Abiotic stresses at different growth stages in the life of plants negatively affect yield productivity. Therefore, plants, including
The
All over the world species from the genus, Amaranthus is also evaluated as a leaf vegetable and ornamental plant [
There are several complex molecular events with several mechanisms that involve the expression of genes responding to undesirable environmental conditions [
Previous studies have illustrated that different plant species have several
Nonredundant protein was checked for the presence of
Characterization of the intron and exon organizations of
Phylogenetic analysis and tree constructs were performed using MEGA v7 through Neighbor-joining Method (N.J.) and clustering was rated with 1000 bootstrap replicates followed by multiple sequence alignments by employing ClustalW [
To find conserved protein,
Cis-acting component analysis of
The gene duplication events were investigated between
Expression profiling analysis of
All putative
Furthermore, some important information about this gene family is given in
Gene ID | Phytozome ID | Chromosomal location | Start | End | Strand | aa | Molecular weight (kDa) | pI | Instability Index | Stabil/Unstable | Subcellular localization |
---|---|---|---|---|---|---|---|---|---|---|---|
AH000120-RA | Scaffold_1 | 1142600 | 1143596 | + | 331 | 38.73 | 9.16 | 52.55 | Unstable | chlo: 6.5, nucl: 4, chlo_mito: 4, cyto: 2, extr: 1 | |
AH000563-RA | Scaffold_1 | 6017582 | 6018425 | − | 280 | 32.11 | 9.07 | 52.94 | Unstable | chlo: 8.5, chlo_mito: 7.33333, mito: 5, cyto_mito: 3.33333 | |
AH000569-RA | Scaffold_1 | 6087530 | 6093619 | + | 638 | 73.47 | 9.18 | 46.82 | Unstable | chlo: 12, nucl: 1, plas: 1 | |
AH000950-RA | Scaffold_1 | 14163323 | 14164226 | − | 300 | 34.36 | 9.45 | 27.76 | Stable | nucl: 4, cyto: 4, pero: 2, mito: 1.5, cyto_mito: 1.5, chlo: 1, plas: 1 | |
AH005893-RA | Scaffold_3 | 14599506 | 14608248 | − | 510 | 58.27 | 9.29 | 41.49 | Unstable | chlo: 13, nucl: 1 | |
AH006852-RA | Scaffold_4 | 4200195 | 4201431 | − | 411 | 47.23 | 8.36 | 41.89 | Unstable | cyto: 12, nucl: 2 | |
AH008278-RA | Scaffold_4 | 28168361 | 28171907 | + | 293 | 33.59 | 9.46 | 45.28 | Unstable | chlo: 7, nucl: 2, mito: 2, cyto: 1, vacu: 1, E.R.: 1 | |
AH008563-RA | Scaffold_5 | 2743848 | 2749626 | − | 598 | 68.01 | 8.95 | 46.70 | Unstable | chlo: 12.5, chlo_mito: 7.5, mito: 1.5 | |
AH008573-RA | Scaffold_5 | 2871990 | 2887061 | − | 775 | 86.91 | 7.04 | 40.65 | Unstable | plas: 10, E.R.: 3, chlo: 1 | |
AH008767-RA | Scaffold_5 | 5385266 | 5386427 | + | 386 | 43.71 | 9.37 | 33.64 | stable | mito: 6, chlo_mito: 5.83333, chlo: 4.5, |
|
AH009043-RA | Scaffold_5 | 11578601 | 11580613 | − | 566 | 65.27 | 8.21 | 32.63 | Stable | chlo: 9, nucl: 1, cyto: 1, plas: 1, extr: 1, E.R.: 1 | |
AH010680-RA | Scaffold_6 | 18554829 | 18557313 | + | 319 | 37.13 | 9.73 | 51.99 | unstable | nucl: 8, cyto: 5, E.R.: 1 | |
AH011694-RA | Scaffold_7 | 14365569 | 14372237 | − | 212 | 24.32 | 5.54 | 48.24 | Unstable | chlo: 7, pero: 3, nucl: 2.5, cyto_nucl: 2, golg: 1 | |
AH011901-RA | Scaffold_7 | 18051832 | 18053492 | − | 505 | 57.30 | 7.13 | 45.32 | Unstable | nucl: 6, cyto: 6, chlo: 1, golg: 1 | |
AH012456-RA | Scaffold_8 | 283979 | 285048 | − | 228 | 26.42 | 9.67 | 39.96 | Stable | cyto_nucl: 5, nucl: 4.5, cyto: 4.5, chlo: 2, cysk: 2, extr: 1 | |
AH012607-RA | Scaffold_8 | 1747795 | 1749381 | − | 504 | 57.18 | 6.04 | 46.74 | Unstable | cyto: 7, chlo: 5, nucl: 1, pero: 1 | |
AH013136-RA | Scaffold_8 | 6751252 | 6752806 | − | 290 | 33.80 | 9.52 | 46.25 | Unstable | chlo: 10, cyto: 2, E.R.: 2 | |
AH014698-RA | Scaffold_9 | 16138092 | 16139506 | + | 298 | 33.58 | 9.21 | 37.49 | Stable | chlo: 8, extr: 3, cyto: 1, mito: 1, E.R.: 1 | |
AH015771-RA | Scaffold_10 | 12327223 | 12328399 | + | 391 | 45.55 | 9.42 | 47.36 | Unstable | mito: 6.5, chlo: 6, cyto_mito: 4, nucl: 1 | |
AH015772-RA | Scaffold_10 | 12339047 | 12342002 | − | 401 | 46.87 | 9.61 | 45.90 | Unstable | mito: 5.5, nucl: 4, cyto_mito: 3.5, chlo: 3, golg_plas: 1 | |
AH018172-RA | Scaffold_12 | 1919980 | 1920573 | − | 155 | 17.90 | 6.9 | 29.94 | Stable | cyto: 9, extr: 3, nucl: 1, cysk: 1 | |
AH019050-RA | Scaffold_12 | 14891414 | 14894228 | − | 397 | 46.02 | 9.48 | 51.84 | Unstable | mito: 6.5, cyto_mito: 4, chlo: 3, nucl: 3, golg_plas: 1 | |
AH021712-RA | Scaffold_15 | 296985 | 297477 | + | 163 | 18.90 | 9.37 | 24.39 | Stable | nucl: 11, vacu: 2, cyto: 1 | |
AH021769-RA | Scaffold_15 | 794905 | 796795 | − | 379 | 43.21 | 9.36 | 48.26 | Unstable | nucl: 6, cyto: 5, chlo: 2.5, chlo_mito: 2 |
Note: +: Forward strand, −: Reverse strand.
