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Gene. 2014 Jan 25;534(2):155-62. doi: 10.1016/j.gene.2013.10.073. Epub 2013 Nov 14.

De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing.

Author information

1
Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
2
Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China. Electronic address: hgli@njfu.edu.cn.

Abstract

Liriodendron chinense (Hemsl.) Sarg is an endangered species and occupies a pivotal position in phylogenetic studies of flowering plants, while its genomic resources are limited. In this study, we performed transcriptome sequencing for L. chinense petals and leaves using the Illumina paired-end sequencing technique. Approximately 17.02-Gb clean reads were obtained, and de novo assembly generated 87,841 unigenes, with an average length of 778 bp. Of these, there were 65,535 (74.61%) unigenes with significant similarity to publically available plant protein sequences. There were 3386 genes identified as significant differentially expressed between petals and leaves, among them 2969 (87.68%) were up-regulated and 417 (12.31%) down-regulated in petals. Metabolic pathway analysis revealed that 25 unigenes were predicted to be responsible for the biosynthesis of carotenoids, with 7 genes differentially expressed between these two tissues. This report is the first to identify genes associated with carotenoid biosynthesis in Liriodendron and represents a valuable resource for future genomic studies on the endangered species L. chinense.

KEYWORDS:

ABA; CCS; COG; CRTISO; Carotenoids biosynthesis; Clusters of Orthologous Groups of proteins; DEGs; Endangered; FBP2; GGPP; GO; Gene Ontology; Gene expression differences; KEGG Ortholog database; KO; LCY; MYB340; Myb-related protein 340; NGS; NR; Nt; PDS; PKS1; PSY; Unigenes; VDE; Z-ISO; ZDS; ZEP; capsanthin/capsorubin synthase; carotenoid isomerase; differentially expressed genes; floral binding protein 2; geranylgeranyl pyrophosphate synthase; lycopene cyclases; next-generation sequencing; non-redundant nucleotide sequences; non-redundant protein database; phytochrome kinase substrate 1; phytoene desaturase; phytoene synthase; phytohormones abscisic acid; violaxanthin de-epoxidase; zeaxanthin epoxidase; ζ-carotene desaturase; ζ-carotene isomerase

PMID:
24239772
DOI:
10.1016/j.gene.2013.10.073
[Indexed for MEDLINE]

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