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Molecular Genetics and Genomics

, Volume 291, Issue 1, pp 383–398 | Cite as

Gene transcript profiles in the desert plant Nitraria tangutorum during fruit development and ripening

  • Jia Wang
  • Zhenhua Dang
  • Huirong Zhang
  • Linlin Zheng
  • Tebuqin Borjigin
  • Yingchun WangEmail author
Original Article

Abstract

Nitraria tangutorum Bobr., a valuable wild shrub distributed in Northwest China, produces edible and medicinal berries. However, little is known about the molecular mechanisms of its fruit development and ripening. We performed de novo transcriptome sequencing of N. tangutorum fruit using the Illumina HiSeq™ 2000 sequencing platform. More than 62.94 million reads were obtained and assembled into 69,306 unigenes (average length, 587 bp). These unigenes were annotated by querying against five databases (Nr, Swiss-Prot, GO, COG, and KEGG); 42,929 and 26,809 unigenes were found in the Nr and Swiss-Prot databases, respectively. In ortholog analyses, 33,363 unigenes were assigned with one or more GO terms, 15,537 hits were aligned to 25 COG classes, and 24,592 unigenes were classified into 128 KEGG pathways. Digital gene expression analyses were conducted on N. tangutorum fruit at the green (S1), yellow (S2), and red (S3) developmental stages. In total, 8240, 5985, and 4994 differentially expressed genes (DEGs) were detected for S1 vs. S2, S1 vs. S3, and S2 vs. S3, respectively. Cluster analyses showed that a large proportion of DEGs related to plant hormones and transcription factors (TFs) showed high expression in S1, down-regulated expression in S2, and up-regulated expression in S3. We analyzed the expression patterns of 23 genes encoding 12 putative enzymes involved in flavonoid biosynthesis. The expression profiles of 10 DEGs involved in flavonoid biosynthesis were validated by Q-PCR analysis. The assembled and annotated transcriptome sequences and gene expression profile analyses provide valuable genetic resources for research on N. tangutorum.

Keywords

Nitraria tangutorum RNA-seq Digital gene expression profiling Fruit development and ripening 

Notes

Acknowledgments

We thank the BGI at Shenzhen for Illumina sequencing and data analysis. This work was supported by the Natural Science Foundation Key Project of Inner Mongolia Autonomous Region (2015ZD03), the Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region (NMGIRT1401), and the Inner Mongolia Autonomous Region Science and Technology Plan Project (20140707).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

438_2015_1116_MOESM1_ESM.tif (780 kb)
Fig S1 Results of homology searches of assembled unigenes against Nr databases (TIFF 780 kb)
438_2015_1116_MOESM2_ESM.tif (602 kb)
Fig S2 GO functional annotation. Unigenes with best BLAST hits were aligned to GO database (TIFF 601 kb)
438_2015_1116_MOESM3_ESM.doc (35 kb)
Table S1 Primer sequences used for Q-PCR. (DOC 35 kb)
438_2015_1116_MOESM4_ESM.xlsx (930 kb)
Table S2 GO functional annotation of genes (XLSX 930 kb)
438_2015_1116_MOESM5_ESM.xlsx (311 kb)
Table S3 COG classifications of genes (XLSX 311 kb)
438_2015_1116_MOESM6_ESM.xlsx (138 kb)
Table S4 Genes annotated in KEGG database (XLSX 137 kb)
438_2015_1116_MOESM7_ESM.xlsx (244 kb)
Table S5 DEGs subjected to GO functional enrichment analyses (XLSX 243 kb)
438_2015_1116_MOESM8_ESM.xlsx (20 kb)
Table S6 DEGs subjected to KEGG pathway enrichment analyses (XLSX 19 kb)
438_2015_1116_MOESM9_ESM.xlsx (12 kb)
Table S7 Differentially expressed genes related to plant hormones during fruit development (XLSX 12 kb)
438_2015_1116_MOESM10_ESM.xlsx (13 kb)
Table S8 Differentially expressed genes related to transcription factors during fruit development (XLSX 13 kb)
438_2015_1116_MOESM11_ESM.xlsx (11 kb)
Table S9 Genes involved in the flavonoid biosynthetic pathway (XLSX 11 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Jia Wang
    • 1
  • Zhenhua Dang
    • 1
  • Huirong Zhang
    • 1
  • Linlin Zheng
    • 1
  • Tebuqin Borjigin
    • 1
    • 2
  • Yingchun Wang
    • 1
    Email author
  1. 1.College of Life SciencesInner Mongolia UniversityHohhotPeople’s Republic of China
  2. 2.College of Mongolian MedicineInner Mongolia Medical UniversityHohhotPeople’s Republic of China

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