Genome-wide Identification, Classification, Expression and Duplication Analysis of GRAS Family Genes in Juglans regia L.

Shaowen Quan,Jianxin Niu,Hang Xu,Li Ma,Yang Qin,Li Zhou

doi:10.1038/s41598-019-48287-x

Shaowen Quan, Jianxin Niu + Show 4 more

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https://doi.org/10.1038/s41598-019-48287-x

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Abstract

Fifty-two GRAS genes are identified in walnut genome. Based on the evolutionary relationship and motif analysis, the walnut GRAS gene family was divided into eight subfamilies, and the sequence features analysis of JrGRAS proteins showed that the JrGRAS protein sequences were both conserved and altered during the evolutionary process. Gene duplication analysis indicated that seven GRAS genes in walnut have orthologous genes in other species, and five of them occurred duplicated events in walnut genome. Expression pattern analysis of the GRAS family genes in walnut showed that two JrGRAS genes (JrCIGRa-b and JrSCL28a) were differentially expressed between flower bud and leaf bud (p < 0.01), and two JrGRAS genes (JrCIGRa-b and JrSCL13b-d) were differentially expressed between the different development stages of flower buds transition (p < 0.01), besides, three hub genes (JrGAIa, JrSCL3f and JrSHRc) were identified by co-expression analysis, which suggested these GRAS genes may play an important role in regulating the development of apical meristem in walnut. This study laid a foundation for further understanding of the function of GRAS family genes in walnut.

Highlights

Walnut is cultivated worldwide for its nutritious fruits and commercially valuable timber, it needs many years before flowering and to become productive[45,46,47]
The walnut genome was assembled only in scaffold-level, and there is no access to the information of walnut Chromosomes until now
The 44 scaffolds which including the 52 JrGRAS genes were used to represent the walnut genome in the synteny and gene duplication analysis, and this may provide a new insight to the analysis of whole genome evolution for the species whose genome assembled in scaffold-level

Summary

Introduction

Walnut is cultivated worldwide for its nutritious fruits and commercially valuable timber, it needs many years before flowering and to become productive[45,46,47]. To better understanding the molecular mechanism of walnut flower bud transition, it is necessary to investigate the GRAS family in walnut. Www.nature.com/scientificreports walnut genome sequences[48] and transcriptome data of the walnut female flower buds and leaf buds, it is possible for us to identify all the GRAS family genes in walnut. GRAS family genes in walnut have been identified in genome-wide. The phylogenetic relationship, sequence alignment, conserved motif composition and gene duplication of the JrGRAS genes were systematically analyzed, and their expression patterns in different tissues (flower bud and leaf bud) and different development stages (before, during, after the flower transition period) were explored using transcriptome data and validated by qRT-PCR experiments. This research lay a foundation for further function investigations of GRAS genes in walnut

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