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Table 3 Presence/absence polymorphisms of introns in ABCB1 in select angiosperms

From: Parallel loss of introns in the ABCB1 gene in angiosperms

  

Intron number

Methodologya

Species

Locus ID

1

2

3

4

5

6

7

8

9

 

Dicots

Intron presence/absenceb

 

Fabaceae

  Phaseolus vulgaris

Phvul.001G179300

Pb

P

P

P

P

P

P

P

P

Seq

  Phaseolus vulgaris

Phvul.007G147400

P

P

P

P

P

P

P

P

P

Seq

  Medicago truncatula

Medtr7g102070

P

P

P

P

P

P

P

P

P

Seq

  Medicago truncatula

Medtr1g063170

P

P

P

P

P

P

P

P

P

Seq

  Trifolium pratense

Tp57577_TGAC_v2_gene32830

P

P

P

P

P

P

P

P

P

Seq

  Glycine max

Glyma.19G184300

P

P

P

P

P

P

P

P

P

Seq

  Glycine max

Glyma.03G183600

P

P

P

P

P

P

P

P

P

Seq

  Glycine max

Glyma.10G055000

P

P

P

P

P

P

P

P

P

Seq

  Glycine max

Glyma.13G142100

P

P

P

P

P

P

P

P

P

Seq

Rosaceae

  Prunus persica

Prupe.7G129600

P

P

P

P

P

P

P

P

P

Seq

  Malus domestica

MDP0000231597

P

P

P

P

P

P

P

P

P

Seq

  Malus domestica

MDP0000183294

P

P

P

P

P

P

P

P

P

Seq

  Fragaria vesca

gene09601-v1.0-hybrid

P

P

P

P

P

P

P

P

P

Seq

Cucurbitaceae

  Cucumis sativus

Cucsa.306720

P

P

P

P

P

P

P

P

A

Seq

Rutaceae

  Citrus clementina

Ciclev10010916m.g

P

P

P

P

P

P

P

P

P

Seq

  Citrus sinensis

orange1.1g000687m.g

P

P

P

P

P

P

P

P

P

Seq

Myrtaceae

  Eucalyptus grandis

Eucgr.K02930

P

P

P

P

P

P

P

P

P

Seq

Malvaceae

  Theobroma cacao

Thecc1EG022244

P

P

P

P

P

P

P

P

P

Seq

  Gossypium raimondii

Gorai.002G246800

P

P

P

P

P

P

P

P

P

Seq

  Gossypium raimondii

Gorai.006G163000

P

P

P

P

P

P

P

P

P

Seq

Brassicaceae

  Eutrema salsugineum

Thhalv10016150m.g

P

P

P

P

P

P

P

A

P

Seq

  Capsella grandiflora

Cagra.0558 s0007

P

P

P

P

P

P

P

P

P

Seq

  Capsella rubella

Carubv10022511m.g

P

P

P

P

P

P

P

P

P

Seq

  Boechera stricta

Bostr.23794 s0400

P

P

P

P

P

P

P

P

P

Seq

  Brassica rape FPsc

Bra023087

P

P

P

P

P

P

P

P

P

Seq

  Brassica rapa FPsc

Bra017216

P

P

P

P

P

P

P

P

P

Seq

  Brassica oleracea

Bo3g031410

P

P

P

P

P

P

P

P

P

Seq

  Brassica oleracea

Bo4g186480

P

P

P

P

P

P

P

P

P

Seq

  Arabidopsis lyrata

934,330

P

P

P

P

P

P

P

P

P

Seq

  Arabidopsis thaliana columbia

AT2G36910

P

P

P

P

P

P

P

P

P

Seq

Caricaceae

  Carica papaya

evm.TU.supercontig_102.36

P

P

P

P

P

P

P

ND

P

Seq

Amaranthaceae

