Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction
Abstract
:1. Introduction
2. Results
2.1. Classification and Annotation of sRNAs in Resistant (HR) and Susceptible (ZS) Cotton Cultivar in Response to Whitefly Infestation
2.2. Abundant lincRNA Act as miRNA Precursor
2.3. Analysis of the miRNA Target Genes Based on Degradome Sequencing
2.4. Tight Linkage Between miRNAs and Their Targets in Cotton in Response to Whitefly Infestation
2.5. Identification of miRNA-mediated phasiRNAs during the Whitefly Infestation Cotton Plants
2.6. mi482a-Triggered phasiRNAs Regulate the Transcriptional in Cotton Response to Whitefly Infestation
2.7. Characterization of the linc1-miR390-tasiARFs Cascade Involved in Cotton Response to Whitefly Infestation
3. Discussion
4. Materials and Methods
4.1. Plant Materials, Whitefly Infestation, and RNA Isolation
4.2. Small RNA and Degradome Library Construction
4.3. miRNA Prediction Pipeline
4.4. Expression Profiles of miRNAs in the HR and ZS Plants during Whitefly Infestation
4.5. Identification and Functional Annotation of the miRNA Target Genes
4.6. Identification of lincRNAs from RNA-Seq Dataset
4.7. Stem-loop qRT-PCR Analysis of miRNAs
4.8. Identification of PHAS Loci
4.9. Validation of lincRNA Function and Corresponding Targets by VIGS
4.10. Data Availability
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample | Raw Reads | Unique Reads | SnoRNA | snRNA | 5S_rRNA | sRNA | Mapping |
---|---|---|---|---|---|---|---|
HR0_R1 | 16,906,187 | 2,276,889 | 567 | 333 | 6957 | 977,245 | 84.19% |
HR0_R2 | 21,306,455 | 2,281,508 | 949 | 554 | 10,990 | 600,015 | 83.81% |
HR0_R3 | 11,613,784 | 729,752 | 213 | 227 | 2721 | 650,351 | 84.12% |
HR24_R1 | 20,313,659 | 2,350,845 | 548 | 394 | 7678 | 824,200 | 81.82% |
HR24_R2 | 22,215,560 | 2,404,771 | 184 | 93 | 1669 | 1,476,308 | 82.16% |
HR24_R3 | 11,306,605 | 833,843 | 245 | 262 | 2932 | 745,572 | 84.45% |
ZS0_R1 | 18,328,323 | 1,838,613 | 97 | 43 | 770 | 1,047,368 | 79.65% |
ZS0_R2 | 21,173,195 | 2,457,802 | 149 | 68 | 1480 | 1,476,875 | 79.93% |
ZS0_R3 | 11,335,617 | 1,086,277 | 232 | 245 | 2977 | 986,067 | 84.21% |
ZS24_R1 | 18,240,711 | 1,104,283 | 70 | 44 | 940 | 636,559 | 81.41% |
ZS24_R2 | 17,720,064 | 1,837,592 | 108 | 69 | 1051 | 507,170 | 82.14% |
ZS24_R3 | 11,416,722 | 1,037,485 | 220 | 232 | 3176 | 925,213 | 83.51% |
MiRNA_ID | miRBase21 | Strand | Chr | Start | End | lincRNA_ID | miRNA Target Annotation |
---|---|---|---|---|---|---|---|
P132 | osa-miR171f-3p | + | A05 | 15999334 | 15999553 | GhA05linc.520 | GRAS |
P147 | ghr-miR166b | + | A07 | 28328142 | 28328522 | GhA07linc.319 | Homeobox-leucine zipper |
P147 | ghr-miR166b | + | A08 | 8999568 | 8999969 | GhA08linc.292 | Homeobox-leucine zipper |
P147 | ghr-miR166b | + | A11 | 67055538 | 67055606 | GhA11linc.93 | Homeobox-leucine zipper |
P149 | NoHits | + | A08 | 103041407 | 103042061 | GhA08linc.135 | |
P168 | gra-miR8733 | - | D06 | 692582 | 692872 | GhD06linc.129 | |
P181 | ath-miR172b-3p | - | A05 | 9079609 | 9079903 | GhA05linc.451 (linc6) | related to AP2.7 |
P187 | ghr-miR390c | + | D09 | 43446164 | 43448093 | GhD09linc.75 (linc1) | TAS3 |
P193 | ghr-miR156d | + | A07 | 2556261 | 2556647 | GhA07linc.14 | SPL |
P72 | gra-miR482c | + | A07 | 9733996 | 9734022 | GhA07linc.38 (linc4) | NB-ARC |
P73 | NoHits | + | D05 | 43103308 | 43103635 | GhD05linc.279 (linc5) | NB-ARC |
P73 | NoHits | - | D05 | 43102918 | 43103615 | GhD05linc.670 (linc2) | NB-ARC |
P81 | NoHits | + | D05 | 43103308 | 43103635 | GhD05linc.279 | NB-ARC |
P81 | NoHits | - | D05 | 43102918 | 43103615 | GhD05linc.670 | NB-ARC |
P87 | NoHits | + | A12 | 84153544 | 84153795 | GhA12linc.146 |
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Li, J.; Hull, J.J.; Liang, S.; Wang, Q.; Chen, L.; Zhang, Q.; Wang, M.; Mansoor, S.; Zhang, X.; Jin, S. Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction. Int. J. Mol. Sci. 2019, 20, 5357. https://doi.org/10.3390/ijms20215357
Li J, Hull JJ, Liang S, Wang Q, Chen L, Zhang Q, Wang M, Mansoor S, Zhang X, Jin S. Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction. International Journal of Molecular Sciences. 2019; 20(21):5357. https://doi.org/10.3390/ijms20215357
Chicago/Turabian StyleLi, Jianying, J. Joe Hull, Sijia Liang, Qiongqiong Wang, Luo Chen, Qinghua Zhang, Maojun Wang, Shahid Mansoor, Xianlong Zhang, and Shuangxia Jin. 2019. "Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction" International Journal of Molecular Sciences 20, no. 21: 5357. https://doi.org/10.3390/ijms20215357