Table 2.
Gene repertoire of the LCSA and gene status in the five Buchnera strainsa
| Type of lossb | No. of genes | Gene(s) in the LCSA | Status of gene in Buchnera strainc: |
||||
|---|---|---|---|---|---|---|---|
| BAp | BSg | BBp | BCc | BCt | |||
| U | 3 | yhhF, ung, miaA | + | ψ | + | + | + |
| U | 21 | fliJ, fliM, pmbA, nth, yabI, apaH, dksA, gloB, ychE, trpA, trpB, trpC, trpD, mviN, flgB, flgC, flgG, ycfF, pepA, yhgN, yggH | + | + | + | − | + |
| U | 15 | rnpB, grpE, pyrH, pgl (ybhE), zwf, yoaE, cyoD, mdlA, mdlB, yqgF, yggW, yggX, pgi, cyaY, repA1 | + | + | + | + | − |
| U | 6 | yraL, yfcN, recB, recD, aroE, sbcB | + | + | + | + | ψ |
| U | 2 | tldD, yccK | + | + | + | ψ | + |
| U | 1 | fabD | ψ | + | + | + | + |
| U | 1 | fabZ | − | + | + | + | + |
| U | 4 | himA (ihfA), yaeT, himD (ihfB), ompA | + | + | − | + | + |
| S5 (BAp-BSg)-(BBp-BCc-BCt) | 1 | hemD | ψ | ψ | − | − | − |
| 1 | ansA | − | ψ | − | − | − | |
| S4 (BSg)-(BBp-BCc-BCt) | 1 | ycfM | + | ψ | ψ | − | − |
| 8 | nlpD, cysN, cysD, cysG, cysH, cysI, cysQ, hemC | + | ψ | − | − | − | |
| 2 | hns, cspC | + | − | − | − | − | |
| S4 (BAp-BSg)-(BCc-BCt) | 3 | cvpA, apbE, cmk | ψ | ψ | + | − | − |
| 7 | mutH, norM, bioC, bioF, pal, yqgE, uspA | − | − | + | − | − | |
| S4 (BAp-BSg)-(BBp)-(BCt) | 1 | pcnB | − | − | − | + | ψ |
| S4 (BAp)-(BBp-BCc-BCt) | 7 | bcp,folE, yqcD, znuA, ygcF, ygcM (ptpS), ybaX | − | + | − | − | − |
| 2 | metR, lolE | ψ | + | − | − | − | |
| S3 (BSg)-(BCc-BCt) | 14 | rnfC or rsxC, yfaE, mrcB, murC, mraY, murF, murE, mltE, bioD, phrB, mrsA (glmM), lgt, pyrE, yjeA | + | ψ | + | − | − |
| 6 | ispE, dxr, ispG, ispF, ispD, dxs | + | + | ψ | − | − | |
| 1 | ycfC | + | − | + | − | − | |
| S3 (BBp-BCc-BCt) | 56 | dnaT, argE, argC, secB, rfaE, cysK, priA, queA, tgt, surA, ribF, nadE, smpA, hpt, panC, panB, mutT, coaE, speD, speE, lpcA, topA, lolC, lolD, glpF, pyrC, flgN, flgA, flgD, flgE, flgK, ompF, pncB, pyrD, ycbY, pyrB, pyrI, yfiO, metK, ygbQ, cysC, cysJ, nadD, argA, mltA, thiL, ispA, tig, smg, argD, yeeX, rnr, ibpA, coaD, yba-4, yhiQ | + | + | − | − | − |
| S3 (BAp-BSg)-(BBp) | 4 | sppA, yebC, zapA, dusA | − | − | − | + | + |
| S3 (BAp)-(BCc-BCt) | 1 | ddlB | ψ | + | + | − | − |
| 5 | yidD, yjeK, ygjT, yebA, ygfA | − | + | + | − | − | |
| S2 (BSg)-(BCt) | 1 | yba3 | + | ψ | + | + | ψ |
| S2 (BCc-BCt) | 100 | atpB, atpE, atpF, atpH, atpA, atpG, atpD, atpC, glmS, glmU, yigL, purH, hupA, murB, yibN, cysE, ribB, bacA, crr, ptsI, ptsH, tRNAAla gene, fliE, fliK, ytfN, dcd, ribE, rnfA or rsxA, rnfB, rnfD or rsxD, rnfG or rsxG, rnfE or rsxE, ydiK, yajC, folA, lytB (ispH), lspA, folC, nrdB, nrdA, yba-2, ppnK, sodA, guaC, pfs, murG, ftsW, murD, ftsI (pbpB), ftsL, htrA, uppS, gpt, yfjF, purB, pyrF, ribA, cls, yciB, sohB, bioB, bioA, znuB, znuC, flgJ, rne, tmk, ptsG, murA, gshA, endA, pyrG, mutS, dsbA, gmk, thyA, ybeX, ribH, ribD, yajR, yrdC, fkpA, yhfC, deoD, deoB, prfC, gshB, yggS, murI, purA, hflC, hflK, mutL, mtlD, mtlA, amiB, pitA, ynfM, yqhA, repA2 | + | + | + | − | − |
| 1 | ppiD | + | + | + | ψ | ψ | |
| S2 (BBp)-(BCt) | 1 | secG | + | + | ψ | + | − |
| 2 | argB, fis | + | + | − | + | − | |
| S2 (BBp)-(BCc) | 1 | yedA | + | + | ψ | − | + |
| 2 | uup, yggJ | + | + | − | − | + | |
| S2 (BAp-BSg) | 1 | bioH | − | ψ | + | + | + |
| S2 (BAp)-(BCc) | 1 | rnhA | ψ | + | + | − | + |
a
B. aphidicola strains are abbreviated as explained in Table 1, footnote b.
b
U, unique loss; S2, S3, S4, and S5, losses in two, three, four, and five strains, respectively. The strains with the gene losses are indicated in parentheses. The number of parentheses indicates the number of probable convergent losses, according to the phylogeny shown in Fig. 1.
c
The status of the gene(s) is indicated as follows: +, gene present; −, gene absent, ψ, pseudogene.