  Chenopodium quinoa

AUR62040338

P

P

P

P

P

P

P

P

P

Seq

  Chenopodium quinoa

AUR62042509

P

P

P

P

P

P

P

P

P

Seq

Euphorbiaceae

  Ricinus communis

30,078.t000079

P

P

P

P

P

P

P

P

P

Seq

  Manihot esculenta

Manes.09G065700

P

P

P

P

P

P

P

P

P

Seq

  Manihot esculenta

Manes.08G011100

P

P

P

P

P

P

P

P

P

Seq

Linaceae

  Linum usitatissimum

Lus10023929.g

P

A

P

P

P

P

P

P

P

Seq

Salicaceae

  Salix purpurea

SapurV1A.1230 s0070

P

P

P

P

P

P

P

P

P

Seq

  Salix purpurea

SapurV1A.0584 s0030

P

P

P

P

P

P

P

P

P

Seq

  Populus trichocarpa

Potri.006G123900

P

P

P

P

P

P

P

P

P

Seq

  Populus trichocarpa

Potri.016G093600

P

P

P

P

P

P

P

P

P

Seq

Solanaceae

  Solanum lycopersicum

Solyc09g008240.2

P

P

P

P

P

P

P

P

P

Seq

  Solanum tuberosum

PGSC0003DMG400003889

P

P

P

P

P

P

P

P

P

Seq

Phrymaceae

  Mimulus guttatus

Migut.J00652

P

P

P

P

P

P

P

P

P

Seq

  Mimulus guttatus

Migut.L01707

P

P

P

P

P

P

A

P

P

Seq

Ranunculaceae

  Aquilegia coerulea Goldsmith

Aquca_030_00072

P

P

P

P

P

P

P

P

P

Seq

  Aquilegia coerulea Goldsmith

Aquca_062_00022

P

P

P

P

P

P

P

P

P

Seq

Non-grass monocots (except Poales)

  Zostera marina

Zosma16g00300

P

A

P

P

P

P

P

A

A

Seq

  Spirodela polyrhiza

Spipo1G0026900

P

P

P

P

P

P

P

P

P

Seq

  Phoenix dactylifera

LOC103714888

P

P

P

P

P

P

P

P

P

Seq

  Phoenix dactylifera

LOC103706998

P

P

P

P

P

P

P

P

P

Seq

  Musa acuminata

GSMUA_Achr4G12130_001

P

P

P

P

P

P

P

P

P

Seq

  Musa acuminata

GSMUA_Achr4G04430_001

P

P

P

P

P

P

P

P

P

Seq

Poales (except Poaceae)

  Ananas comosus

Aco010196

P

P

P

P

P

P

P

P

P

Seq

  Typha latifolia

Not assigned

P

P

P

P

P

P

P*

P

P

LR-PCR/Seq

  Ecdeiocolea spp.

Not assigned

A

P

P

P

P

P

P

P

P

LR-PCR/Seq

  Mayaca spp.

Not assigned

P

P

P

A

P

P

P

P

A

LR-PCR/Seq

Poaceae

  Streptochaeta spp.

Not assigned

A

P

P

P

P

P

P

P

P

LR-PCR/Seq

  Anomochloa spp.

Not assigned

A*

P*

P*

A*

ND

P

P*

P

A

PCR/Seq

  Pharus mezhii

Not assigned

A*

P*

P

P*

P

P*

ND

P

ND

PCR/Seq

  Leersia perrieri

LPERR08G20590

A

A

A

A

A

A

P

A

A

Seq

  Oryza sativa ssp. indica

BGIOSGA029208

A

A

A

A

P

A

P

A

A

Seq

  Oryza sativa ssp. japonica

LOC_Os08g45030

A

A

A

A

P

A

P

A

A

Seq

  Aulonemia spp.

Not assigned

A*

P*

A*

A*

P

ND

P

A

ND

PCR/Seq

  Bambusa spp.

Not assigned

A

P

A

A

P

P

P*

A

A

PCR/Seq

  Phyllostachys spp.

