Table 3

Shared single copy nuclear genes are a rich source of phylogenetic information.

ATH

Annotation

# SEQ

# NT

# VAR

PI

>50 MP

>50 ML


At2 g13360

AGT1

49

1203

703

51%

63%

65%

At3 g47810

MAIGO 1

91

573

359

49%

66%

73%

At2 g32520

dienelactone hydrolase family protein

73

721

536

64%

75%

81%

At3 g52300

ATPQ

129

519

395

62%

65%

66%

At5 g06360

Ribosomal protein S8e

51

780

449

47%

58%

58%

At5 g04600

RNA recognition motif (RRM)-containing protein

63

579

475

74%

68%

71%

At2 g21870

probable atp synthase 24 kda subunit, mitochondrial precursor

95

606

492

68%

78%

78%

At4 g33250

eukaryotic translation initiation factor 3 subunit 11 (eif3k)

60

662

453

59%

68%

66%

At4 g30010

fiber protein Fb15

129

251

217

77%

62%

63%

At1 g77710

Probable ubiquitin-fold modifier 1 precursor

143

254

202

55%

46%

45%

At4 g08230

glycine-rich protein

51

413

286

54%

60%

68%

At4 g31720

STG1, TAFII15

64

448

323

51%

63%

67%

At4 g37830

putative cytochrome c oxidase subunit VIa precursor

151

216

192

71%

43%

45%

At5 g47570

similar to hypothetical protein 25.t00006 [Brassica oleracea]

90

387

288

64%

58%

65%

At5 g23290

putative c-myc binding protein

69

404

289

64%

62%

69%

At1 g27530

expressed protein

60

525

332

51%

68%

71%

At3 g20390

Endoribonuclease L-PSP, putative

132

372

313

69%

70%

70%

At5 g63135

hypothetical protein

64

448

323

51%

65%

63%

Concatenated alignment of 13 shared single copy genes

69

7701

5072

55%

81%

87%


This table provides the following information about the 18 shared single copy genes that were used for phylogenetic analysis based on EST and finished cDNA sequences: the Arabidopsis thaliana locus ID (ATH); the TAIR annotation in Arabidopsis (Annotation); the number of sequences in the final alignment (# SEQ); the number of nucleotides in the final alignment (# NT); the number of variable characters in the final alignment (# VAR); the percentage of characters that are parsimony-informative (% PI); the percent of nodes in the MP bootstrap consensus trees that are supported in greater than 50% of the bootstrap replicates; the percent of nodes in the ML bootstrap consensus trees that are supported in greater than 50% of the bootstrap replicates.

Duarte et al. BMC Evolutionary Biology 2010 10:61   doi:10.1186/1471-2148-10-61

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