The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification
Frontiers in Plant Science(2020)
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, which were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between these species, this study offers insights about Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq, identifying significant similarities between Sbi and Ssp. Moreover, through coexpression networks, we inferred a core structure of kinase interactions with specific key elements. This study is the first to categorize the allele specificity of a kinome and provides a wide reservoir of molecular and genetic information, enhancing the understanding of the evolutionary history of Sbi and Ssp PKs.
Highlight This study describes the catalog of kinase gene family in Saccharum spontaneum and Sorghum bicolor , providing a reservoir of molecular features and expression patterns based on RNA-Seq and co-expression networks.
### Competing Interest Statement
The authors have declared no competing interest.
* Aco
: Aquilegia coerulea
AGC
: cyclic AMP-dependent protein kinase (cAPK), cGMP-dependent protein kinase, and lipid signaling kinase families
Aly
: Arabidopsis lyrata
Ath
: Arabidopsis thaliana
B-lectin
: D-mannose-binding lectin
Bdi
: Brachypodium distachyon
CAMK
: calcium- and calmodulin-regulated kinase
Ccl
: Citrus clementina
CDS
: DNA coding sequence
CK1
: casein kinase 1
CMGC
: cyclin-dependent kinase, mitogen-activated protein kinase, glycogen synthase kinase and cyclin-dependent kinase-like kinase
Cpa
: Carica papaya
Cre
: Chlamydomonas reinhardtii
Csa
: Cucumis sativus
Csi
: Citrus sinensis
DUF26
: Domain of Unknown Function 26
Egr
: Eucalyptus grandis
ER
: endoplasmic reticulum
GM
: gene model
Gma
: Glycine max
GO
: Gene Ontology
GUB
: galacturonan-binding
HMM
: hidden Markov model
IRE1
: inositol-requiring kinase 1
Ka
: Nonsynonymous substitution rates
Ks
: Synonymous substitution rates
LRR
: leucine-rich repeat
LRRNT
: leucine-rich repeat N-terminal domain
Mes
: Manihot esculenta
Mgu
: Mimulus guttatus
Mtr
: Medicago truncatula
MW
: molecular weight
MYA
: million years ago
Osa
: Oryza sativa
PEK
: pancreatic eukaryotic initiation factor-2alpha kinase
PK
: protein kinase
pI
: isoelectric point
Ppa
: Physcomitrella patens
Ppe
: Prunus persica
Ptr
: Populus trichocarpa
Rco
: Ricinus communis
RLK
: receptor-like kinase
S-locus-glycop
: S-locus glycoprotein
Sbi
: Sorghum bicolor
Sit
: Setaria italica
Smo
: Selaginella moellendorffii
Ssp
: Saccharum spontaneum
STE
: serine/threonine kinase
TKL
: tyrosine kinase-like kinase
TPM
: Transcripts per million
Vca
: Volvox carteri
Vvi
: Vitis vinifera
WAK
: wall-associated receptor kinase
WGD
: whole-genome duplication
Zma
: Zea mays
MoreTranslated text
AI Read Science
Must-Reading Tree
Example
Generate MRT to find the research sequence of this paper
Chat Paper
Summary is being generated by the instructions you defined