Pan-Genome Analysis of TRM Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber
Abstract
:1. Introduction
2. Materials and Method
2.1. Identification of TRM Genes in Cucumber
2.2. Protein Length, Motif Composition, and Gene Structure Analysis Amino Acid Variations
2.3. Gene Duplication and Synteny Analysis
2.4. Transcriptome Profiling of CsTRMs in Fruit
2.5. Transcriptome Profiling of CsTRMs in Response to Abiotic and Biotic Stresses
2.6. RNA Isolation and Quantitative Real-Time PCR (qRT-PCR) Analysis
3. Result
3.1. Identification of CsTRM Genes Based on the Cucumber Pan-Genome
3.2. Analysis of Protein Length and Amino Acid Variations in the CsTRM Proteins
3.3. Synteny Analysis of CsTRM Genes
3.4. Expression Profiles of CsTRM Genes in the Fruit
3.5. Expression Patterns of CsTRM Genes under Abiotic and Biotic Stresses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | 9930 | XTMC | Cu2 | Cuc80 | PI | Cuc64 | W4 | W8 | Hx14 | Hx117 | Cuc37 | Gy14 | 9110gt |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CsTRM01 | 1G003000 | 1G002960 | 1G003190 | 1G003020 | 1G02950 | 1G003020 | 1G003020 | 1G003050 | 1G008150 | 1G003070 | 1G003050 | 1G002970 | 1G003150 |
CsTRM02 | 1G006080 | 1G006040 | 1G006230 | 1G006090 | 1G06220 | 1G006110 | 1G006160 | 1G006130 | 1G012280 | 1G009330 | 1G006130 | 1G005930 | 1G006390 |
CsTRM03 | 1G024390 | 1G023100 | 1G019380 | 1G034690 | 1G022250 | 1G022640 | 1G033380 | 1G035450 | 1G025870 | 1G016710 | 1G021460 | ||
CsTRM04 | 1G036240 | 1G038300 | 1G031670 | 1G23930 | 1G045200 | 1G039460 1G050980 | 1G048780 | 1G052690 | 1G036240 | 1G023410 | 1G034790 | ||
CsTRM05 | 2G013800 | 2G013420 | 2G014430 | 2G016150 | 2G11310 | 2G012220 | 2G015170 | 2G022290 | 2G022190 | 2G018160 | 2G012230 | 2G011350 | 2G015370 |
CsTRM06 | 2G002210 | 2G001130 | 2G002170 | 2G01120 | 2G001150 | 2G001150 | 2G002120 | 2G002150 | 2G001120 | 2G001120 | 2G002200 | ||
CsTRM07 | 2G006910 | 2G004780 | 2G004780 | 2G005680 | 2G04550 | 2G004690 | 2G004760 | 2G005690 | 2G006680 | 2G005730 | 2G004660 | 2G004680 | 2G005790 |
CsTRM08 | 3G000320 | 3G000290 | 3G000270 | 3G00310 | 3G000310 | 3G000300 | 3G000290 | 3G000310 | 3G000300 | 3G000310 | 3G000260 | 3G000300 | |
CsTRM09 | 3G008900 | 3G014120 | 3G011330 | 3G009320 | 3G08770 | 3G009130 | 3G011320 | 3G009390 | 3G013030 | 3G018440 | 3G009280 | 3G008870 | 3G011230 |
CsTRM10 | 3G009320 | 3G014570 | 3G09200 | 3G009570 | 3G011790 | 3G009840 | 3G013470 | 3G018890 | 3G009740 | 3G009280 | 3G011660 | ||
CsTRM11 | 3G016640 | 3G023990 | 3G019120 | 3G016980 | 3G16440 | 3G027380 | 3G019160 | 3G017460 | 3G023810 | 3G029290 | 3G017050 | 3G016550 | 3G018960 |
CsTRM12 | 3G020250 | 3G028160 | 3G024300 | 3G021230 | 3G20290 | 3G031530 | 3G023320 | 3G021650 | 3G030910 | 3G038450 | 3G021080 | 3G020040 | 3G025120 |
