Presentation for Botany 2015 in Edmonton, Alberta, Canada. Abstract here: http://www.botanyconference.org/engine/search/index.php?func=detail&aid=625

1. Transposable elements of
Agavoideae
Kate L Hertweck (@k8hert)
The University of Texas at Tyler
Alexandros Bousios
University of Sussex
Michael McKain
Donald Danforth Plant Science Center
en.wikipedia.org en.wikipedia.org

2. Why Agavoideae? (besides the obvious)
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Asparagaceae subfamily Agavoideae: 23 genera, 637 species
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agave, yucca, Joshua Tree
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Economically important:
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tequila, food starches
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biofuels
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ornamentals
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interesting morphological, ecological, life history traits
●
Recent diversification correlated with ecological traits
(Good-Avila, 2006)
gizmodo.com
Hertweck et al., TEs in Agavoideae
commons.wikimedia.org

3. Agavoideae genomics
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Emerging genomic/transcriptomic resources
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Polyploidy, bimodality (McKain et al., 2012)
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Variation in TEs (Bousios et al., 2007) and genome size (Zonneveld, 2003)
Darlington 1963
Hertweck et al., TEs in Agavoideae
Guadelupe et al., 2008

4. Transposable elements as a model system
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TEs, mobile genetic elements, or jumping genes
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Parasitic, self-replicating, move independently in the genome
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Many different types; some similar to or derived from viruses
Class I: Retrotransposons
(copy and paste)
LTR (Gypsy,
Copia/Sireviruses,
Caulimoviruses)
LINE
SINE
Class II: DNA transposons
(cut and paste)
TIR (EnSpm, hAT, MuDR,
TcMar, PIF)
MITE
Helitron
Hertweck et al., TEs in Agavoideae
●
TE proliferation is associated with modifications across the genome,
including changes to gene expression and genome size
●
TE composition/abundance may interact with organismal changes, like
hybridization, polyploidy, phenotype, life history

5. Mine existing genomic resources across Agavoideae to characterize
repetitive elements
Estimate abundance and diversity of transposable elements (TEs)
Cross validate results from different methods
The big questions:
Is transposon composition in Agavoideae genomes related to
hypothesized patterns of genomic evolution?
Do transposon proliferation and other genomic traits correlate with life
history traits in Agavoideae?
Hertweck et al., TEs in Agavoideae
Our goals

6. Aphyllanthes
Lomandra
Sansevieria
Asparagus
Ledebouria
Dichelostemma
Agapanthis
Allium
Haworthia
Hosta
Scadoxus
0%
10%
20%
30%
40%
50%
60%
70%
0
5000
10000
15000
20000
25000
Agavoideae includes substantial diversity
(even by Asparagales standards)
Unknown contigs
Known repeats
Genomesize(Mb/1C)
Percentageofsequence
readsfromnucleargenome
Hertweck, 2013, Genome
●
Genomes are difficult to assemble
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Genome size varies

7. Repeat characterization methods
Genome survey sequences
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most from MonAToL
project (Illumina SE, 30-
100 bp)
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quality control of fastq files
with PRINSEQ
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assembled with
MaSuRCA v2.3.2 or
RepARK v1.3.0
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organellar sequences
filtered with BLAST
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0.02-0.38x coverage
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12 taxa, only 8 with
sufficient contigs to analyze
Scripts available:
github.com/k8hertweck/REpipe
Hertweck et al., TEs in Agavoideae
Nuclear contigs
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assembled contigs are
consensus of most
abundant TEs in the
genome
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TEs must exist in high copy
to have sufficient reads for
detection (assembly)
●
the older a TE insertion,
the more likely it has
accumulated mutations
which will inhibit detection
●
data presented as
percentage of TE type in
nuclear genome (relative
abundance)
en.wikipedia.org

8. Repeat characterization methods
Genome survey sequences
Scripts available:
github.com/k8hertweck/REpipe
Hertweck et al., TEs in Agavoideae
Transcriptomes
●
various sources, tissues,
coverage, assembly
methods
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downloaded assemblies
(no other filtering)
Nuclear contigs
●
contigs represent actively
transcribed TEs, which
may or may not relate to
abundance in the genome
●
even relatively rare TEs
may be detectable
●
data presented as
percentage of transcripts
(relative expressed
diversity)
en.wikipedia.org

9. Repeat characterization methods
Genome survey sequences
Scripts available:
github.com/k8hertweck/REpipe
Hertweck et al., TEs in Agavoideae
TranscriptomesNuclear contigs
RepeatMasker
●
Liliopsida library (mostly
references from grasses)
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searches many types of
TEs, including parts
without genes
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some ambiguous results
(same contig, multiple
types of TE)
Domain searching
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rpstblastn against protein
domain models (CDD)
for TE-specific genes
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clustering with
CD-HIT-EST
Repeat contigs
Unknown contigs
read mapping
Wikimedia
Commons

10. Detectable repeats vary across species
Hertweck et al., TEs in Agavoideae
Repeat abundance
●
percentage of total reads
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repeat annotations from
RepeatMasker
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most reads map to unannotated
contigs (or remain unmapped)
Repeat diversity
●
percentage of nuclear contigs
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annotations from RepeatMasker
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most contigs are LTRs
●
transcriptomes represent broader
variation in diverse TEs (because
of the overall number of contigs)
GSS transcriptome

11. Sampled taxa possess same diversity of DNA TE families,
but at different abundance
Hertweck et al., TEs in Agavoideae
GSS data
●
percentage of nuclear genome
●
annotations from RepeatMasker
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most taxa have a single family
present in high abundance
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may reflect karyotype
Transcriptome data
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percentage of contigs
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annotations from RepeatMasker
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all families present (active?) in all
taxa
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minor variation in family-level
diversity for some taxa
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not incongruent with GSS data

12. Patterns of LTR abundance rely on annotation method
Hertweck et al., TEs in Agavoideae
●
Gypsy more abundant in
most genomes, although
proportions vary
●
no relationship with LTR
abundance and genome
size
●
including CDD annotations
can double LTR
abundance in some
genomes
●
Proportion of Copia:Gypsy
remains same for some
taxa (Schoenolirion), but
changes for others (Hosta)
●
LTR diversity (numbers of
contigs) shows similar
patterns
tetraploid,
largest (known) genome in dataset

13. Hertweck et al., TEs in Agavoideae
Conclusions
●
Mine existing genomic resources across Agavoideae to characterize
repetitive elements
●
Methods matter; bias is not evenly distributed and patterns difficult to
discern
●
Low proportion of GSS data assemble for Agavoideae
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large numbers of ancestral (inactive) insertions, related to whole
genome duplication event?
●
low-level diversity in abundant TEs just different enough from available
libraries to remain undetectable
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DNA transposon dominance may differ among clades
●
Gypsy more abundant in most genomes

14. Hertweck et al., TEs in Agavoideae
Future work
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Future work:
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Improve annotations (build custom repeat libraries) and analyze TE
subtaxonomy
●
improve quantification of repeats (P-clouds, RepeatExplorer)
●
validate results using multiple sequencing attempts/data types
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Big questions:
●
Is transposon composition in Agaviodeae genomes related to
hypothesized patterns of genomic evolution?
●
Do transposon proliferation and other genomic traits correlate with life
history traits in Agavoideae?

15. Acknowledgements
MonAToL
Texas Advanced Computing Center (TACC)
National Evolutionary Synthesis Center (NESCent, Duke U)
Research
https://sites.google.com/site/k8hertweck
Blog:
k8hert.blogspot.com
Twitter @k8hert
Google+ k8hertweck@gmail.com