new and old regions for barcoding n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
New and old regions for Barcoding PowerPoint Presentation
Download Presentation
New and old regions for Barcoding

Loading in 2 Seconds...

play fullscreen
1 / 13

New and old regions for Barcoding - PowerPoint PPT Presentation


  • 80 Views
  • Uploaded on

New and old regions for Barcoding . Teun Boekhout CBS. Problems with Mitochondrial Genomes. Taphrinomycotina versus Saccharomycotina versus Pezizomycotina Cryptococcus gattii. (3). (1). (2). Pezizomycotina. Saccharomycotina. Saccharomycotina. Pezizomycotina. Taphrinamycotina.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'New and old regions for Barcoding' - osma


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
problems with mitochondrial genomes
Problems with Mitochondrial Genomes
  • Taphrinomycotina versus Saccharomycotina versus Pezizomycotina
  • Cryptococcus gattii
three published scenario s on fission yeasts

(3)

(1)

(2)

Pezizomycotina

Saccharomycotina

Saccharomycotina

Pezizomycotina

Taphrinamycotina

Taphrinamycotina

Saccharomycotina

Taphrinamycotina

Pezizomycotina

Mitochondrial support

Most nuclear genes

No support

Three published scenario’s on fission yeasts
cryptococcus gattii
Cryptococcus gattii
  • 4 monophyletic lineages (phylogenetic species)
  • 6 nuclear concordant nuclear gene phylogenies
  • Mitochondrial versus nuclear genes incongruent
  • [ATP 6 & MtLrRNA] vs [CNLAC, TEF1α, RPB1, RPB2, ITS, IGS1]
  • Mitochondrial loci incongruent
  • Mitochondrial recombination
slide5

CBS6998

CBS1622/CBS6992

100

ATP6 haplotype 3

MtLrRNA haplotype 2

M3

CBS6290

63

60

48A/56A

64

CBS8273/RV20186T

74

Nucleus

CBS6289

93

Mitochondrion

ATP6 haplotype 4

MtLrRNA haplotype 2

M1

WM830

MtLrRNA

ATP6

WM276

60

blue = AFLP4

green = AFLP6

purple = AFLP4 like

yellow = AFLP6 like

red = chimera AFLP4/AFLP6

WM176

99

5032738

CBS7229T/RV54130

60

E566

WM179R

ATP6 haplotype 1

MtLrRNA haplotype 2

M2

CBS919T

64

CBS7748

CBS883T

10

ATP6 haplotype 2

MtLrRNA haplotype 1

M5

ATP6 haplotype 2

MtLrRNA haplotype 4

M4

Nuclear AFLP/MLST 4 with varying mitochondria

slide6

WM714

WM714

H99

H99

Cryptococcus neoformans

125.91

125.91

CBS6886

CBS6886

JEC20

JEC20

RAM2

ICB184

ICB184

HEC11102

A1MR265

CBS1930

A1MR406

CBS6956

A1M368

CBS7750

CBS1930

CBS8684

CBS6956

A1MR269

AFLP6

VGII

MLST 6

CBS8684

A1MR368

WM178

WM178

A1MR409

A1MR406

95

HEC11102

A1MR409

A1MF2866

A1MF2932

A1MF2932

A1MR265

A1MR269

A1MR271

A1MR271

A1MF2866

100

CBS7750

RAM2

(M5)

(M5)

WM179

WM179

(M5)

(M5)

E566

E566

(M4)

63

84

(M4)

CBS919

CBS883

(M4)

(M4)

CBS883

CBS7748

(M4)

(M4)

CBS7748

CBS919

65

(M3)

(M3)

CBS1622

CBS1622

(M3)

(M3)

AFLP4

VGI

MLST4

CBS6992

CBS6992

(M2)

(M2)

CBS7229

CBS7229

(M2)

(M2)

RV54130

RV54130

(M2)

100

(M2)

WM176

WM176

(M2)

(M2)

75

5032738

5032738

(M2)

(M2)

WM276

WM276

(M2)

(M2)

WM830

WM830

62

AFLP7

VGIV

MLST7

B5748

97

B5748

B5742

B5742

WM779

M27055

M27055

WM779

(M1)

(M1)

CBS6290

CBS6290

(M1)

93

(M1)

