MARS and RNAcmap3:The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search

sequences found in the huge,integrated database of protein sequences(Big Fantastic Database).In contrast,the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search.Here,we built a comprehensive database by incorporating the non-coding RNA(ncRNA)sequences from RNAcentral,the transcriptome assembly and metagenome assembly from metagenomics RAST(MG-RAST),the genomic sequences from Genome Warehouse(GWH),and the genomic sequences from MGnify,in addition to the nucleotide(nt)database and its subsets in National Center of Biotechnology Information(NCBI).The resulting Master database of All possible RNA sequences(MARS)is 20-fold larger than NCBI’s nt database or 60-fold larger than RNAcentral.The new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art techniques.It also yields more accurate and more sensitive multiple sequence alignments(MSAs)than manually curated MSAs from Rfam for the majority of structured RNAs mapped to Rfam.The results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on MSAs.MARS is accessible at https://ngdc.cncb.ac.cn/omix/release/OMIX003037,and RNAcmap3 is accessible at http://zhouyq-lab.szbl.ac.cn/download/.

Predicting the Reproduction Strategies of Several Microalgae Through Their Genome Sequences

Documenting the sex and sexual reproduction of the microalgae is very difficult, as most of the results are based on the microscopic observation that can be heavily influenced by genetic, physiological and environmental conditions. Understanding the reproduction strategy of some microalgae is required to breed them in large scale culture industry. Instead of direct observation of sex and sexual reproduction under microscope, the whole set or the majority of core meiosis genes may evidence the sex and sexual reproduction in the unicellular algae, as the meiosis is necessary for maintaining the genomic stability and the advantages of genetic recombination. So far, the available genome sequences and bioinformatic tools （in this study, homolog searching and phylogenetic analysis） allow us to propose that at least 20 core meiosis genes （among them 〉6 must be meiosis specific） are enough for an alga to maintain its sexual reproduction. According to this assumption and the genome sequences, it is possible that sexual reproduction was carried out by Micromonas pusilla and Cyanidiosehyzon merolae, while asexual reproduction was adopted by Bigelowiella natans, Guillardia theta, Nannochloropsis gaditana, N. oeeanica, Chlorella variablis, Phaeodactylum tricornutum and Thalassiosira pseu- donana. This understanding will facilitate the breeding trials of some economic microalgae （e.g., N. gaditana, N. oceanica, C. vari- ablis and P. tricornutum）. However, the reproduction strategies of these microalgae need to be proved by further biological experiments.