The red flesh trait gives red pitayas more healthful components and a higher price, while the genetic mechanism behind this trait is unknown. In this manuscript, transcriptome analysis was employed to discover the genetic differences between white and red flesh in pitayas. A total of 27.99 Gb clean data were obtained for four samples. Unigenes, 79,049 in number, were generated with an average length of 1333 bp, and 52,618 Unigenes were annotated. Compared with white flesh, the expression of 10,215 Unigenes was up-regulated, and 4853 Unigenes were down-regulated in red flesh. The metabolic pathways accounted for 64.6% of all differentially expressed Unigenes in KEGG pathways. The group with high betalain content in red flesh and all structural genes, related to betalain biosynthesis, had a higher expression in red flesh than white flesh. The expression of the key gene, tyrosine hydroxylase CYP76AD1, was up-regulated 245.08 times, while 4,5-DOPA dioxygenase DODA was up-regulated 6.46 times. Moreover, the special isomers CYP76AD1α and DODAα were only expressed in red flesh. The competitive anthocyanin biosynthesis pathway had a lower expression in red flesh. Two MYB transcription factors were of the same branch as BvMYB1, regulating betalain biosynthesis in beet, and those transcription factors had expression differences in two kinds of pitayas, which indicated that they should be candidate genes controlling betalain accumulation in red pitayas. This research would benefit from identifying the major gene controlling red flesh trait and breed new cultivars with the red flesh trait. Future research should aim to prove the role of each candidate gene in betalain biosynthesis in red pitayas.

Jerusalem artichoke (Helianthus tuberosus L.) is a characteristic crop in the Qinghai-Tibet Plateau which has rapidly developed and gained socioeconomic importance in recent years. Fructans are abundant in tubers and represent the foundation for their formation, processing and utilization of yield; and are also widely used in new sugar-based materials, bioenergy processing, ecological management, and functional feed. To identify key genes in the metabolic pathway of fructans in Jerusalem artichoke, high-throughput sequencing was performed using Illumina Hi Seq™ 2500 equipment to construct a transcriptome library. Qinghai-Tibet Plateau Jerusalem artichoke “Qingyu No.1” was used as the material; roots, stems, leaves, flowers and tubers of Jerusalem artichoke in its flowering stage were mixed into a mosaic of the Jerusalem artichoke transcriptome library, obtaining 63,089 unigenes with an average length of 713.6 bp. Gene annotation through the Nr, Swiss Prot, GO, KOG and KEGG databases revealed 34.95 and 46.91% of these unigenes had similar sequences in the Nr and Swiss Prot databases. The GO classification showed the Jerusalem artichoke unigenes were divided into three ontologies, with a total of 49 functional groups encompassing biological processes, cellular components, and molecular functions. Among them, there were more unigenes involved in the functional groups for cellular processes, metabolic processes, and single-organism processes. 38,999 unigenes were annotated by KOG and divided into 25 categories according to their functions; the most common annotation being general function prediction. A total of 13,878 unigenes (22%) were annotated in the KEGG database, with the largest proportion corresponding to pathways related to carbohydrate metabolism. A total of 12 unigenes were involved in the synthesis and degradation of fructan. Cluster analysis revealed the candidate 12 unigene proteins were dispersed in the 5 major families of proteins involved in fructan synthesis and degradation. The synergistic effect of INV gene is necessary during fructose synthesis and degradation in Jerusalem artichoke tuber development. The sequencing data from the transcriptome of this species can provide a reliable data basis for the identification and assessment of the expression of the members of the INV gene family.A simple sequence repeat (SSR) loci search was performed on the transcriptome data of Jerusalem artichoke, identifying 6635 eligible SSR loci with a large proportion of dinucleotide and trinucleotide repeats, and the most different motifs were repeated 5 times and 6 times. Dinucleotide and trinucleotide repeat motifs were the most frequent, with AG/CT and ACC/GGT repeat motifs accounting for the highest proportion. In this study, a database search of the transcriptome of the Jerusalem artichoke from the Qinghai Tibet Plateau was conducted by high throughput sequencing technology to obtain important transcriptional and SSR loci information. This allowed characterization of the overall expression features of the Jerusalem artichoke transcriptome, identifying the key genes involved in metabolism in this species. In turn, this offers a foundation for further research on the regulatory mechanisms of fructan metabolism in Jerusalem artichoke.