The Gene structure of 24
The chromosome mapping analysis was performed on the MapChart tool to explore genetic variations in the
Gene or genome duplications contribute to genomic evolution. Both tandemly and segmentally duplicated gene pairs were identified among all
Gene 1 | Gene 2 | Ka | Ks | Ka/Ks | Selection pressure | Duplication type |
---|---|---|---|---|---|---|
0,154 | 0,308 | 0,500 | Purifying | Tandem | ||
0,261 | 0,574 | 0,455 | Purifying | WGD/Segmental |
Note: Ka, non-synonymous substitution rate; Ks, synonymous substitution rate.
The ratio of Ka/Ks > 1 and Ka/Ks = 1 values show positive selection and neutral selection, respectively [
These results demonstrated that the Ka/Ks ratio in tandemly duplicated (
To analyze the
The lowest number of
The orthologous association of
Gene 1 | Gene 2 | Ka | Ks | Ka/Ks | Selection pressure |
---|---|---|---|---|---|
AUR62011331 | 0,215 | 1,001 | 0,215 | Purifying | |
AUR62016730 | 0,149 | 0,939 | 0,159 | Purifying | |
AUR62011322 | 0,098 | 0,740 | 0,132 | Purifying | |
AUR62013212 | 0,064 | 0,841 | 0,077 | Purifying | |
AUR62024319 | 0,200 | 0,601 | 0,333 | Purifying | |
AUR62017060 | 0,051 | 0,534 | 0,096 | Purifying | |
AUR62027731 | 0,284 | 0,814 | 0,349 | Purifying | |
AUR62018915 | 0,265 | 0,843 | 0,314 | Purifying | |
AUR62023431 | 0,212 | 0,735 | 0,289 | Purifying | |
AUR62013723 | 0,215 | 0,717 | 0,300 | Purifying | |
AUR62035531 | 0,315 | 0,771 | 0,408 | Purifying | |
AUR62041650 | 0,298 | 0,872 | 0,342 | Purifying | |
AUR62029735 | 0,380 | 1,289 | 0,295 | Purifying | |
AUR62002686 | 0,140 | 1,020 | 0,137 | Purifying | |
AT2G21710.1 | 0,316 | 4,995 | 0,063 | Purifying | |
AT5G06810.1 | 0,489 | 1,793 | 0,273 | Purifying | |
AT5G55580.1 | 0,163 | NaN | NaN | Purifying | |
AT2G34620.1 | 0,254 | NaN | NaN | Purifying | |
AT2G36000.1 | 0,475 | 2,464 | 0,193 | Purifying |
The MEME 5.0.5 online tool was utilized to distinguish the conserved motifs of
Moreover,
ID | Width | Best possible match |
---|---|---|
Motif-1 | 15 | PQILGYSIEKNMKPR |
Motif-2 | 15 | YLKSMGWSKDDIGRM |
Motif-3 | 21 | FRRCPQCFCCSEAKLKQGMDY |
Motif-4 | 21 | WMLNMPEHVFIHRYVTKYSDT |
Motif-5 | 28 | MGIPPDHPMYIHAIRVMNSLSEESWERK |
Motif-6 | 21 | AIRRGPWILTADWENMQQNLD |
Motif-7 | 24 | HQHLMERGVHCPLNDMLACSDHEF |
Motif-8 | 15 | YLVQEMGRPIQEVVE |
Motif-9 | 29 | SNQSFCIQYLTNSCGLSLHSAISISKKVT |
Motif-10 | 21 | IHFFKENGFSGCHIPQFIVKY |
Previous studies showed that
While Families of plant
The
Gene duplications are very important in the independent mechanisms ending up with segmental and tandem duplication, including novel functions, the evolution of related close genes, gene expansion, and enhancing stress tolerance [
Moreover,
The cluster relationships analysis between m
The functions of several
24
The author received no specific funding for this study.
The author declares that they have no conflicts of interest to report regarding the present study.