Bacterial Small RNAs in the Genus Herbaspirillum spp.
Abstract
:1. Introduction
2. Results
2.1. Prediction of New ncRNAs in the Genus Herbaspirillum spp.
2.2. ncRNAs Differential Expression in RNA-Seq
2.3. Comparative Analysis of the Secondary Structure of 6S of H. seropedicae SmR1
2.4. Candidate sRNA Target Identification
2.5. Prediction of CRISPR
3. Discussion
4. Materials and Methods
4.1. Genomes of Bacteria of the Genus Herbaspirillum
4.2. RNA-Seq Data
4.3. Prediction of ncRNAs in Silico
4.4. ncRNA Sequence Annotation
4.5. Mapping and Visualization of Sequence Reads
4.6. Transcriptome Analysis
4.7. Target Prediction
4.8. Identifying CRISPR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Genus Herbaspirillum | ncRNAs |
Herbaspirillum seropedicae Z67 | ohsC_RNA, Rhizobiales-2 and UPD-PKc |
Herbaspirillum lusitanum P6-12 | Absence |
Herbaspirillum hiltneri N3 | ar14, Acido-1, Alpha_RBS, ar14, asX2, asX3, Bp2_287, csRNA, isrN, istR, Ms_AS-4, Ms_IGR-8, ncr1175, NsiR1, P26, P5, PrrB_RsmZ, RsmY, RydC, sau-5971, SpF41_sRNA, Spot_42, Xoo5, sraA, sX9, TB10Cs4H2, TB11Cs5H2 and TB9Cs1H1 |
Herbaspirillum frisingense GSF30 | Entero_5_CRE, P10 and STnc430 |
Herbaspirillum spp. estirpe B65 | snoZ248 |
Herbaspirillum rubrisubalbicans M1 | ALIL, Alpha_RBS, Archaea_SRP, asX2, b55, BjrC1505, C4, ceN84, istR, K_chan_RES, MAT2A_B, MEG3_2, NRF2_IRES, OrzO-P, P36, pRNA, PtaRNA1, rli60, rox2, rseX, sau-6072, sau-63, SpF25_sRNA, SpR10_sRNA, sroB, sX15, TB9Cs1H1 and TB9Cs1H2. |
Herbaspirillum huttiense subsp. Putei estirpe IAM 15032 | asX2, Cardiovirus_CRE, Chloroflexi-1, MEG3_2, SBWMV2_UPD-PKk, sroB, veev_FSE, asX2, Cardiovirus_CRE, Chloroflexi-1, MEG3_2, SBWMV2_UPD-PKk, sroB and veev_FSE. |
Herbaspirillum autotrophicum IAM 14942 | MIR1444 and SpF10_sRNA. |
Herbaspirillum spp. estirpe B501 | Absence |
Herbaspirillum spp. estirpe GW103 | sX2, Flavi_CRE, RyeB, SAM-IV, sau-6072 e sroB. |
Herbaspirillum spp. estirpe RV1423 | psRNA2, sbcD and STnc40. |
Herbaspirillum rhizosphaerae UMS-37 | NRF2_IRES, NsiR1, Pseudomon-groES and sX9. |
Herbaspirillum rubrisubalbicans spp. estirpe Os34 | ryfA, SpR20_sRNA and asX2. |
Herbaspirillum rubrisubalbicans spp. estirpe Os45 | asX2, ROSE_2 and ryfA. |
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Carvalho Garcia, A.; Dos Santos, V.L.P.; Santos Cavalcanti, T.C.; Collaço, L.M.; Graf, H. Bacterial Small RNAs in the Genus Herbaspirillum spp. Int. J. Mol. Sci. 2019, 20, 46. https://doi.org/10.3390/ijms20010046
Carvalho Garcia A, Dos Santos VLP, Santos Cavalcanti TC, Collaço LM, Graf H. Bacterial Small RNAs in the Genus Herbaspirillum spp. International Journal of Molecular Sciences. 2019; 20(1):46. https://doi.org/10.3390/ijms20010046
Chicago/Turabian StyleCarvalho Garcia, Amanda, Vera Lúcia Pereira Dos Santos, Teresa Cristina Santos Cavalcanti, Luiz Martins Collaço, and Hans Graf. 2019. "Bacterial Small RNAs in the Genus Herbaspirillum spp." International Journal of Molecular Sciences 20, no. 1: 46. https://doi.org/10.3390/ijms20010046