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Genome-wide characterization of phenylalanine ammonia-lyase gene family in watermelon (Citrullus lanatus)

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Abstract

Phenylalanine ammonia-lyase (PAL), the first enzyme in the phenylpropanoid pathway, plays a critical role in plant growth, development, and adaptation. PAL enzymes are encoded by a gene family in plants. Here, we report a genome-wide search for PAL genes in watermelon. A total of 12 PAL genes, designated ClPAL1-12, are identified . Nine are arranged in tandem in two duplication blocks located on chromosomes 4 and 7, and the other three ClPAL genes are distributed as single copies on chromosomes 2, 3, and 8. Both the cDNA and protein sequences of ClPALs share an overall high identity with each other. A phylogenetic analysis places 11 of the ClPALs into a separate cucurbit subclade, whereas ClPAL2, which belongs to neither monocots nor dicots, may serve as an ancestral PAL in plants. In the cucurbit subclade, seven ClPALs form homologous pairs with their counterparts from cucumber. Expression profiling reveals that 11 of the ClPAL genes are expressed and show preferential expression in the stems and male and female flowers. Six of the 12 ClPALs are moderately or strongly expressed in the fruits, particularly in the pulp, suggesting the potential roles of PAL in the development of fruit color and flavor. A promoter motif analysis of the ClPAL genes implies redundant but distinctive cis-regulatory structures for stress responsiveness. Finally, duplication events during the evolution and expansion of the ClPAL gene family are discussed, and the relationships between the ClPAL genes and their cucumber orthologs are estimated.

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Abbreviations

ABA:

Abscisic acid

ABRE:

ABA-responsive element

AuxRE:

Auxin-responsive element

CRT:

C-repeat

ERE:

Ethylene-responsive element

GA:

Gibberellin

GARE:

GA-responsive element

HSE:

Heat shock-responsive element

LTRE:

Low temperature-responsive element

MIO:

4-Methylidene-imidazolone-5-one

ORF:

Open reading frame

PAL:

Phenylalanine ammonia-lyase

RT-PCR:

Reverse transcription-polymerase chain reaction

SA:

Salicylic acid

SARE:

SA-responsive element

UTR:

Untranslated region

WGD:

Whole-genome duplication

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Acknowledgments

We thank the members of our laboratory for their helpful advice and discussions. This work is supported by the Young Scientists Fund of the National Natural Science Foundation of China (No. 31101548) and China Agriculture Research System (CARS-25). This work is also supported by Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture.

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Authors and Affiliations

  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China

    Chun-Juan Dong & Qing-Mao Shang

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  1. Chun-Juan Dong
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  2. Qing-Mao Shang
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Correspondence to Qing-Mao Shang.

Electronic supplementary material

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Supplementary Table S1 Primers used for cloning and RT-PCR analysis of ClPAL genes.

Supplementary Table S2 Sequence identities among the coding regions of the ClPAL genes.

Supplementary Table S3 Sequence identities among the ClPAL proteins.

Supplementary Figure S1 Nucleic acid sequence and the deduced amino acid sequences of ClPAL1-12.

Supplementary Figure S2 Promoter sequences and the predicted cis-elements of ClPAL1-12 genes. The putative transcription initiation site was designated as +1. The predicted cis-elements were shown in bold and boxed and annotated below.

Supplementary Figure S3 RNA transcript levels of three housekeeping genes in different tissues of cucumber.

Supplementary material 1 (DOC 2038 kb)

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Dong, CJ., Shang, QM. Genome-wide characterization of phenylalanine ammonia-lyase gene family in watermelon (Citrullus lanatus). Planta 238, 35–49 (2013). https://doi.org/10.1007/s00425-013-1869-1

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