Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

Abstract

The plant sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs) are key regulators in the interconnection of various signaling pathways. However, little is known about the SnRK family in strawberries. In this study, a total of 26 FvSnRKs including one FvSnRK1, nine FvSnRK2s and 16 FvSnRK3s were identified from the strawberry genome database. They were respectively designated as FvSnRK1.1, FvSnRK2.1 to FvSnRK2.9 and FvSnRK3.1 to FvSnRK3.16, according to the conserved domain of each subfamily and multiple sequence alignment with Arabidopsis. FvSnRK family members were unevenly distributed in seven chromosomes. The number of exons or introns varied among FvSnRK1s, FvSnRK2s and FvSnRK3s, but highly conserved in the same subfamily. The FvSnRK1.1 had 10 exons. Most of FvSnRK2s had nine exons or eight introns, except FvSnRK2.4, FvSnRK2.8 and FvSnRK2.9. FvSnRK3 genes were divided into intron-free and intron-harboring members, and the number of introns in intron-harboring group ranged from 11 to 15. Moreover, the phylogenetic analysis showed SnRK1, SnRK2 and SnRK3 subfamilies respectively clustered together in spite of the different species of strawberry and Arabidopsis, indicating the genes were established prior to the divergence of the corresponding taxonomic lineages. Meanwhile, conserved motif analysis showed that FvSnRK sequences that belonged to the same subgroup contained their own specific motifs. Cis-element in promoter and expression pattern analyses of FvSnRK1.1 suggested that FvSnRK1.1 was involved in cold responsiveness, light responsiveness and fruit ripening. Taken together, this comprehensive analysis will facilitate further studies of the FvSnRK family and provide a basis for the understanding of their function in strawberry.

Genomic Characterization and Expression Analysis of the SnRK Family Genes in Dendrobium officinale Kimura et Migo (Orchidaceae)

“…A total of 36 DoSnRK members were identified in D. officinale . Compared with the number of SnRK members in other species, the number in D. officinale was similar to that in Arabidopsis and in Eucalyptus grandis [ 16 ], but D. officinale has 10 more than strawberry [ 12 ] and fewer than Brassica napus [ 42 ] and Brachypodium distachyon [ 41 ]. Among the three subfamilies, the DoSnRK1 subfamily had only one member (DoSnRK1.1), which is the same as that in strawberry [ 12 ] but less than that in other species.…”

“…Compared with the number of SnRK members in other species, the number in D. officinale was similar to that in Arabidopsis and in Eucalyptus grandis [ 16 ], but D. officinale has 10 more than strawberry [ 12 ] and fewer than Brassica napus [ 42 ] and Brachypodium distachyon [ 41 ]. Among the three subfamilies, the DoSnRK1 subfamily had only one member (DoSnRK1.1), which is the same as that in strawberry [ 12 ] but less than that in other species. The DoSnRK2 subfamily contained moderate members, as in sugar beet [ 13 ], tea [ 44 ], E. grandis [ 16 ], and strawberry [ 12 ], but some species contained more than 10 members [ 41 , 42 , 45 , 46 , 47 , 48 , 49 ].…”

“…Among the three subfamilies, the DoSnRK1 subfamily had only one member (DoSnRK1.1), which is the same as that in strawberry [ 12 ] but less than that in other species. The DoSnRK2 subfamily contained moderate members, as in sugar beet [ 13 ], tea [ 44 ], E. grandis [ 16 ], and strawberry [ 12 ], but some species contained more than 10 members [ 41 , 42 , 45 , 46 , 47 , 48 , 49 ]. The DoSnRK3 subfamily contained the most members, similar to B. distachyon [ 41 ] and E. grandis [ 16 ], but fewer than Brassica.…”

“…SnRK2 and SnRK3 subfamilies are specific to plants and contain more members than the SnRK1 subfamily. SnRK2 and SnRK3 subfamilies are thought to evolve from SnRK1 and form more functions during evolution [ 12 ]. The SnRK2 subfamily contains a kinase domain and an ATP-binding domain.…”

“…D. officinale plants prefer to grow in hot tropical areas and show strong resistance to stresses, particularly to drought [ 37 ]. Although SnRK members have been identified in various plants, such as Arabidopsis [ 10 , 39 ], apple [ 40 ], Brachypodium distachyon L. [ 41 ], Eucalyptus grandis [ 16 ], strawberry [ 12 ], and Brassica napus [ 42 ], there is no report on the SnRK family in orchid plants. In the present research, a comprehensive investigation of the SnRK family in D. officinale was carried out.…”