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Table 1 Material and gene sequences used

From: Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae)

Species

Taxonomic group (base chromosome number)

2n

x

GenBank accession ID

Voucher ID

Viola congesta

sect. Andinium (x = 7)

--

2x

a: GU289564; b: GU289615

Marcussen 641 (O)

Viola biflora

sect. Chamaemelanium (x = 6)

2n = 12

2x

a: GU289574; b: GU289625

Marcussen 775 (O)

Viola brevistipulata

sect. Chamaemelanium (x = 6)

2n = 12

2x

a: GU289575; b: GU289626, GU289627

Marcussen 803 (O)

Viola canadensis

sect. Chamaemelanium (x = 6)

2n = 12, 24

4x

aa: GU289576; ba: GU289637

Marcussen 802 (O)

Viola nuttallii

sect. Chamaemelanium (x = 6)

2n = 24

4x

a: GU289577, GU289578, GU289579; b: GU289628, GU289629

Marcussen 801 (O)

Viola pubescens

sect. Chamaemelanium (x = 6)

2n = 12

2x

a: GU289580; b: GU289630

Marcussen 637 (O)

Viola maculata

sect. Chilenium

--

8x

a: GU289570, GU289571, GU289572, GU289573; b: GU289616, GU289617, (GU289618b), GU289619

Marcussen 804 (O)

Viola banksii

sect. Erpetion

--

8x-10x

a: GU289565, GU289566, GU289567c, GU289568c, (GU289569b); b: (GU289620c), GU289621, GU289622b, GU289623, GU289624

Marcussen 630 (O)

Viola bicolor

sect. Melanium

2n = 34

12x?

a: GU289603, GU289604, GU289605c, GU289606b, GU289607c, GU289608b

Marcussen 743 (O)

Viola calcarata

sect. Melanium

2n = 20

12x?

a: GU289609, GU289610, GU289611, GU289612c, GU289613, GU289614

Marcussen 672 (O)

Viola dirimliensis

sect. Melanium

2n = 8

8x?

a: GU289599, GU289600, GU289601, GU289602c

Marcussen 650 (O)

Viola epipsila

sect. Viola (x = 10, 12)

2n = 24

4x

a: GU289587, GU289588; b: GU289635b

Marcussen 661 (O)

Viola hirta

sect. Viola (x = 10, 12)

2n = 20

4x

a: GU289581, GU289582

Marcussen 682 (O)

Viola mirabilis

sect. Viola (x = 10, 12)

2n = 20

4x

a: GU289583, GU289584; b: GU289631

Marcussen 683 (O)

Viola selkirkii

sect. Viola (x = 10, 12)

2n = 24

4x

a: GU289589, GU289590; b: GU289634b

Marcussen 698 (O)

Viola spathulata

sect. Viola (x = 10, 12)

--

8x?

a: GU289593, GU289594, GU289595b, GU289596b, GU289597, GU289598; b: GU289636b

Marcussen 670 (O)

Viola uliginosa

sect. Viola (x = 10, 12)

2n = 20

4x

a: GU289585, GU289586; b: GU289632

Marcussen 662 (O)

Viola verecunda

sect. Viola (x = 10, 12)

2n = 24

4x

a: GU289591, GU289592; b: GU289633

Marcussen 697 (O)

Allexis batangae

Violaceae (outgroup)

--

2x

a: GU289562; b: GU289563c

Bos 4241 (UPS)

Anchietea parvifolia

Violaceae (outgroup)

--

2x

GU289559c

Myndel Pedersen 13944 (UPS)

Corynostylis arborea

Violaceae (outgroup)

--

2x

GU289560

Asplund 14509 (UPS)

Cubelium concolor (= Hybanthus concolor)

Violaceae (outgroup)

2n = 48

2x

GU289561

Pläck & Bodin s.n. (UPS)

Hybanthus enneaspermus

Violaceae (outgroup)

2n = 16, 32

2x

GU289558

unknown 2001-05-13 (UPS)

Rinorea ilicifolia

Violaceae (outgroup)

--

2x

GU289557

Friis et al. 2445 (UPS)

Populus trichocarpa

Salicaceae (outgroup)

2n = 38

--

a: DT509274; b: CV227572

--

Manihot esculenta

Euphorbiaceae (outgroup)

2n = 36, 54, 72

--

a: DV448133; b: (CK652029)

--

Euphorbia esula

Euphorbiaceae (outgroup)

2n = 20, 48-60

--

DV145650

--

  1. Taxa used in this study, with respective GenBank accessions for DNA sequences and voucher information. For each taxon systematic affinity (sections within Viola for ingroup, and families within Malpighiales for outgroup), chromosome counts (2n, where available), and putative ploidal levels (x, inferred from the NRPD2/E2 data), are indicated. GenBank accession IDs are sorted by paralog (a and b), and by homoeolog (ascending numbers); gene copies excluded from phylogenetic analysis, because they were considered too short for reliable analysis, are put in brackets. Note that NRPD2/E2-a and NRPD2/E2-b are arbitrary labels, and that NRPD2/E2-a and NRPD2/E2-b in Euphorbiaceae, Salicaceae and Violaceae are not orthologous to each other. Herbarium acronyms for voucher specimen deposition (i.e., O, U) follow Holmgren and Holmgren [50].
  2. a the secondarily duplicated gene copies in Viola canadensis differed only in 3 (NRPD2/E2-a) and 8 (NRPD2/E2-b) substitutions, and their respective consensuses were used as single sequences in the analyses
  3. b partial sequence (exon 6 to exon 7); PCR 1 failed (see Figure 1)
  4. c partial sequence (exon 5 to intron 6); PCR 2 failed (see Figure 1)