seq data created in this study will be served as resources for gene discovery and detailed genomic information for grapevine breeding programs.