De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading

Abstract

BackgroundLitchi (Litchi chinensis Sonn.) is one of the most important fruit trees cultivated in tropical and subtropical areas. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying fruit set and fruit development in litchi. Shading during early fruit development decreases fruit growth and induces fruit abscission. Here, high-throughput RNA sequencing (RNA-Seq) was employed for the de novo assembly and characterization of the fruit transcriptome in litchi, and differentially regulated genes, which are responsive to shading, were also investigated using digital transcript abundance(DTA)profiling.ResultsMore than 53 million paired-end reads were generated and assembled into 57,050 unigenes with an average length of 601 bp. These unigenes were annotated by querying against various public databases, with 34,029 unigenes found to be homologous to genes in the NCBI GenBank database and 22,945 unigenes annotated based on known proteins in the Swiss-Prot database. In further orthologous analyses, 5,885 unigenes were assigned with one or more Gene Ontology terms, 10,234 hits were aligned to the 24 Clusters of Orthologous Groups classifications and 15,330 unigenes were classified into 266 Kyoto Encyclopedia of Genes and Genomes pathways. Based on the newly assembled transcriptome, the DTA profiling approach was applied to investigate the differentially expressed genes related to shading stress. A total of 3.6 million and 3.5 million high-quality tags were generated from shaded and non-shaded libraries, respectively. As many as 1,039 unigenes were shown to be significantly differentially regulated. Eleven of the 14 differentially regulated unigenes, which were randomly selected for more detailed expression comparison during the course of shading treatment, were identified as being likely to be involved in the process of fruitlet abscission in litchi.ConclusionsThe assembled transcriptome of litchi fruit provides a global description of expressed genes in litchi fruit development, and could serve as an ideal repository for future functional characterization of specific genes. The DTA analysis revealed that more than 1000 differentially regulated unigenes respond to the shading signal, some of which might be involved in the fruitlet abscission process in litchi, shedding new light on the molecular mechanisms underlying organ abscission.

De Novo Assembly and Characterization of the Fruit Transcriptome of Chinese Jujube (Ziziphus jujuba Mill.) Using 454 Pyrosequencing and the Development of Novel Tri-Nucleotide SSR Markers

“…Similar results were observed in other studies [46], [47]. The functional annotation that was provided by the SwissProt database was considered to be more reliable because it is a high-quality annotated and non-redundant protein sequence database [46].…”

De Novo Assembly and Characterization of Pericarp Transcriptome and Identification of Candidate Genes Mediating Fruit Cracking in Litchi chinensis Sonn.

“…A total of 46,641 unigenes (≥200 bp) were identified. The mean unigene size was 993 bp, which was longer than that reported in other studies using a similar approach, such as 601 bp by Li et al [21]. More than 69% of unigenes identified in the present study matched the NR database, which was comparable with the results of other studies using the same technology (e.g., 59% by Li et al [21]).…”

“…The mean unigene size was 993 bp, which was longer than that reported in other studies using a similar approach, such as 601 bp by Li et al [21]. More than 69% of unigenes identified in the present study matched the NR database, which was comparable with the results of other studies using the same technology (e.g., 59% by Li et al [21]). These results indicate that the litchi pericarp transcriptome presented here is comprehensive, accurate, and useful for future genetic research of litchi pericarp and pericarp of other Sapindaceae family plant species.…”

Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum

“…Our assembly yielded 57,939 contigs, 64.3% of which have a BLASTx hit with the nr database (Supplemental Table 3). This value is higher than those in other published de novo dicot transcriptome data sets; e.g., 44.7% in the chickpea de novo assembly based solely on 454 reads, 43.3% in tea (Camellia sinensis) unigenes (Shi et al, 2011), and 59.65% in Litchi chinensis (Li et al, 2013). Thus, our de novo assembled transcriptome provides reasonable coverage of P. japonicum genes with an enrichment of transcripts expressed at different stages of haustorium development, thereby representing an excellent resource for mining essential genes during haustorium development.…”