Transcriptome and weighted gene co-expression network analysis of jujube(Ziziphus jujuba Mill.)fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation

Proanthocyanidin(PA)is an important bioactive compound with multiple physiological benefits in jujube(Ziziphus jujube Mill.).However,the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated.Here,the profiling of PA,(+)-catechin and(–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed.The levels of total PAs and catechin exhibited a decreased trend over jujube ripening,and epicatechin content of two jujube cultivars increased first and then declined.Transcriptome analysis revealed that the differentially expressed genes(DEGs)were mainly enriched in ribosome,glycolysis/gluconeogenesis,fructose and mannose metabolism.17 DEGs encoding PAL,CHS,CHI,CHS,F3'H,LAR,ANR,C4Hs,4CLs,FLSs,DFRs and UFGTs involved in PA biosynthesis were relatively abundant.The highly transcribed LAR gene may greatly contribute to epicatechin accumulation.A weighted gene co-expression network analysis(WGCNA)was performed,and a network module including 1620 genes highly correlated with content of Pas and catechin was established.We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module.Sixteen genes encoding 9 families of transcriptional factors(i.e.,MYB,bHLH,ERF,bZIP,NAC,SBP,MIKC,HB,WRKY)were considered as hub genes.The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data.These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding.

Transcriptome analysis to identify candidate genes related to chlorogenic acid biosynthesis during development of Korla fragrant pear in Xinjiang

Korla fragrant pear(KFP)with special fragrance is a unique cultivar in Xinjiang,China.In order to explore the biosynthesis molecular mechanism of chlorogenic acid(CGA)in KFP,the samples at different development periods were collected for transcriptome analysis.High performance liquid chromatography analysis showed that CGA contents of KFP at 88,118 and 163 days after full bloom were(20.96±1.84),(12.01±0.91)and(7.16±0.41)mg/100 g,respectively,and decreased with the fruit development.Pears from these typical 3 periods were selected for de novo transcriptome assemble and 68059 unigenes were assembled from 444037960 clean reads.One‘phenylpropanoid biosynthesis’pathway including 57 unigenes,11 PALs,1 PTAL,64CLs,9 C4Hs,25 HCTs and 5 C3’Hs related to CGA biosynthesis was determined.It was found that the expression levels of 11 differentially expressed genes including 1 PAL,2 C4Hs,34CLs and 5 HCTs were consistent with the change of CGA content.Quantitative polymerase chain reaction analysis further showed that 8 unigenes involved in CGA biosynthesis were consistent with the RNA-seq data.These findings will provide a comprehensive understanding and valuable information on the genetic engineering and molecular breeding in KFP.

Comparative transcriptome analysis on candidate genes involved in lipid biosynthesis of developing kernels for three walnut cultivars in Xinjiang

Walnut(Juglans regia L.)is a good source of lipids and polyunsaturated fatty acids(PUFAs).In order to explore the biosynthesis molecular mechanism of oil accumulation and fatty acid(FA)synthesis in walnut,the samples at different development periods of three walnut cultivars,’Zhipi’(ZP),’Xinwu 417’(W417)and’Xinwen 81’(W81)were collected for transcriptomic analysis.The analysis of oil accumulation and FA profiles showed that the oil content in mature walnut kernel was nearly 70%,and over 90%of FAs were PUFAs.We identified 126 candidate genes including 64 genes for FA de novo synthesis,45 genes for triacylglycerol assembly,and 17 genes for oil bodies involved in lipid biosynthesis by RNA-sequencing.Ten key enzymes including ACCase,LACS6,LACS8,SAD,FAD2,FAD3,LPAAT1,DGAT2,PDAT2,and PLC encoded by 19 genes were highly associated with lipid biosynthesis.Quantitative PCR analysis further validated 9 important genes,and the results were well consistent with our transcriptomic data.Finally,5 important transcription factors including WRI1,ABI3,FUS3,PKL and VAL1 were identified,and their main regulatory genes might contain ACCase,KASII,LACS,FAD3 and LPAAT which were determined through correlation analysis of expression levels for 27 walnut samples.These findings will provide a comprehensive understanding and valuable information on the genetic engineering and molecular breeding in walnut.

Comparative transcriptome analysis of candidate genes involved in chlorogenic acid biosynthesis during fruit development in three pear varieties of Xinjiang Uygur Autonomous Region

Pear is one of the main fruits with thousands of years of cultivation history in China.There are more than 2000 varieties of pear cultivars around the world,including more than 1200 varieties or cultivars in China(Legrand et al.,2016).Xinjiang Uygur Autonomous Region is an important pear production region in China with 30 of varieties or cultivars.Pyrus sinkiangensis is the most popular variety,which is mainly distributed in Xinjiang(Zhou et al.,2018).Chlorogenic acid(CGA),p-coumaric acid.