CsTRM13 | 3G028590 | 3G044970 | 3G034490 | 3G039640 | 3G27110 | 3G050790 | 3G034230 | 3G032590 | 3G049730 | 3G053340 | 3G043310 | 3G025270 | 3G034790 |
CsTRM14 | 3G033690 | 3G052230 | 3G039760 | 3G045880 | 3G31210 | 3G055180 | 3G039400 | 3G038880 | 3G057040 | 3G059810 | 3G049600 | 3G029050 | 3G041170 |
CsTRM15 | 3G035160 | 3G053700 | 3G041160 | 3G047320 | 3G32570 | 3G056620 | 3G040870 | 3G040290 | 3G058490 | 3G061290 | 3G050990 | 3G030380 | 3G042680 |
CsTRM16 | 3G036950 | 3G056500 | 3G043950 | 3G049050 | 3G34290 | 3G032070 | 3G044470 | ||||||
CsTRM17 | 3G045060 | 3G067760 | 3G055880 | 3G057270 | 3G42630 | 3G066680 | 3G051990 | 3G050610 | 3G070610 | 3G071560 | 3G061110 | 3G040150 | 3G052920 |
CsTRM18 | 4G024630 | 4G030170 | 4G024030 | 4G078840 | 4G14290 | 4G027840 | 4G018900 | 4G021930 | 4G026900 | 4G030090 | 4G084710 | 4G013800 | 4G026010 |
CsTRM19 | 4G031780 | 4G042910 | 4G034540 | 4G090510 | 4G21450 | 4G044030 | 4G027440 | 4G033570 | 4G040430 | 4G039790 | 4G095540 | 4G020000 | 4G035410 |
CsTRM20 | 5G002760 | 5G003630 | 5G003640 | 5G002610 | 5G05360 | 5G003650 | 5G002590 | 5G005490 | 5G006540 | 5G003570 | 5G002660 | 5G003770 | |
CsTRM21 | 5G003260 | 5G004130 | 5G004140 | 5G003110 | 5G05880 | 5G003020 | 5G003100 | 5G004990 | 5G007040 | 5G004090 | 5G003170 | 5G003160 | 5G004310 |
CsTRM22 | 5G005590 | 5G007580 | 5G007530 | 5G005560 | 5G08200 | 5G000650 | 5G006510 | 5G001620 | 5G009400 | 5G009680 | 5G005630 | 5G005580 | |
CsTRM23 | 5G026190 | 5G042130 | 5G041190 | 5G050680 | 5G17200 | 5G021470 | 5G028290 | 5G024190 | 5G042910 | 5G054980 | 5G043620 | 5G016900 | 5G034200 |
CsTRM24 | 5G038540 | 5G060730 | 5G054610 | 5G063070 | 5G29400 | 5G043920 | 5G040890 | 5G049340 | 5G063180 | 5G067580 | 5G056820 | 5G028860 | 5G046740 |
CsTRM25 | 6G016870 | 6G024320 | 6G018060 | 6G025320 | 6G14470 | 6G015450 | 6G015250 | 6G019390 | 6G025200 | 6G018200 | 6G015300 | 6G014340 | 6G017280 |
CsTRM26 | 6G022550 | 6G035270 | 6G023850 | 6G053560 | 6G17180 | 6G022100 | 6G019950 | 6G023190 | 6G032860 | 6G030040 | 6G019540 | 6G016650 | 6G023980 |
CsTRM27 | 6G040450 | 6G052040 | 6G035430 | 6G079450 | 6G25260 | 6G035100 | 6G032700 | 6G033070 | 6G052400 | 6G045570 | 6G036810 | 6G024690 | 6G035970 |
CsTRM28 | 7G025430 | 7G031600 | 7G024250 | 7G035470 | 7G13640 | 7G025890 | 7G021920 | 7G034950 | 7G031600 | 7G031470 | 7G037050 | 7G012470 | 7G023340 |
CsTRM29 | UnG00530 |
Protein Number | 9930 | XTMC | Cu2 | Cuc80 | PI | Cuc64 | W4 | W8 | Hx14 | Hx117 | Cuc37 | Gy14 | 9110gt |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CsTRM01 | 1048 | 1048 | 1048 | 1048 | 1048 | 1048 | 1043 | 1048 | 1048 | 1048 | 1048 | 1063 | 1048 |
CsTRM02 | 1040 | 1067 | 1067 | 1067 | 1067 | 1067 | 1067 | 1067 | 1067 | 1067 | 1067 | 1067 | 1067 |
CsTRM03 | 780 | 788 | 788 | 788 | 781 | 781 | 781 | 781 | 781 | 788 | 781 | ||
CsTRM04 | 402 | 402 | 402 | 402 | 402 | 402/402 | 402 | 402 | 402 | 402 | 402 | ||
