On 2017 Jun 12, Bastian Fromm commented:

Summary The author describes the results of a combined smallRNA sequencing and blasting approach in Taenia ovis. Specifically RNA was retrieved from Tov metacercaria and then mapped to the genome of T. solium. Mapping reads are then blasted against miRBase and so the author describes 34 miRNAs as present in Tov.

Major problems

1. The author uses miRBase as reference for cestode miRNAs although it is very outdated (last update 2014). The author should rather have used available literature for comparisons (1-9).
2. Consequently (?) the author fails to acknowledge his results in the light of standard work in the field of miRNA evolution in flatworms (10-12) and to draw conclusions about the completeness of his predictions.
3. The approach of mapping a smallRNA sequencing library of a given species against another is problematic and I cannot understand why no the author does not at least try to use classical PCR to confirm loci.

Minor problems 1) page 3 line 61 author should make sentence more clear. It looks like author removed all reads that had adapter sequences. Recommendation 1) Author should get all available PRE-sequences for cestodes and ma his Tov reads with liberal settings to them and report results.

1. Jiang, S., Li, X., Wang, X., Ban, Q., Hui, W. and Jia, B. (2016) MicroRNA profiling of the intestinal tissue of Kazakh sheep after experimental Echinococcus granulosus infection, using a high-throughput approach. Parasite, 23, 23.
2. Kamenetzky, L., Stegmayer, G., Maldonado, L., Macchiaroli, N., Yones, C. and Milone, D.H. (2016) MicroRNA discovery in the human parasite Echinococcus multilocularis from genome-wide data. Genomics, 107, 274-280.
3. Macchiaroli, N., Cucher, M., Zarowiecki, M., Maldonado, L., Kamenetzky, L. and Rosenzvit, M.C. (2015) microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach. Parasit Vectors, 8, 83.
4. Jin, X., Guo, X., Zhu, D., Ayaz, M. and Zheng, Y. (2017) miRNA profiling in the mice in response to Echinococcus multilocularis infection. Acta tropica, 166, 39-44.
5. Bai, Y., Zhang, Z., Jin, L., Kang, H., Zhu, Y., Zhang, L., Li, X., Ma, F., Zhao, L., Shi, B. et al. (2014) Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus. BMC genomics, 15, 736.
6. Cucher, M., Prada, L., Mourglia-Ettlin, G., Dematteis, S., Camicia, F., Asurmendi, S. and Rosenzvit, M. (2011) Identification of Echinococcus granulosus microRNAs and their expression in different life cycle stages and parasite genotypes. International journal for parasitology, 41, 439-448.
7. Ai, L., Xu, M.J., Chen, M.X., Zhang, Y.N., Chen, S.H., Guo, J., Cai, Y.C., Zhou, X.N., Zhu, X.Q. and Chen, J.X. (2012) Characterization of microRNAs in Taenia saginata of zoonotic significance by Solexa deep sequencing and bioinformatics analysis. Parasitology research, 110, 2373-2378.
8. Wu, X., Fu, Y., Yang, D., Xie, Y., Zhang, R., Zheng, W., Nie, H., Yan, N., Wang, N., Wang, J. et al. (2013) Identification of neglected cestode Taenia multiceps microRNAs by illumina sequencing and bioinformatic analysis. BMC veterinary research, 9, 162.
9. Ai, L., Chen, M.-X., Zhang, Y.-N., Chen, S.-H., Zhou, X.-N. and Chen, J.-X. (2014) Comparative analysis of the miRNA profiles from Taenia solium and Taenia asiatica adult. African Journal of Microbiology Research, 8, 895-902.
10. Fromm, B., Worren, M.M., Hahn, C., Hovig, E. and Bachmann, L. (2013) Substantial Loss of Conserved and Gain of Novel MicroRNA Families in Flatworms. Molecular biology and evolution, 30, 2619-2628.
11. Cai, P., Gobert, G.N. and McManus, D.P. (2016) MicroRNAs in Parasitic Helminthiases: Current Status and Future Perspectives. Trends Parasitol, 32, 71-86.
12. Fromm, B., Ovchinnikov, V., Hoye, E., Bernal, D., Hackenberg, M. and Marcilla, A. (2016) On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica. Parasite immunology.

