Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd)

Abstract

BackgroundPear (Pyrus spp) is an important fruit species worldwide; however, its genetics and genomic information is limited. Combining the Solexa/Illumina RNA-seq high-throughput sequencing approach (RNA-seq) with Digital Gene Expression (DGE) analysis would be a powerful tool for transcriptomic study. This paper reports the transcriptome profiling analysis of Chinese white pear (P. bretschneideri) using RNA-seq and DGE to better understand the molecular mechanisms in fruit development and maturation of Chinese white pear.ResultsDe novo transcriptome assembly and gene expression analysis of Chinese white pear were performed in an unprecedented depth (5.47 gigabase pairs) using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system. Approximately, 60.77 million reads were sequenced, trimmed, and assembled into 90,227 unigenes. These unigenes comprised 17,619 contigs and 72,608 singletons with an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR, and COGs at NCBI, Pfam, InterPro, and KEGG) found that 61,636 unigenes can be annotated with gene descriptions, conserved protein domains, or gene ontology terms. By BLASTing all 61,636 unigenes in KEGG, a total of 31,215 unigenes were annotated into 121 known metabolic or signaling pathways in which a few primary, intermediate, and secondary metabolic pathways are directly related to pear fruit quality. DGE libraries were constructed for each of the five fruit developmental stages. Variations in gene expression among all developmental stages of pear fruit were significantly different in a large amount of unigenes.ConclusionExtensive transcriptome and DGE profiling data at five fruit developmental stages of Chinese white pear have been obtained from a deep sequencing, which provides comprehensive gene expression information at the transcriptional level. This could facilitate understanding of the molecular mechanisms in fruit development and maturation. Such a database can also be used as a public information platform for research on molecular biology and functional genomics in pear and other related species.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-823) contains supplementary material, which is available to authorized users.

Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size

“…In horticultural crops, only in a few cases, transcriptome sequence analysis has been used for the prediction of genes related to fruit development- as in case of Annona squamosa, Musa accuminata , Prunusavium , Pyrusbrets chneideri etc78910. Comparative analysis of transcriptome in litchi has been used to speculate on the processes involved in the regulation of floral initiation by phytohormones, expression of flowering related genes11, genes related to shading stress12, fruit cracking13, reactive oxygen species (ROS) induced abortion of rudimentary leaves14, fruit abscission15, maturation, coloration16, abscission induced by carbohydrate stress17 and fruit ripening after cold storage18.…”

Genome-Wide Comparative Analysis of the β-glucosidase Family in Five Rosaceae Species and their Potential Role on Lignification of Stone Cells in Chinese White Pear

“…Moreover, these two genes were clustered together with AtBGLU1-6 which related to the accumulation of avonoids in Arabidopsis [2], so PbBGLU28 and PbBGLU29 may participate in the accumulation of avonoids in pear. The expression levels of the three genes PbBGLU1, PbBGLU15 and PbBGLU16 have similar characteristics, they are relatively high in leaves and owers, and relatively low in buds and stems, all three genes were expressed at different stages of fruit development, and its expression shows a trend of rising rst and then falling, with similar trend of the content of lignin and stone cells in "Dangshan Su" pear fruit [35,36], and the three genes had similar expression patterns with the key genes involved in regulation of the lignin synthesis pathway [44]. These results suggested that the three genes PbBGLU1, PbBGLU15, and PbBGLU16 in PbBGLUs IV-B may be functional genes involved in the hydrolysis of monolignol glucosides in the pear lignin synthesis pathway.…”

“…Arabidopsis AtBGLU12-17 was related to the use of Arabidopsis avonoids, AtBGLU15 can catalyze the hydrolysis of Q3G7R, K3G7R and avonol 3-O-glucosides [4], these genes and PbBGLU19 (group III) were clustered together, and it is speculated that PbBGLU19 may be involved in the hydrolysis of avonoid glycosides in pear. PbBGLUs IV-A was clustered together with AtBGLU (40,41,43,44) and some poplar BGLU genes, but the functions of these genes have not yet been explored. The functions of AtBGLU45, AtBGLU46, AtBGLU47 in Arabidopsis and PtrBGLU6 in Poplar had been clari ed, they can catalyze the hydrolysis of monolignol glucosides during ligni cation [16,17,19 ], the three genes PbBGLU1, PbBGLU15 and PbBGLU16 in the PbBGLUs group IV-B were clustered together with these functional genes, speculating that PbBGLU1, PbBGLU15 and PbBGLU16 may be able to affect the ligni cation by catalyze the hydrolysis of monolignol glucosides in pear fruit, which in turn affects the development of pear stone cells.…”

Transcriptomic and metabolomic analysis provides insights into anthocyanin and procyanidin accumulation in pear

“…Pear is an important fruit for human consumption, and its total global production is ranked third after grape and apple [1]. Pear is cultivated commercially in 76 countries or regions worldwide [2], among which China is the world's leading pear producer. In 2017, China produced 16.4 million tons (Mt) of pear fruits, accounting for 68% of global pear production (24.2 Mt) (FAOSTAT, 2017).…”