Table 1.
Expression of Genes Potentially Involved in Organic Osmolyte Synthesis and Transport in Halocafeteria seosinensis
| Sequence Name | TPM |
EBSeq |
DESeq2 |
Limma |
Annotation | ||||
|---|---|---|---|---|---|---|---|---|---|
| Opt | Max | PPDE | Post FC | P Value | log2 FC | P Value | log2 FC | ||
| Ectoine biosynthesis | |||||||||
| m.89065 | 289 | 261 | 0.04 | 0.7 | 0.172 | −0.5 | 0.233 | −0.5 | EctA |
| m.89060 | 238 | 397 | 1.0 | 1.3 | 1E−04 | 0.4 | 0.052 | 0.4 | EctB |
| m.89066 | 504 | 239 | 0.7 | 0.4 | 3E−05 | −1.4 | 0.015 | −1.4 | EctC |
| m.14216 | 0.7 | 216 | 1.0 | 220 | NA | 7.4 | 0.001 | 7.8 | Ectoine hydroxylase (EctD) |
| m.89063 | 113 | 259 | 1.0 | 1.8 | 4E−04 | 0.9 | 0.017 | 0.9 | Aspartate kinase |
| Amino acid transport | |||||||||
| m.15646 | 8 | 83 | 1.0 | 7.9 | 2E−59 | 3.0 | 2E−04 | 3.0 | Sodium-amino acid symporter |
| m.82938 | 4 | 38 | 1.0 | 7.1 | 2E−09 | 2.7 | 0.009 | 2.8 | Amino acid transporter |
| m.16444 | 9 | 245 | 1.0 | 22.6 | 2E−28 | 4.3 | 4E−04 | 4.5 | Amino acid transporter |
| m.16489 | 2 | 80 | 1.0 | 29.3 | 8E−50 | 4.7 | 3E−04 | 4.9 | Amino acid transporter |
| m.62883 | 29 | 25 | 1.0 | 0.7 | 2E−05 | −0.6 | 0.022 | −0.6 | Amino acid transporter |
| m.11656 | 16 | 11 | 1.0 | 0.5 | 2E−05 | −0.9 | 0.012 | −0.9 | Amino acid transporter |
| m.18092 | 55 | 36 | 1.0 | 0.5 | 2E−11 | −1.0 | 0.004 | −1.0 | Amino acid transporter |
| m.41609 | 18 | 14 | 1.0 | 0.6 | 4E−06 | −0.7 | 0.014 | −0.6 | Amino acid transporter |
| m.1357 | 48 | 44 | 1.0 | 0.7 | 3E−06 | −0.5 | 0.029 | −0.5 | Amino acid transporter |
| Myo-inositol transport | |||||||||
| m.89752 | 3 | 76 | 1.0 | 18.0 | 3E-44 | 4.1 | 2E-04 | 4.3 | Myo-inositol transporter |
| m.27262 | 5 | 62 | 1.0 | 9.4 | 1E-26 | 3.2 | 4E-04 | 3.4 | Myo-inositol transporter |
| m.25988 | 6 | 14 | 1.0 | 1.9 | 7E-06 | 0.9 | 0.012 | 0.9 | Myo-inositol transporter |
| m.27173 | 2 | 5 | 0.6 | 2.3 | 0.042 | 1.1 | 0.102 | 1.1 | Myo-inositol transporter |
Note.—TPM, average mRNA Transcripts Per Million at optimal (Opt) and at maximal (Max) salt concentrations; PPDE, Posterior Probability of being Differentially Expressed; Post FC, Posterior Fold Change for maximal over optimal salt concentration; EctA, l-2,4-diaminobutyrate acetyltransferase; EctB, l-2,4-diaminobutyrate transaminase; EctC, ectoine synthase. P values calculated by DESeq2 and limma were corrected for multiple testing. (NA: due to low mean normalized count at optimal concentration.)