## 2 Materials and Methods  
### Dataset Collection  
Previous studies have demonstrated that a stringent dataset is essential for building a robust predictive model. We collected seven 6 mA site datasets of six species including _Rice_, _Arabidopsis thaliana_ (_A. thaliana_), _Rosa chinensis_ (_R. chinensis_), _Fragaria vesca_ (_F. vesca_), _Hono sapiens_ (_H. sapiens_) and _Drosophila melanogaster_ (_D. melanogaster_). There are two benchmark datasets 6 mA-rice-Lv and 6 mA-rice-Chen for _Rice_. The 6 mA-rice-Lv dataset include 15,400 positive samples and 15,400 negative samples which are obtained from NCBI Gene Expression Omnibus (GEO) ([[https://www.ncbi.nlm.nih.gov/genome/10](https://www.ncbi.nlm.nih.gov/genome/10)]([https://www.ncbi.nlm.nih.gov/genome/10](https://www.ncbi.nlm.nih.gov/genome/10)) (accessed on 20 August 2021)) following the steps proposed by [PERSON] et al. [23]. The 6 mA-rice-Chen benchmark dataset includes the 880 rice 6 mA sites and 880 non-6 mA sites which are obtained from GEO ([[https://www.ncbi.nlm.nih.gov/geo/](https://www.ncbi.nlm.nih.gov/geo/)]([https://www.ncbi.nlm.nih.gov/geo/](https://www.ncbi.nlm.nih.gov/geo/)) (accessed on 20 August 2021)) under the accession number GSE103145 following the steps proposed by [PERSON] et al. [20].  
To demonstrate that our model has the ability to predict the 6 mA sites of other species and 6 mA shares similar patterns across different species, we collected DNA 6 mA sequences of _Arabidopsis thaliana_ and _Drosophila melanogaster_ from the MethSMRT database ([[http://sysbio.gzzoc.com/methsmrt/](http://sysbio.gzzoc.com/methsmrt/)]([http://sysbio.gzzoc.com/methsmrt/](http://sysbio.gzzoc.com/methsmrt/)) (accessed on 20 August 2021)) [35] and also obtained the DNA 6 mA sequences of _Fragaria vesca_ and _Rosa chinensis_ from the MDR database [36]. Preliminary trials indicated that, when the length of the segments is 41 bp with the 6 mA in the center, the highest predictive results could be obtained. Thus, the sequences of all positive samples are 41 bp. In order to construct a high-quality benchmark dataset, the following two steps were performed. Firstly, according to the the Methylome AnalysisTechnical Note [35], the sequences with modQV no less than 30 are left for the subsequent analysis. It should be noted that, in order to obtain statistically significant results, if the raw data are too small, this step was ignored to get more samples. Secondly, to avoid redundancy and reduce homology bias, sequences with more than 80% sequence similarity were removed using the CD-HIT program [37]. After the above two steps, the objective and strict positive datasets for the above species were obtained. Negative samples for _Arabidopsis thaliana_, _Drosophila melanogaster_, _Fragaria vesca_, and _Rosa chinensis_ were also collected. These samples are 41 nt long sequences with Adenine in the center and were proved to be unmethylated by experiments. For convenience, we used the _Homo sapiens_ dataset ([[http://lin-group.cn/server/iDNA-MS/download.html](http://lin-group.cn/server/iDNA-MS/download.html)]([http://lin-group.cn/server/iDNA-MS/download.html](http://lin-group.cn/server/iDNA-MS/download.html)) (accessed on 20 August 2021)) [38] directly, including 18,335 positive samples and 18,335 negative samples. The details of the datasets are presented in Table 1.