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Comparative study of the leaf transcriptomes and ionoms of Juglans regia and its wild relative species Juglans cathayensis

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Abstract

Juglans regia ‘Yuanfeng’ is an elite walnut cultivar in China. Juglans cathayensis, a close relative species of Juglans regia originated from China, possesses some superior traits such as strong disease resistance and high fruit number per branch. So far, transcriptomes of either J. regia or J. cathayensis have not been studied and made available to public yet. In the present study, the transcriptomes of J. regia and J. cathayensis leaves were profiled using Illumina HiSeq 2000 platform. A total of 41,914 unigenes were obtained from the combined clean reads of J. regia and J. cathayensis with an average length of 1363 bp and 2529 differentially expressed genes (DEGs) were detected. Gene annotation analyses revealed that 38,483 unigenes (91.81%) were annotated in at least one of the five databases such as Gene Ontology (GO), etc. Meanwhile, the Ca, Mg, Fe, Zn, K and protein contents in the leaves of J. regia and J. cathayensis were compared and significant differences between J. regia and J. cathayensis in terms of the Ca, Mg, Fe and protein contents were discovered. In addition, DEGs associated with the Ca, Mg and Fe content variations between J. regia and J. cathayensis were investigated. Our comparative transcriptomes’ analysis between J. regia and J. cathayensis could provide a useful resource for genetic characterization and improvements of J. regia.

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Abbreviations

ACA:

Auto-inhibited Ca2+-ATPases

Atp2c:

Calcium-transporting ATPase-type 2C

CAX:

Cation/proton exchanger

Ca-P60A:

Calcium ATPase at 60A

DEG:

Differentially expressed gene

ECA:

Er-type Ca2+-ATPase

eggNOG:

Evolutionary genealogy of genes: Non-supervised Orthologous Groups

FRD:

Ferric reductase defective

GO:

Gene ontology

IRT:

Iron-regulated transporter

KEGG:

Kyoto Encyclopedia of Genes and Genomes

KO:

KEGG orthology

MHX:

Magnesium/proton exchanger

MTP:

Metal tolerance protein

NGS:

Next generation sequencing

nr:

Non-redundant database

NRAMP:

Natural resistance-associated macrophage protein

PPO:

Polyphenol oxidase

RNA-seq:

RNA sequencing

RPKM:

Reads per kb per million reads

SRA:

Short read archive

TPC:

Two-pore calcium channel

YSL:

Yellow stripe-like

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Acknowledgements

We thank Mr. Xuejun Ge of Lianchuang Walnut Plantation Co., Ltd., Suizhou, China, for providing experimental materials. Sequencing services were provided by Personal Biotechnology Co., Ltd., Shanghai, China. We also thank Tao Xu of Bionovogene Biotech Co., Ltd., Suizhou, China, for bioinformatics assistance. This work was jointly supported by the Demonstration Project of Forestry Science and Technology funded by the Central Government of China (the plan of Forestry Department of Hubei province, China, [2013]98) and the Natural Science Foundation of Hubei province, China (2012FFC031).

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  1. Zhongcheng Zhou and Muxian Han contributed equally to this work.

Authors and Affiliations

  1. Department of Forestry Ecology, Hubei Ecology Vocational College, No.110, Zhifang Street, Jiangxia District, Wuhan, 430200, China

    Zhongcheng Zhou, Mei Hou, Rui Tian & Shuifa Min

  2. State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, No.1 Dongxiaofu, Haidian District, Beijing, 100091, China

    Zhongcheng Zhou

  3. College of Life Sciences, Hubei Normal University, No.11, Cihu Road, Huangshi, 435002, China

    Muxian Han

  4. General Forestry Station of Sanmenxia City, No.2, Liufeng Road, 472000, Sanmenxia, Henan, China

    Xiaojing Deng

  5. Laboratory of Bio-technology, Xiangyang Academy of Agricultural Sciences, No. 81, Dengcheng Road, Hi-Tec Development Zone, Xiangyang, 441057, China

    Jinbo Zhang

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  1. Zhongcheng Zhou
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Correspondence to Shuifa Min or Jinbo Zhang.

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Communicated by M Stobiecki.

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Zhou, Z., Han, M., Hou, M. et al. Comparative study of the leaf transcriptomes and ionoms of Juglans regia and its wild relative species Juglans cathayensis . Acta Physiol Plant 39, 224 (2017). https://doi.org/10.1007/s11738-017-2504-8

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  • DOI: https://doi.org/10.1007/s11738-017-2504-8

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