On 2017 Jun 12, Bastian Fromm commented:

Summary The author describes the results of a combined smallRNA sequencing and blasting approach in Taenia ovis. Specifically RNA was retrieved from Tov metacercaria and then mapped to the genome of T. solium. Mapping reads are then blasted against miRBase and so the author describes 34 miRNAs as present in Tov.

Major problems

1. The author uses miRBase as reference for cestode miRNAs although it is very outdated (last update 2014). The author should rather have used available literature for comparisons (1-9).
2. Consequently (?) the author fails to acknowledge his results in the light of standard work in the field of miRNA evolution in flatworms (10-12) and to draw conclusions about the completeness of his predictions.
3. The approach of mapping a smallRNA sequencing library of a given species against another is problematic and I cannot understand why no the author does not at least try to use classical PCR to confirm loci.

Minor problems 1) page 3 line 61 author should make sentence more clear. It looks like author removed all reads that had adapter sequences. Recommendation 1) Author should get all available PRE-sequences for cestodes and ma his Tov reads with liberal settings to them and report results.

1. Jiang, S., Li, X., Wang, X., Ban, Q., Hui, W. and Jia, B. (2016) MicroRNA profiling of the intestinal tissue of Kazakh sheep after experimental Echinococcus granulosus infection, using a high-throughput approach. Parasite, 23, 23.
2. Kamenetzky, L., Stegmayer, G., Maldonado, L., Macchiaroli, N., Yones, C. and Milone, D.H. (2016) MicroRNA discovery in the human parasite Echinococcus multilocularis from genome-wide data. Genomics, 107, 274-280.
3. Macchiaroli, N., Cucher, M., Zarowiecki, M., Maldonado, L., Kamenetzky, L. and Rosenzvit, M.C. (2015) microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach. Parasit Vectors, 8, 83.
4. Jin, X., Guo, X., Zhu, D., Ayaz, M. and Zheng, Y. (2017) miRNA profiling in the mice in response to Echinococcus multilocularis infection. Acta tropica, 166, 39-44.
5. Bai, Y., Zhang, Z., Jin, L., Kang, H., Zhu, Y., Zhang, L., Li, X., Ma, F., Zhao, L., Shi, B. et al. (2014) Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus. BMC genomics, 15, 736.
6. Cucher, M., Prada, L., Mourglia-Ettlin, G., Dematteis, S., Camicia, F., Asurmendi, S. and Rosenzvit, M. (2011) Identification of Echinococcus granulosus microRNAs and their expression in different life cycle stages and parasite genotypes. International journal for parasitology, 41, 439-448.
7. Ai, L., Xu, M.J., Chen, M.X., Zhang, Y.N., Chen, S.H., Guo, J., Cai, Y.C., Zhou, X.N., Zhu, X.Q. and Chen, J.X. (2012) Characterization of microRNAs in Taenia saginata of zoonotic significance by Solexa deep sequencing and bioinformatics analysis. Parasitology research, 110, 2373-2378.
8. Wu, X., Fu, Y., Yang, D., Xie, Y., Zhang, R., Zheng, W., Nie, H., Yan, N., Wang, N., Wang, J. et al. (2013) Identification of neglected cestode Taenia multiceps microRNAs by illumina sequencing and bioinformatic analysis. BMC veterinary research, 9, 162.
9. Ai, L., Chen, M.-X., Zhang, Y.-N., Chen, S.-H., Zhou, X.-N. and Chen, J.-X. (2014) Comparative analysis of the miRNA profiles from Taenia solium and Taenia asiatica adult. African Journal of Microbiology Research, 8, 895-902.
10. Fromm, B., Worren, M.M., Hahn, C., Hovig, E. and Bachmann, L. (2013) Substantial Loss of Conserved and Gain of Novel MicroRNA Families in Flatworms. Molecular biology and evolution, 30, 2619-2628.
11. Cai, P., Gobert, G.N. and McManus, D.P. (2016) MicroRNAs in Parasitic Helminthiases: Current Status and Future Perspectives. Trends Parasitol, 32, 71-86.
12. Fromm, B., Ovchinnikov, V., Hoye, E., Bernal, D., Hackenberg, M. and Marcilla, A. (2016) On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica. Parasite immunology.