Table 2

List of 12 linked sets involving the duplication of more than one gene locus in S. cerevisiae with KS < 0.35

Linked set

Paralogous set A

Paralogous set B

KS

Average KS

Structural categories

Chromosomal location

Duplication span (bp)


1

YLR154C-H

YLR157C-C

0.0000

0.0000

Complete

XII/XII

7,167

YLR155C

YLR158C

0.0000

Complete

YLR156W

YLR159W

0.0000

Complete

YLR156C-A

YLR159C-A

0.0000

Complete

YLR157C

YLR160C

0.0000

Complete

YLR157W-D

YLR161W

0.0000

Partial

2

YHR053C

YHR055C

0.0000

0.0000

Complete

VIII/VIII

1,816

YHR054C

YHR056C

0.0000

Partial

3

YCL065W

YCR041W

-

0.0019

Chimeric

III/III

2,509

YCL066W

YCR040W

0.0000

Complete

YCL067C

YCR039C

0.0000

Complete

YCL068C

YCR038C

0.0058

Chimeric

4

YNL033W

YNL019C

0.0000

0.0077

Complete

XIV/XIV

4,247

YNL034W

YNL018C

0.0450

Complete

5

YAR073W/75W

YHR216W

0.1074

0.0087

Complete

I/VIII

7,445

YAR071W

YHR215W

0.0069

Complete

YAR070C

YHR214C-B

0.0000

Complete

YAR069C

YHR214C-D

0.0000

Complete

6*

YKR106W

YCL073C

0.0359

0.0243

Complete

XI/III

6,928

YKR105C

YCL069W

0.0127

Complete

7

YDR543C

YER188C

0.0608

0.0377

Complete

IV/V

7,481

YDR545W

YER189W

0.0147

Complete

8

YJR162C

YNL337W

0.0000

0.0409

Complete

X/IV

2,916

YJR161C

YNL336W

0.0818

9

YCR107W/AAD3

YOL165C

0.0430

0.0430

Complete

III/XV

5,952

YCR108C

YOL166W

-

Complete

10

YAR050W

YHR211W

0.3081

0.0449

Complete

I/VIII

19,614

YAR060C

YHR212C

0.0000

Complete

YAR061W

YHR212W-A

0.0000

Complete

YAR062W

YHR213W

0.0000

Complete

YAR064W

YHR213W-B

0.0000

Complete

YAR066W

YHR214W

0.0066

Complete

YAR068W

YHR214W-A

0.0000

Complete

11

YNR073C

YEL070W

0.0482

0.0817

Complete

XIVI/V

4,611

YNR072C

YEL069C

0.1152

Complete

12

YAR033W

YGL051W

0.0280

0.0973

Complete

I/VII

6,461

YAR031W

YGL053W

0.1667

Complete


Columns 2 and 3 list the systematic names of the group of loci representing each paralogous set as per the Saccharomyces Genome Database. Column 4 lists the synonymous-site divergence (KS) between two paralogs within a linked set as computed by the Nei and Gojobori method with a correction for multiple hits. Column 5 presents the averaged KS value for all paralogous pairs within a linked set. Column 6 lists the particular category of structural resemblance (complete, partial or chimeric) for each duplicate pair. Column 7 lists the chromosomal location of paralogs 1 and 2, respectively. Column 8 provides a minimal estimate of the length of the duplicated region, based on current visual inspection of the extent of sequence homology across the paralogs' coding and flanking regions. *A linked set that has been classified as an ohnolog resulting from a WGD event. Dashes indicate an inability to compute synonymous divergence between the paralogs due to an altered reading frame in one or both gene copies.

Katju et al. Genome Biology 2009 10:R75   doi:10.1186/gb-2009-10-7-r75

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