Genome-Wide Analysis of SPL Gene Families Illuminate the Evolution Patterns in Three Rubber-Producing Plants
Abstract
:1. Introduction
2. Materials and Methods
2.1. SPL Identification across the Genome and Phylogenetic Analysis
2.2. Physicochemical Characterization and Structural Analysis of the Protein
2.3. Analysis of Protein Domains and Conserved Motifs
2.4. Collinearity Analysis
2.5. Analysis of Expression Patterns across Several Developmental Stages and Tissue Types
3. Results
3.1. SPL Identification across the Genome and Phylogenetic Analysis
3.2. Physicochemical Properties and Secondary and Three-Dimensional Structural Analysis
3.3. Analysis of Protein Domains and Conserved Motifs
3.4. Cis-Acting Elements and Collinearity Analysis
3.5. Analysis of Expression Patterns across Several Developmental Stages and Tissue Types
4. Discussion
4.1. SPL Identification across the Genome and Phylogenetic Analysis
4.2. Analysis of Protein Domains and Conserved Motifs
4.3. Analysis of Responses and Expression Patterns
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | gene ID | Chr ID | Gene Range | Exon | Intron | CDS | UTR | Size/aa | MW/kD | PI | Instability Index |
---|---|---|---|---|---|---|---|---|---|---|---|
TkSPL1 | GWHPBCHF001261 | GWHBCHF00000001 | 14822969:14828316 | 12 | 11 | 11 | 3 | 927 | 103,394.48 | 6.2 | 53.89 |
TkSPL2 | GWHPBCHF002675 | GWHBCHF00000002 | 2073280:2078116 | 11 | 10 | 10 | 3 | 748 | 83,959.66 | 5.95 | 58.08 |
TkSPL3 | GWHPBCHF006473 | GWHBCHF00000002 | 100814431:100818025 | 4 | 3 | 4 | 0 | 261 | 29,108.21 | 7.73 | 74.85 |
TkSPL4 | GWHPBCHF019170 | GWHBCHF00000004 | 830539:832919 | 3 | 2 | 2 | 3 | 302 | 34,271.32 | 9.08 | 68.14 |
TkSPL5 | GWHPBCHF020579 | GWHBCHF00000004 | 30786520:30796342 | 5 | 4 | 5 | 2 | 357 | 39,818.25 | 9 | 51.09 |
TkSPL6 | GWHPBCHF020580 | GWHBCHF00000004 | 30786520:30796342 | 5 | 4 | 4 | 3 | 349 | 38,902.15 | 9.1 | 51.1 |
TkSPL7 | GWHPBCHF022201 | GWHBCHF00000004 | 84269226:84270914 | 4 | 3 | 4 | 2 | 298 | 33,372.53 | 8.41 | 56.09 |
TkSPL8 | GWHPBCHF023484 | GWHBCHF00000004 | 107063807:107065169 | 2 | 1 | 2 | 2 | 198 | 22,079.54 | 9.24 | 65.76 |
TkSPL9 | GWHPBCHF024887 | GWHBCHF00000004 | 129182786:129185573 | 2 | 1 | 2 | 2 | 192 | 22,005.9 | 8.36 | 70.5 |
TkSPL10 | GWHPBCHF025127 | GWHBCHF00000004 | 132569671:132571972 | 3 | 2 | 3 | 2 | 298 | 33,497.02 | 8.76 | 53.76 |
TkSPL11 | GWHPBCHF026791 | GWHBCHF00000004 | 155862873:155865148 | 4 | 3 | 3 | 3 | 279 | 30,897.47 | 9.74 | 67.09 |
TkSPL12 | GWHPBCHF028134 | GWHBCHF00000005 | 14701253:14704746 | 4 | 3 | 3 | 3 | 351 | 37,175.07 | 7.61 | 52.58 |
TkSPL13 | GWHPBCHF029402 | GWHBCHF00000005 | 33473738:33478697 | 11 | 10 | 10 | 3 | 1042 | 115,521.09 | 8.36 | 56.28 |
