PHYLOGENOMIC APPLICATIONS

OF REPETITIVE ELEMENTSDaniel Vitales

Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona)

Laboratori de Botànica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona

I Simposio Anual de Botánica Española:

Filogenómica para comprender la diversidad y evolución de grupos complejos de plantas

February 8th, 2020

REPETITIVE ELEMENTS: INTRODUCTION

TANDEM REPEATS DISPERSED REPEATS

TRANSPOSONS OTHER DISPERSED(e.g. tRNA-like,

retropseudogens)

DNATRANSPOSONS

RNATRANSPOSONS

LTR RETROTRANSPOSONS

(e.g. copia, gypsy)

NON-LTR RETROTRANSPOSONS

(e.g. LINEs, SINEs)

TANDEM REPEAT GENES

SATELLITES

• SATELLITES

• MINISATELLITES

• MICROSATELLITES

• RIBOSOMAL DNA

• OTHER MULTIPLE-COPY GENES(e.g. histones)

“REPEATOME”REPETITIVE FRACTION OF

THE GENOME

Genlisea aurea 63.6 Mbp SMALLEST PLANT GENOMEArabidopsis thaliana 125 Mbp 25%Sugar beet Beta vulgaris 758 Mbp 63% Broad bean Vicia faba 12000 Mbp 85% Rye Secale cereale 8800 Mbp 92% Onion Allium cepa 15100 Mbp 95%Paris japonica 149000 Mbp LARGEST PLANT GENOMEHuman Homo sapiens 3000 Mbp >50%

Species Genome size Repeat content

Liu et al. 2013. International journal of molecular sciences, 14(7), 13559-13576.

7th Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis in Plants. Ceske Budejovice. 22-24 May 2018.http://repeatexplorer.org/

Plant genome composition

Plant repeatome composition

REPETITIVE ELEMENTS: INTRODUCTION

• Limitations caused by short length of NGS sequences

• Repeat length > Read Length

• Copies of the repetitive elements accumulate mutations,

diverging along time

• (unless concerted evolution!)

Nieto Feliner & Rosselló. 2012. Plant genome diversity volume 1, 171-193.

Caveats of using repetitive elements for phylogenetic reconstruction

Repeats

Reads?

? ?

?

e.g. retrotransposon length: ~ 1000 - 20000bp

read length: 100~300nt

?

?

?

?

?

?

?

?

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REPETITIVE ELEMENTS: INTRODUCTION

Identification of sequences clusters

Reconstruction of repetitive elements

Shotgun genomic sequencing

Dispersed RE(eg. transposons)

Tandem Repeats(e.g. rDNA, satellites)

Reads

Each cluster is a set of reads that frequently overlap and that are part of the same family of repetitive elements.

Novák, P., Neumann, P., Pech, J., Steinhaisl, J., & Macas, J. (2013). RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitiveelements from next-generation sequence reads. Bioinformatics, 29(6), 792-793.

REPETITIVE ELEMENTS: CHARACTERIZATION

7th Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis in Plants. Ceske Budejovice. 22-24 May 2018.http://repeatexplorer.org/

REPETITIVE ELEMENTS: CHARACTERIZATION

7th Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis in Plants. Ceske Budejovice. 22-24 May 2018.http://repeatexplorer.org/

7th Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis in Plants. Ceske Budejovice. 22-24 May 2018.http://repeatexplorer.org/

Cluster annotation and quantification

REPETITIVE ELEMENTS: CHARACTERIZATION

7th Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis in Plants. Ceske Budejovice. 22-24 May 2018. http://repeatexplorer.org/

Proportion of reads

Novák et al. 2014. PloS one, 9(6).

Clu

ster

s

CL1CL2CL3CL4CL5CL6CL7CL8CL9CL10CL11CL12CL13CL14CL15CL16CL17

CL18CL19CL20CL21--

REPETITIVE ELEMENTS: CHARACTERIZATION

Dodsworth et al. 2015. Systematic biology, 64(1), 112-126.

REPETITIVE ELEMENTS: PHYLOGENOMIC METHODSPhylogenetic reconstruction based on comparative repeat abundances

Phylogenetic reconstruction based on comparative repeat abundances

Dodsworth et al. 2015. Systematicbiology, 64(1), 112-126.

