Table 2.
A partial list of P. jirovecii full-length msg isoforms (~3 kb) identified in a clinical sample by PacBio sequencing and clustering-based analysis
| Contig no. | Length (bp) | Matched msg gene | Status | Identity to the known (%) | PCR verification |
|---|---|---|---|---|---|
| Contig0020 | 3086 | EF371022 | Known | 98.92 | ND |
| Contig0007 | 3086 | EF371023 | Known | 99.87 | ND |
| Contig0021 | 3008 | EF371024 | Known | 99.83 | ND |
| Contig0025 | 3011 | EF371025 | Known | 99.60 | ND |
| Contig0133 | 3068 | EF371026 | Known | 99.71 | ND |
| Contig0022 | 3104 | EF371028 | Known | 99.58 | ND |
| Contig0006 | 3062 | EF371029 | Known | 99.97 | ND |
| Contig0008 | 3041 | EF371030 | Known | 99.87 | ND |
| Contig0026 | 3032 | EF371031 | Known | 98.76 | ND |
| Contig0012 | 3005 | EF371032 | Known | 99.70 | ND |
| Contig0013 | 2996 | EF371033 | Known | 99.87 | ND |
| Contig0011 | 3092 | EF371035 | Known | 99.88 | ND |
| Contig0003 | 3038 | EF371036 | Known | 99.97 | ND |
| Contig0005 | 3002 | EF371038 | Known | 99.90 | ND |
| Contig0010 | 2996 | EF371040 | Known | 99.80 | ND |
| Contig0015 | 3129 | EF371041 | Known | 99.78 | ND |
| Contig0001 | 3002 | EF371042 | Known | 99.37 | ND |
| Contig0027 | 3065 | EF371045 | Known | 99.64 | ND |
| Contig0014 | 3077 | EF371050 | Known | 99.71 | ND |
| Contig0018 | 3044 | EF371051 | Known | 99.70 | ND |
| Contig0009 | 3029 | EF371052 | Known | 99.87 | ND |
| Contig0017 | 3023 | EF371053 | Known | 99.50 | ND |
| Contig0016 | 3050 | EF371055 | Known | 99.84 | ND |
| Contig0004 | 3026 | EF371056 | Known | 99.97 | ND |
| Contig0010b | 3060 | No | Novel | NA | 99.53 |
| Contig0004b | 3086 | No | Novel | NA | 99.45 |
| Contig0015b | 3039 | No | Novel | NA | 99.20 |
| Contig0053b | 3077 | No | Novel | NA | 98.91 |
| Contig0006b | 3062 | No | Novel | NA | 98.50 |
| Contig0054b | 3074 | No | Novel | NA | 98.32 |
| Contig0138b | 3041 | No | Novel | NA | ND |
A total of 72 unique msg isoforms identified in this study, with only 31 of them shown in this table. The first 24 contigs matched in full-length with the 24 previously identified msg genes from the same clinical sample [22] as shown in the third column with GenBank accession no, NA not applicable, ND not determined by PCR. Additional file 4 contains a complete list of sequences for 72 Msg isoforms