CsTRM05 | 776 | 803 | 803 | 803 | 803 | 803 | 803 | 803 | 803 | 803 | 803 | 803 | 803 |
CsTRM06 | 722 | 722 | 722 | 722 | 722 | 722 | 722 | 750 | 722 | 722 | 722 | ||
CsTRM07 | 893 | 478 | 893 | 891 | 891 | 893 | 893 | 899 | 893 | 891 | 891 | 922 | 891 |
CsTRM08 | 893 | 879 | 879 | 893 | 879 | 879 | 879 | 893 | 879 | 879 | 904 | 879 | |
CsTRM09 | 930 | 933 | 933 | 933 | 932 | 933 | 933 | 933 | 933 | 933 | 933 | 932 | 933 |
CsTRM10 | 346 | 346 | 344 | 344 | 344 | 344 | 346 | 344 | 346 | 305 | 346 | ||
CsTRM11 | 616 | 616 | 616 | 616 | 616 | 616 | 616 | 616 | 616 | 616 | 616 | 616 | 616 |
CsTRM12 | 953 | 953 | 954 | 954 | 953 | 953 | 953 | 953 | 953 | 952 | 953 | 954 | 953 |
CsTRM13 | 963 | 963 | 963 | 963 | 963 | 963 | 963 | 963 | 963 | 963 | 963 | 927 | 963 |
CsTRM14 | 353 | 353 | 353 | 353 | 353 | 353 | 353 | 353 | 353 | 353 | 353 | 353 | 353 |
CsTRM15 | 888 | 888 | 888 | 888 | 888 | 888 | 888 | 888 | 888 | 888 | 888 | 888 | 888 |
CsTRM16 | 472 | 472 | 550 | 550 | 472 | 472 | 550 | ||||||
CsTRM17 | 1091 | 1038 | 1091 | 1091 | 1091 | 1091 | 210 | 353 | 440 | 600 | 1091 | 1058 | 357 |
CsTRM18 | 961 | 961 | 961 | 961 | 961 | 922 | 961 | 961 | 961 | 961 | 961 | 961 | 961 |
CsTRM19 | 903 | 903 | 987 | 987 | 906 | 987 | 906 | 906 | 906 | 906 | 906 | 906 | 906 |
CsTRM20 | 785 | 785 | 785 | 785 | 781 | 781 | 781 | 781 | 785 | 785 | 745 | 785 | |
CsTRM21 | 476 | 476 | 476 | 476 | 476 | 476 | 476 | 476 | 476 | 476 | 476 | 476 | 476 |
CsTRM22 | 495 | 495 | 495 | 495 | 495 | 495 | 495 | 495 | 495 | 495 | 495 | 449 | |
CsTRM23 | 794 | 794 | 794 | 848 | 795 | 795 | 794 | 795 | 794 | 794 | 795 | 794 | 736 |
CsTRM24 | 1049 | 1049 | 1049 | 1049 | 1049 | 1049 | 1049 | 1049 | 1049 | 1049 | 1049 | 1049 | 958 |
CsTRM25 | 1011 | 1011 | 1011 | 1011 | 902 | 959 | 1009 | 1011 | 1022 | 1009 | 1011 | 940 | 1011 |
CsTRM26 | 936 | 936 | 936 | 936 | 936 | 936 | 938 | 936 | 936 | 936 | 936 | 936 | 936 |
CsTRM27 | 505 | 505 | 505 | 505 | 505 | 505 | 505 | 736 | 505 | 473 | 505 | 505 | 505 |
CsTRM28 | 960 | 960 | 960 | 959 | 959 | 994 | 995 | 1047 | 895 | 995 | 995 | 976 | 978 |
CsTRM29 | 788 |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Zhao, L.; Wang, K.; Wang, Z.; Chu, S.; Chen, C.; Wang, L.; Ren, Z. Pan-Genome Analysis of TRM Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber. Horticulturae 2024, 10, 908. https://doi.org/10.3390/horticulturae10090908
Zhao L, Wang K, Wang Z, Chu S, Chen C, Wang L, Ren Z. Pan-Genome Analysis of TRM Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber. Horticulturae. 2024; 10(9):908. https://doi.org/10.3390/horticulturae10090908
Chicago/Turabian StyleZhao, Lili, Ke Wang, Zimo Wang, Shunpeng Chu, Chunhua Chen, Lina Wang, and Zhonghai Ren. 2024. "Pan-Genome Analysis of TRM Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber" Horticulturae 10, no. 9: 908. https://doi.org/10.3390/horticulturae10090908