TkSPL14 | GWHPBCHF029413 | GWHBCHF00000005 | 33656280:33661229 | 11 | 10 | 10 | 3 | 1039 | 115,165.69 | 8.36 | 57.09 |
TkSPL15 | GWHPBCHF035319 | GWHBCHF00000006 | 28696570:28698241 | 2 | 1 | 2 | 2 | 183 | 20,547.1 | 9.49 | 44.27 |
TkSPL16 | GWHPBCHF039801 | GWHBCHF00000007 | 11469584:11479658 | 5 | 4 | 5 | 2 | 357 | 39,883.37 | 9.1 | 53.96 |
TkSPL17 | GWHPBCHF039802 | GWHBCHF00000007 | 11469584:11479658 | 5 | 4 | 4 | 3 | 349 | 38,967.27 | 9.19 | 54.04 |
TkSPL18 | GWHPBCHF040059 | GWHBCHF00000007 | 13895402:13897881 | 3 | 2 | 2 | 3 | 171 | 19,026.37 | 8.94 | 60.4 |
TkSPL19 | GWHPBCHF044300 | GWHBCHF00000008 | 4487440:4488774 | 2 | 1 | 2 | 2 | 296 | 32,163.23 | 9.48 | 57.94 |
TkSPL20 | GWHPBCHF044302 | GWHBCHF00000008 | 4501786:4503817 | 3 | 2 | 2 | 3 | 261 | 29,845.17 | 7.03 | 73.8 |
TkSPL21 | GWHPBCHF050461 | GWHBCHF00000009 | 9840573:9843749 | 5 | 4 | 4 | 2 | 275 | 30,724.02 | 9.55 | 73.95 |
TkSPL22 | GWHPBCHF052188 | GWHBCHF00000009 | 28195236:28196956 | 3 | 2 | 3 | 2 | 316 | 35,456.72 | 9.36 | 68.57 |
TkSPL23 | GWHPBCHF053518 | GWHBCHF00000009 | 42852554:42856744 | 10 | 9 | 9 | 3 | 928 | 104,212.96 | 6.82 | 46.08 |
TkSPL24 | GWHPBCHF053519 | GWHBCHF00000009 | 42852554:42856744 | 9 | 8 | 9 | 2 | 924 | 103,871.69 | 6.95 | 45.77 |
TkSPL25 | GWHPBCHF056162 | GWHBCHF00000009 | 103280194:103281999 | 2 | 1 | 2 | 2 | 137 | 15,812.68 | 8.56 | 63.94 |
EuSPL1 | GWHPAAAL001077 | GWHAAAL00000030 | 988480:992976 | 11 | 10 | 11 | 0 | 178 | 20,179.44 | 9.03 | 55.87 |
EuSPL2 | GWHPAAAL003913 | GWHAAAL00000058 | 2037987:2040046 | 3 | 2 | 3 | 0 | 547 | 60,636.72 | 6.91 | 54.8 |
EuSPL3 | GWHPAAAL004171 | GWHAAAL00000080 | 203789:215644 | 2 | 1 | 2 | 0 | 369 | 41,404.83 | 8.07 | 72.6 |
EuSPL4 | GWHPAAAL007895 | GWHAAAL00000112 | 735958:741319 | 5 | 4 | 5 | 0 | 133 | 15,322.89 | 7.69 | 84.16 |
EuSPL5 | GWHPAAAL008461 | GWHAAAL00000115 | 1029716:1033122 | 5 | 4 | 5 | 0 | 968 | 107,979.44 | 7.33 | 57.38 |
EuSPL6 | GWHPAAAL008647 | GWHAAAL00000172 | 475295:476266 | 2 | 1 | 2 | 0 | 978 | 109,120.78 | 8.36 | 51.07 |
EuSPL7 | GWHPAAAL012748 | GWHAAAL00000184 | 1290342:1300388 | 11 | 10 | 11 | 0 | 347 | 37,321.69 | 8.1 | 64.57 |
EuSPL8 | GWHPAAAL012866 | GWHAAAL00000249 | 1634971:1649669 | 12 | 11 | 12 | 0 | 875 | 98,038.82 | 6.26 | 58.57 |
EuSPL9 | GWHPAAAL016673 | GWHAAAL00006095 | 779825:852698 | 9 | 8 | 9 | 0 | 259 | 28,558.46 | 8.79 | 61.98 |
EuSPL10 | GWHPAAAL020125 | GWHAAAL00014124 | 1676:4668 | 3 | 2 | 3 | 0 | 363 | 38,927.58 | 9.01 | 64.09 |
EuSPL11 | GWHPAAAL025240 | GWHAAAL00017881 | 529023:533014 | 3 | 2 | 3 | 0 | 354 | 40,444.43 | 8.94 | 48.71 |
EuSPL12 | GWHPAAAL026381 | GWHAAAL00020293 | 536331:540436 | 3 | 2 | 3 | 0 | 696 | 77,869.21 | 8.88 | 53.91 |
EuSPL13 | GWHPAAAL026606 | GWHAAAL00026424 | 227394:229146 | 3 | 2 | 3 | 0 | 131 | 15,166.23 | 10.47 | 72.74 |