Not assigned

A

P

A

A

P

P

P

A

A

LR-PCR/Seq

  Phyllostachys edulis

PH01000979

A

P

A

A

P

P

P

A

A

Seq

  Phyllostachys edulis

PH01001487

A

P

A

A

P

P

P

A

A

Seq

  Brachypodium distachyon

Bradi3g12627

A

A

A

A

P

A

P

A

A

Seq

  Brachypodium stacei

Brast03G311000

A

A

A

A

P

A

P

A

A

Seq

  Hordeum vulgare

MLOC_5438

A

A

A

A

P

P

P

A

A

Seq

  Aegilops tauschii

F775_52675

A

A

A

A

P

P

P

A

A

Seq

  Triticum urartu

TRIUR3_22724

A

A

A

ND

P

P

P

A

A

Seq

  Eragrostis tef

JN672670

A

A

A

A

A

P

P

A

A

Seq

  Eragrostis tef

JN672669

A

A

A

A

A

P

P

A

A

Seq

  Zoysia spp.

Not assigned

A

A

A

A

A

A

P

A

A

LR-PCR/Seq

  Oropetium thomaeum

Oropetium_20150105_14444

A

P

A

A

A

A

P

A

A

Seq

  Eleusine coracana

Not assigned

A

P

A

A

A

A

P

A

A

Seq

  Micraira subilifolia

Not assigned

A*

A*

A*

A*

P

P

ND

A

A

PCR/Seq

  Phragmites australis

Not assigned

A*

P*

A*

A*

P

P

ND

A

A

PCR/Seq

  Danthoniopsis dinteri

Not assigned

A

P

A

A

P

ND

ND

A

A

PCR

  Chasmanthium laxum

Not assigned

A

P

A

A

P

P

P

A

A

Seq

  Paspalum vaginatum

Not assigned

A

P

A

A

A

P

P

A

A

LRPCR/Seq

  Zea mays

GRMZM2G315375

A

P

A

A

P

P

P

A

A

Seq

  Sorghum bicolor

AY372819.1

A

P

A

A

P

P

P

A

A

Seq

  Arundinella hirta

Not assigned

A

P

A

A

P

ND

P*

A

A

PCR/Seq

  Andropogon virginicus

Not assigned

A

P

A

A

P

P

P

A

A

Seq

  Andropogon gerardii

Not assigned

A

P

A

A

P

ND

P*

A

A

PCR/Seq

  Acroceras macrum

Not assigned

A

P

A

A

A

ND

P*

A

ND

PCR/Seq

Sacciolepis myosuroides

Not assigned

A

P

A

A

P

ND

P*

A

A

PCR/Seq

  Dichanthelium

oligosanthes

Not assigned

A

P

A

A

A

P

P

A

A

Seq

  Panicum virgatum

Pavir.6NG364900

A

P

A

A

A

P

P

A

A

Seq

  Panicum virgatum

Pavir.6KG414900

A

P

A

A

A

P

P

A

A

Seq

  Panicum hallii

Pahal.F00317

A

P

A

A

A

P

P

A

A

Seq

  Setaria italica

Seita.6G253500

A

A

A

A

A

P

P

A

A

Seq

  Setaria viridis

Sevir.6G258000

A

A

A

A

A

P

P

A

A

Seq

  Cenchrus americanus

CaABCB1

A

A

A

A

A

P

P

A

A

Seq

  Brachiaria spp.

Not assigned

A

A

A

A

A

P

ND

A

ND

PCR

  Urochloa abyss

Urochola_abyss_gt1kb

A

A

A

A

A

P

P

A

A

Seq

Basal angiosperm

  Amborella trichopoda

evm_27.TU.AmTr_v1.0_scaffold00076.86

P

P

P

P

P

P

P

P

P

Seq

  1. a Seq: Sequence information from cloned genes or whole-genome sequencing; PCR: PCR amplification across two introns (1 + 2, 3 + 4) or single introns; PCR/Seq: PCR amplification across introns followed by sequencing of some of the amplicons (Sanger sequenced amplicons are indicated with an asterisk (*)); LR-PCR/Seq: Long-range PCR across all introns followed by sequencing of the amplification product
  2. b P present, A absent; ND indicates introns for which no data is available on intron status
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BMC Ecology and Evolution

ISSN: 2730-7182

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