56A

56A

(M1)

(M1)

74

CBS8273

AFLP4

VGI

MLST4

CBS8273

(M1)

(M1)

48A

48A

(M1)

(M1)

CBS6289

CBS6289

(M1)

(M1)

CBS6998

CBS6998

(M1)

(M1)

RV20186

RV20186

CBS6993

CBS6996

WM161

380C

WM728

CBS6955

94

AFLP5

VGIII

MLST5

CBS5758

CBS6993

81

CBS8755

384C

WM726

WM161

b

a

380C

CBS5758

82

CBS6955

WM726

ATP6

MtLrRNA

0.1

CN043

1

CBS8755

CBS6996

CN043

98

384C

WM728

the old alternative
The ‘old’ alternative
  • rDNA universally present
  • ITS + D1/D2 LSU rDNA (Kurtzman > 20years)
  • Basidio + Asco yeasts
  • Yeast book chapters: both needed
  • Clinical yeasts (C. glabrata / C. nivariensis / C. bracarensis)
  • Large datasets available
  • Proven useful for ID (Kurtzman, Fell, CBS, et al.)
  • Luminex technology (ID, M. Diaz, Miami)
  • Cryptococcus, Trichosporon, Candida, Malassezia
alternatives 2
Alternatives 2
  • ‘Unique’ fungal pathways
  • E.g. Ergosterol pathway (membranes)
  • Concatenated ERG genes resolve TOL
  • ERG7 (lanosterol synthase) fungi/animals
  • ERG1 (squalene epoxidase) fungi/animals/plants
  • ERG11 (lanosterol C14 demethylase) fungi/animals
alternatives 3
Alternatives 3
  • Comparative Genomics
  • 33 Fungal Genomes
  • 4852 KOGs
  • 70 single protein Kogs (paralogs!)
  • 32 gene KOs not viable (S. cerevisae) > essential genes
  • Reference tree based on 531 KOGs
  • KOG2671 showed highest correlation (0.97) with 531 KOG tree
  • Cophenetic correlation between individual protein NJ trees > 0.5 > 64 KOGs remaining
  • Development phylogenetic signal
slide10

64 concatenated proteins

Sac. cerevisiae RM11-1a

*

Sac. cerevisiae S288c

*

Sac. paradoxus

*

Sac. mikatae

*

*

Sac. kudriavzevii

* > 80%

*

Sac. bayanus

*

Sac. castellii

IA

Can. glabrata

*

Ash. gossypii

Kluyveromyces lactis

Sac. kluyveri

*

Can. guilliermondii

*

Debaromyces hansenii

*

*

Can. albicans

I

Can. lusitaniae

Yarrowia lipolytica

Chaetomium globosum

*

Neurospora crassa

*

IB1

*

*

Magnaporthe grisea

Fusarium graminearum

*

IB

IB2

Sclerotinia sclerotiorum

*

Botritys cinerea

*

Asp. fumigatus

*

IB3

*

Asp. nidulans

*

Coccidioides immitis

IB4

Stagonospora nodorum

IC

*

Schizosaccharomyces pombe

Coprinopsis cinereus

*

IIA

Phanerochaete chrysosporium

II

*

Cry. neoformans var. neoformans JEC21

*

*

Cry. neoformans var. grubii H99

IIB

Ustilago maydis

III

IIIA

Rhizopus oryzae

Caenorhabditis elegans

0.1

development of phylogenetic signal
Development of phylogenetic signal

Mainly Information storage and Processing & Cellular processes and signaling

potential barcoding candidates
Potential Barcoding candidates
  • KOG2671 Putative RNA methylase
  • KOG0340 ATP-dependent RNA helicase
  • KOG4089 Predicted mitochondrial ribosomal protein L23
  • KOG0173 20S proteasome
  • KOG2728 Uncharacterized conserved protein
  • Etc. Etc.

Top 5 orthologues with high discriminatory potential

my suggestions
My suggestions
  • There may be alternative genes
  • D1/D2 + ITS 1+2!
  • Panfungal / Paneukaryotic / Single copy / PCRable
  • Need to be investigated further for Barcoding (and TOL) potential
  • Option: Multilocus Barcoding ?
  • Webtool: Different loci per (higher) taxon
  • Selection depends on taxonomic resolution