Table 2

Identity and sequence details of the set of 19 genes targeted for phylogenetic purposes

Candidate gene designation

Original Musa EST (NCBI accession number) a

Blast homology

Corresponding O. sativa chromosome

Homologous region on the O. sativa chromosome (bp) b

Amplified successfully from the outgroup species (S. nicolai)

Intron fraction in the final alignment (%)

Aligned sequence length (bp) c

Mean GC content (%) c


g-1

FF561021.1

ATP:citrate lyase

Chr. 1

11000940 - 11002303

yes

81.5

840 [761]

34.8 [34.6]

g-2

ES433688.1

Stomatal cytokinesis defective protein

Chr. 1

22165522 - 22168085

yes

39.0

776 [720]

39.4 [39.5]

g-3

FF558855.1

Electron transport protein SCO1/SenC family protein

Chr. 2

3229271 - 3231294

yes

90.8

882 [869]

33.3 [33.4]

g-4

ES437588.1

Putative non-phototropic hypocotyl 3 (NPH3)

Chr. 2

21628715 - 21631333

no

33.5

529

62.7

g-5

ES436517.1

Endoribonuclease dicer homolog

Chr. 3

1177218 - 1178862

yes

45.3

890 [827]

36.9 [37.5]

g-6

FF559301.1

CASP protein-like

Chr. 3

28468384 - 28470215

yes

75.6

897 [863]

37.6 [37.8]

g-7

FF559765.1

Zeaxanthin epoxidase

Chr. 4

22349032 - 22350073

no

70.5

909

40.4

g-8

ES437560.1

Na/H antiporter

Chr. 5

2717353 - 2718249

no

33.2

487

47.6

g-9

FF561211.1

Protein of unknown function; DUF89 family protein

Chr. 6

12551039 - 12553284

yes

86.9

1045 [942]

33.5 [33.5]

g-10

ES436526.1

T-complex protein 1, eta subunit (TCP-1-eta)

Chr. 6

28301038 - 28302942

no

69.3

1154

34.1

g-11

ES434922.1

NAD+ synthase domain containing protein

Chr. 7

3637535 - 3641458

yes

54.5

794 [747]

36.5 [36.3]

g-12

FF561580.1

Ribosomal protein s6 RPS6-2

Chr. 7

25669518 - 25671532

no

67.7

755

39.7

g-13

FF559780.1

mRNA capping enzyme, large subunit family protein

Chr. 8

4670797 - 4673706

no

91.2

1433

37.2

g-14

FF560522.1

Methylcrotonyl-CoA carboxylase beta chain

Chr. 8

20354213 - 20356265

no

87.8

767

34.1

g-15

FF560378.1

Annexin-like protein

Chr. 9

13652033 - 13655072

no

92.5

737

38.7

g-16

ES436518.1

Succinoaminoimidazole-carboximide ribonucleotide synthetase family protein

Chr. 9

17688901 - 17690929

no

72.0

587

36.2

g-17

FF558349.1

Methionine aminopeptidase 1

Chr. 10

18996256 - 18997164

no

73.4

746

35.9

g-18

FF559189.1

Initiation factor 2B family protein

Chr. 10

12576657 - 12577797

yes

95.9

915 [915]

34.1 [34.1]

g-19

ES436684.1

DNA polymerase delta catalytic subunit

Chr. 11

4368226 - 4369480

yes

74.0

878 [760]

35.4 [36.2]


a The Musa EST sequence from which the corresponding gene fragment was derived.

b Genomic location in rice.

c Data in square brackets include the outgroup S. nicolai.

Christelov√° et al. BMC Evolutionary Biology 2011 11:103   doi:10.1186/1471-2148-11-103

Open Data