Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

Abstract

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.

Figure 1

A simple evolutionary scenario under which the COG algorithm groups paralogous sequences.

Figure 2

Suitable case of a witness. A duplication occurred before all speciations and Z is a witness of the non-orthology between the sequences x₁ and y₂.

Figure 3

Unsuitable cases of witnesses. To the left, duplication occurred only in Z, and therefore z₃ and z₄ are in-paralogs with respect to (X, Y) and cannot act as witness of non-orthology. To the right, X speciated before the duplication event. Hence, x₁ is orthologous to all three other proteins and cannot act as witness of non-orthology.

Figure 4

Unrooted phylogenetic consensus tree constructed from a Bayesian analysis of a subgroup from COG0508. Posterior probabilities are indicated to the right of the nodes and clan-supporting bootstrap values are indicated below the probability value. Predicted clans are indicated by the vertical bars on the right side. The leaf labels correspond to the following COG identifiers: Agrobacterium tumefaciens (2: AGl2719, 3: AGc4775, 4: AGc2641), Brucella melitensis (2: BMEII0746, 3: BMEI0141, 4: BMEI0856), Buchnera sp. (1: BU206, 3: BU303), E.coli K12 (COG identifier corresponds to the gene name: aceF, sucB), E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471, 3: mll4300, 4a: mlr0385, 4b: mll3627), Rhizobium meliloti (2: SMc03203, 3a: SMc02483, 3b: SMb20019, 4: SMc01032), Rickettsia conorii (3: RC0226, 4: RC0764), Rickettsia prowazekii (3: RP179, 4: RP530), Vibrio cholerae (1: VC2413, 3: VC2086), Y.pestis (1: YPO3418, 3: YPO1114).

Figure 5

Unrooted phylogenetic consensus tree for COG0513, constructed from a Bayesian analysis. Posterior probabilities are drawn to the right of the nodes and clan-supporting bootstrap values are below the relevant nodes. The vertical bars bars to the right indicate the prediced clans. The leaf labels correspond to the COG identifiers: A.tumefaciens (2: AGl1362, 5: AGc4238, 6: AGc3366), B.melitensis (2: BMEI1824, 5: BMEI0934, 6: BMEI1035), E.coli K12 (COG identifier corresponds to the gene name: dbpA, deaD, rhlB, rhlE, srmB), H.influenzae (1: HI0422, 3: HI0231, 4: HI0892), P.multocida (1: PM1840, 3: PM1112, 4: PM1921), P.aeruginosa (2: PA0455, 3: PA2840, 4: PA3861, 5: PA0428), R.loti (2: mlr4393, 5: mlr0349, 6: mll0224), R.meliloti (2: SMc01090, 5: SMb20880, 6: SMc00522), V.cholerae (1: VC0660, 2: VC2564, 4: VC0305, 5: VCA0204), Y.pestis (1: YPO2708, 2: YPO1776, 3: YPO3488, 4: YPO3869).

Figure 6

Phylogenetic consensus tree rooted by outgroups for COG1113, constructed from a Bayesian analysis of a data subgroup from COG1113. Posterior probabilities of the Bayesian analysis are drawn to the right of the nodes and clan-supporting bootstrap values below relevant nodes. Predicted clans are indicated by vertical bars to the right. The leaf labels correspond to the COG identifiers: A.tumefaciens C58 (6: AGl2082), Bacillus halodurans (out: BH2171), B.melitensis (5: BMEII0038), E.coli K12 (COG identifier corresponds to the gene name: ansP, aroP, cycA, gabP, pheP, proY, yifK), E.coli H7 EDL933 (1: ZpheP, 2: ZaroP, 3: ZyifK, 4: ZproY, 5: ZcycA, 6: ZansP, 7: ZgabP), E.coli H7 (1: ECs0614, 2: ECs0116, 3: ECs4729, 4: ECs0452, 5: ECs5186, 6: ECs2057, 7: ECs3524), P.aeruginosa (2a: PA3000, 2b: PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859, 6: YPO1937).