HbSPL1 | GT021460.t1 | CM021228.1 | 13875757:13877545 | 2 | 1 | 2 | 0 | 531 | 57,107.57 | 7.27 | 46.45 |
HbSPL2 | GT021495.t1 | CM021228.1 | 13970213:13972002 | 2 | 1 | 2 | 0 | 442 | 48,140.64 | 8.2 | 48.31 |
HbSPL3 | GT010583.t1 | CM021228.1 | 86118185:86120916 | 4 | 3 | 4 | 0 | 194 | 21,651.15 | 9.06 | 64.25 |
HbSPL4 | GT010615.t1 | CM021233.1 | 98164232:98172531 | 10 | 9 | 10 | 0 | 194 | 21,651.15 | 9.06 | 64.25 |
HbSPL5 | GT017984.t1 | CM021234.1 | 94639220:94645994 | 4 | 3 | 4 | 0 | 458 | 49,852.23 | 8.87 | 56.52 |
HbSPL6 | GT003116.t1 | CM021238.1 | 65041899:65062959 | 24 | 23 | 24 | 0 | 707 | 79,038.55 | 7.23 | 55.88 |
HbSPL7 | GT030712.t1 | CM021238.1 | 65225362:65248838 | 24 | 23 | 24 | 0 | 1065 | 117,893.71 | 8.75 | 46.86 |
HbSPL8 | GT030809.t1 | CM021239.1 | 12363240:12365845 | 3 | 2 | 3 | 0 | 1005 | 110,811.41 | 8.33 | 48.37 |
HbSPL9 | GT019690.t1 | CM021239.1 | 23400072:23405078 | 10 | 9 | 10 | 0 | 293 | 32,788.22 | 9.21 | 64.77 |
HbSPL10 | GT039310.t1 | CM021239.1 | 26622170:26632180 | 12 | 11 | 12 | 0 | 995 | 110,256.79 | 6.4 | 43.85 |
HbSPL11 | GT033052.t1 | CM021239.1 | 39504948:39506565 | 3 | 2 | 3 | 0 | 339 | 37001.37 | 9.5 | 59.73 |
HbSPL12 | GT019861.t1 | CM021240.1 | 72675955:72677659 | 3 | 2 | 3 | 0 | 686 | 77,405.9 | 5.86 | 55.24 |
HbSPL13 | GT025439.t1 | CM021241.1 | 2028142:2034204 | 10 | 9 | 10 | 0 | 368 | 41,070.02 | 9.44 | 51.55 |
HbSPL14 | GT042310.t1 | CM021241.1 | 27863168:27864903 | 3 | 2 | 3 | 0 | 862 | 97,241.22 | 6.29 | 47.94 |
HbSPL15 | GT040479.t1 | JAAGAX010000040.1 | 559530:565521 | 4 | 3 | 4 | 0 | 398 | 44,823.71 | 8.64 | 49.13 |
HbSPL16 | GT028737.t1 | JAAGAX010000040.1 | 620658:626675 | 4 | 3 | 4 | 0 | 404 | 44,567.07 | 8.41 | 55.27 |
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Su, R.; Yuan, B.; Yang, Y.; Ao, G.; Wang, J. Genome-Wide Analysis of SPL Gene Families Illuminate the Evolution Patterns in Three Rubber-Producing Plants. Diversity 2023, 15, 983. https://doi.org/10.3390/d15090983
Su R, Yuan B, Yang Y, Ao G, Wang J. Genome-Wide Analysis of SPL Gene Families Illuminate the Evolution Patterns in Three Rubber-Producing Plants. Diversity. 2023; 15(9):983. https://doi.org/10.3390/d15090983
Chicago/Turabian StyleSu, Renping, Boxuan Yuan, Yang Yang, Guoen Ao, and Juanying Wang. 2023. "Genome-Wide Analysis of SPL Gene Families Illuminate the Evolution Patterns in Three Rubber-Producing Plants" Diversity 15, no. 9: 983. https://doi.org/10.3390/d15090983
APA StyleSu, R., Yuan, B., Yang, Y., Ao, G., & Wang, J. (2023). Genome-Wide Analysis of SPL Gene Families Illuminate the Evolution Patterns in Three Rubber-Producing Plants. Diversity, 15(9), 983. https://doi.org/10.3390/d15090983