Fritillaria

Asclepias

Orobanche Fabeae

Drosophila

REPETITIVE ELEMENTS: PHYLOGENOMIC METHODS

Similarity A-B [CL n] = Observed N edges A-B [CL n]

Expected N edges A-B [CL n]

=Observed N edges A-B [CL n]

(N reads A + N reads B) [CL n]

N reads total [cluster n]

Vitales, Garcia & Dodsworth. 2019. BioRxiv. doi: https://doi.org/10.1101/624064

REPETITIVE ELEMENTS: PHYLOGENOMIC METHODSPhylogenetic reconstruction based on repeat similarities

Vitales, Garcia & Dodsworth. 2019. BioRxiv. doi: https://doi.org/10.1101/624064

REPETITIVE ELEMENTS: PHYLOGENOMIC METHODSPhylogenetic reconstruction based on repeat similarities

Vitales, Garcia & Dodsworth. 2019. BioRxiv. doi: https://doi.org/10.1101/624064

REPETITIVE ELEMENTS: PHYLOGENOMIC METHODSPhylogenetic reconstruction based on repeat similarities

Straub et al. 2012. American Journal of Botany, 99(2), 349-364.

Asclepias Sonoran Desert Clade

Vitales, Garcia & Dodsworth. 2019. BioRxiv. doi: https://doi.org/10.1101/624064

REPETITIVE ELEMENTS: PHYLOGENOMIC METHODSPhylogenetic reconstruction based on repeat similarities

repeat abundances repeat similarities

Phylogenetic reconstruction based on repeat similaritiesGenome representation Repeat types

REPETITIVE ELEMENTS: PHYLOGENOMIC METHODS

Vitales, Garcia & Dodsworth. 2019. BioRxiv. doi: https://doi.org/10.1101/624064

Bello et al. 2012. Annals of Botany 112, 1597-1612.

GS (pg)

13.6

8.3

10.7

12.4

11.8

10.6

9.5

13.4

10.1

Rosato et al. 2018. Annals of Botany 122(3), 387-395.

SpeciesN pop

(N ind)ITR site N

Heliocauta atlantica 3 (10) 6-17

A. clavatus 14 (38) 0-14

A. homogamos 2 (8) 0

A. linearilobus 3 (5) 19

A. maroccanus 3 (9) 0

A. monanthos 3 (10) 0-4

A. radiatus 3 (8) 0

A. pyrethrum 2 (6) 26-45

A. valentinus 9 (31) 0-10

Interstitial telomeric-like repeats (ITR) variability

Rosato et al. 2017. PloS one, 12(10).

REPETITIVE ELEMENTS: ANACYCLUS STUDY CASE

Hypothesis: activation of the repeat

machinery drive homoploid changes in GS

Karyological 45S rDNA site phenotypes

Vitales et al. 2019. Annals of Botany (in press). doi: https://doi.org/10.1093/aob/mcz183

Conservation levels of highly abundant TEs are decoupled from the actual GS of the species

REPETITIVE ELEMENTS: ANACYCLUS STUDY CASE

Comparative repeat composition of Anacyclus species Sequence conservation by differential stringency mapping

Alternative hypothesis: recombination events between

homologous chromosomes derived from distinct genomes

(i.e. from homoploid hybridization) leading to

chromosome arm exchanges, which would result in

different genome sizes.

REPETITIVE ELEMENTS: ANACYCLUS STUDY CASE

Vitales et al. 2019. Annals of Botany (in press). Doi: https://doi.org/10.1093/aob/mcz183

• Shallow sequencing of gDNA (genome skimming) might result in a depth characterization of repetitive DNA.

• Genomic repeat abundances and repeat sequence similarities contain phylogenetic signals and can be used as a complementary markers to infer evolutionary histories.

• Combined application of phylogenetic approaches based on repeat abundances and repeat sequence similarities can be helpful to understand mechanisms governing genome and repeatome evolution.

• Further development of these methods should focus on automating the data processing and obtaining support values for phylogenetic trees and networks.

SUMMARY

Acknowledgements:

Institut Botànic de Barcelona, CSIC-ICUBSònia GarciaTeresa GarnatjeJaume PellicerJoan Pere Pascual

Real Jardín Botánico, CSICGonzalo Nieto-FelinerInés ÁlvarezJavier Fuertes

Universitat de BarcelonaJoan VallèsOriane Hidalgo

Institute of Biophysics, BrnoAleš Kovařík

Jardí Botànic de la Universitat de ValènciaMarcela RosatoJosep Antoni Rosselló

University of BedfordshireSteven Dodsworth