Genome-Wide Investigation and Expression Analysis of K + -Transport-Related Gene Families in Chinese Cabbage ( Brassica
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Genome‑Wide Investigation and Expression Analysis of K+‑Transport‑Related Gene Families in Chinese Cabbage (Brassica rapa ssp. pekinensis) Changwei Shen1 · Jingping Yuan2 Received: 21 May 2020 / Accepted: 18 September 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Potassium (K+) transport and channel systems play vital roles in plant growth, development and responses to various stresses. In this study, 44 putative K+-transport-related genes (18K+ uptake permease (KUP)/high-affinity K+ (HAK)/ K+ transporter (KT) family genes and 26 channel genes, including 18 Shaker family genes and 8 K+ channel outward (KCO) family genes) were identified in the genome of Chinese cabbage (Brassica rapa ssp. pekinensis). To clarify the molecular evolution of each family in Chinese cabbage, phylogenetic analysis and assessments of the gene structures, conserved motifs, chromosomal locations, gene duplications, expression patterns and cis-acting elements of the 44 putative K+-transport-related genes were performed. The phylogenetic analysis showed that these genes could be classified into five clades [KUP/HAK/KTs, KCOs, Kout, Kin (KAT) and Kin (AKT)] and that the members of a given clade shared conserved exon–intron distributions and motif compositions. These K +-transport-related genes were unevenly distributed over all ten chromosomes, including four duplicated gene pairs that implied an expansion of K+-transport-related genes in Chinese cabbage. Analyses of Illumina RNA-seq data for these 4 4K+-transport-related genes indicated tissue-/organ-specific expression patterns. In addition, an overall evaluation showed that the expression levels of KUP/HAK/KT genes were significantly higher than those of potassium channel genes in six tissues. Promoter cis-acting element analysis revealed that these 44K+-transport-related genes may be associated with responses to 10 abiotic stresses, primarily light, methyl jasmonate (MeJA) and abscisic acid (ABA). Our results provide a systematic and comprehensive overview of K +-transport-related gene families in Chinese cabbage and establish a foundation for further research on K+ absorption and transport functions.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s1052 8-020-10004-z) contains supplementary material, which is available to authorized users. Extended author information available on the last page of the article
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Vol.:(0123456789)
Biochemical Genetics
Keywords Chinese cabbage · K+-transport-related genes · Phylogenetic tree · Conserved domain · Cis-acting elements · Expression pattern
Introduction Potassium (K+) is the most widely distributed inorganic cation in plant cells, accounting for 10% of plant dry matter (Leigh and Wyn Jones 1984). K+ is critical for the regulation of plant growth and is involved in many basic functions, such as protein biosynthesis, stomatal movement, cell length, osmotic adjustment, photosynthesis and maintenance of plasma membrane potential. Due
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