This document discusses the genomic effects of transposable elements (TEs). It begins with an overview of TEs and their impact on genomes. It then discusses three areas of research: 1) using TEs as a model system to study patterns of genome expansion and contraction, 2) examining the relationship between genomic changes driven by TEs and life history evolution in the plant order Asparagales, and 3) investigating the role of TEs in aging using experimental populations of fruit flies selected for long and short lifespans. The document outlines approaches, preliminary results, and conclusions from each area of research. It emphasizes that TEs contribute significantly to genome size and evolution, and that comparative genomic methods can provide insights into their relationships
BITS - Comparative genomics on the genome levelBITS
This is the third presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on the gene
Thanks to Klaas Vandepoele of the PSB department.
Detection of genomic homology in eukaryotic genomesKlaas Vandepoele
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.
Nucleic Acids Res. 2012 Jan;40(2):e11.
Comparative genomics is a powerful means to gain insight into the evolutionary processes that shape the genomes of related species. As the number of sequenced genomes increases, the development of software to perform accurate cross-species analyses becomes indispensable. However, many implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements, limiting the number of genomes that can be analyzed in one run. Here, we present a software package to unveil genomic homology based on the identification of conservation of gene content and gene order (collinearity), i-ADHoRe 3.0, and its application to eukaryotic genomes. The use of efficient algorithms and support for parallel computing enable the analysis of large-scale data sets. Unlike other tools, i-ADHoRe can process the Ensembl data set, containing 49 species, in 1 h. Furthermore, the profile search is more sensitive to detect degenerate genomic homology than chaining pairwise collinearity information based on transitive homology. From ultra-conserved collinear regions between mammals and birds, by integrating coexpression information and protein-protein interactions, we identified more than 400 regions in the human genome showing significant functional coherence. The different algorithmical improvements ensure that i-ADHoRe 3.0 will remain a powerful tool to study genome evolution.
BITS - Comparative genomics on the genome levelBITS
This is the third presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on the gene
Thanks to Klaas Vandepoele of the PSB department.
Detection of genomic homology in eukaryotic genomesKlaas Vandepoele
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.
Nucleic Acids Res. 2012 Jan;40(2):e11.
Comparative genomics is a powerful means to gain insight into the evolutionary processes that shape the genomes of related species. As the number of sequenced genomes increases, the development of software to perform accurate cross-species analyses becomes indispensable. However, many implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements, limiting the number of genomes that can be analyzed in one run. Here, we present a software package to unveil genomic homology based on the identification of conservation of gene content and gene order (collinearity), i-ADHoRe 3.0, and its application to eukaryotic genomes. The use of efficient algorithms and support for parallel computing enable the analysis of large-scale data sets. Unlike other tools, i-ADHoRe can process the Ensembl data set, containing 49 species, in 1 h. Furthermore, the profile search is more sensitive to detect degenerate genomic homology than chaining pairwise collinearity information based on transitive homology. From ultra-conserved collinear regions between mammals and birds, by integrating coexpression information and protein-protein interactions, we identified more than 400 regions in the human genome showing significant functional coherence. The different algorithmical improvements ensure that i-ADHoRe 3.0 will remain a powerful tool to study genome evolution.
Dissecting plant genomes with the PLAZA 2.5 comparative genomics platformKlaas Vandepoele
Dissecting plant genomes with the PLAZA comparative genomics platform.
Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K.
Plant Physiol. 2012 Feb;158(2):590-600.
With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.
A cloning vector is a genome that can accept the target DNA and increase the number of copies through its own autonomous replication.
An adapter or adaptor, or a linker in genetic engineering is a short, chemically synthesized, single-stranded or double-stranded oligonucleotide that can be ligated to the ends of other DNA or RNA molecules. It may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid much more efficiently.
A retrospective look at the state of many famous modern genome sequences, and a cautionary tale of the dangers in assuming that genome sequence and/or its annotations are finished.
It is a circular DNA molecule 4.6 million base pairs in length, containing 4288 annotated protein-coding genes (organized into 2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) genes.
Whole genome sequencing of arabidopsis thalianaBhavya Sree
arabidopsis is the representative of plant kingdom or the 'model plant'.it is the first plant genome sequenced. the sequences lead to the overall understanding of the plant kingdom, better understanding of various genes,the important metabolic pathways, evolution etc
DNA-based methods for bioaerosol analysisjordanpeccia
Information for producing phylogenetic/taxonomic libraries of airborne bacteria and fungi. Includes fundamental background information, approaches for sequencing and data analysis, two case studies, and a review of sampling methods
Dissecting plant genomes with the PLAZA 2.5 comparative genomics platformKlaas Vandepoele
Dissecting plant genomes with the PLAZA comparative genomics platform.
Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K.
Plant Physiol. 2012 Feb;158(2):590-600.
With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.
A cloning vector is a genome that can accept the target DNA and increase the number of copies through its own autonomous replication.
An adapter or adaptor, or a linker in genetic engineering is a short, chemically synthesized, single-stranded or double-stranded oligonucleotide that can be ligated to the ends of other DNA or RNA molecules. It may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid much more efficiently.
A retrospective look at the state of many famous modern genome sequences, and a cautionary tale of the dangers in assuming that genome sequence and/or its annotations are finished.
It is a circular DNA molecule 4.6 million base pairs in length, containing 4288 annotated protein-coding genes (organized into 2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) genes.
Whole genome sequencing of arabidopsis thalianaBhavya Sree
arabidopsis is the representative of plant kingdom or the 'model plant'.it is the first plant genome sequenced. the sequences lead to the overall understanding of the plant kingdom, better understanding of various genes,the important metabolic pathways, evolution etc
DNA-based methods for bioaerosol analysisjordanpeccia
Information for producing phylogenetic/taxonomic libraries of airborne bacteria and fungi. Includes fundamental background information, approaches for sequencing and data analysis, two case studies, and a review of sampling methods
Developing an undergraduate bioinformatics courseKate Hertweck
Poster presentation at UT Tyler Teaching Symposium in spring 2015. Describes course objectives, curriculum, and implementation of a newly developed undergraduate bioinformatics course.
"Estimation of Divergence Times in Asparagales in the Presence of Hybridization," presented in symposium "Insights and Benefits from Monocot Palaeobiology: Fossils, DNA, and Phylogenies" at Monocots V (5th International Conference on Comparative Biology of Monocotyledons, The New York Botanical Garden, July 2013).
lightning talk for iEvoBio2013, June 25, 2013, delivered by Arlin Stoltzfus on behalf of HIP and the hackathon participants. Phylotastic is a distributed delivery system for expert knowledge of species phylogeny (the tree of life).
Presented at Evolution 2014 in Raleigh, NC (http://evolution2014.org)
Jumping genes and life history: De novo transposable element insertions respond to selection for accelerated and delayed development times
Kate L Hertweck, NESCent, k8hertweck@gmail.com
Mira Han, UNLV, mira.han@unlv.edu
Lee F Greer, University of California, Irvine, lgreer@uci.edu
Mark A Phillips, UC Irvine, mphillips6789@gmail.com
Michael R Rose, University of California, Irvine, mrrose@uci.edu
Joseph L Graves, JSNN, North Carolina A&T State University, gravesjl@ncat.edu
A wealth of scientific literature has speculated on the response of both the genome and organism to proliferation of transposable elements (TEs, or jumping genes). In particular, the relationship between TEs and aging has been addressed by both theory and empirical studies. Theory suggests TEs may contribute to life history features such as aging, by introducing detrimental somatic mutation. However, a comparison TEs between organisms indicate the number of copies may increase, decrease, or have no effect on lifespan, depending on the model system and type of TE investigated. Long-term studies in experimental evolution allow explicit testing of such hypothesis using replicated populations. Our data represent pooled population genome-wide resequencing from Drosophila selected for both delayed and accelerated reproduction times and development. Our previous results indicate that insertion frequencies of ancestral TEs (i.e., annotated in the fully sequenced reference genome) respond fairly consistently to selection. For the present study, we use two independent approaches (PoPoolation TE and RelocaTE) to identify de novo TE insertions. We find that the magnitude of TE proliferation varies among multiple families of LTRs, LINEs, and DNA transposons. We present methodological considerations for interpreting such results.
Bayesian Divergence Time Estimation – Workshop LectureTracy Heath
**These lecture slides are no longer being updated. For the most current version please go to: https://figshare.com/articles/Bayesian_Divergence-Time_Estimation_Lecture/6849005
A lecture on Bayesian divergence-time estimation by Tracy A. Heath (http://phyloworks.org/).
Digital Experimental Phylogenetics - Evolution2014Cory Kohn
This talk introduces the use of experimental phylogenetics via digital evolution as being a complementary tool to other methods that investigate phylogenetic accuracy.
Unlike the experimental generation of evolutionary histories using biological organisms, digital evolution is immensely more feasible, allows a large range of experimental treatment investigation, and maintains a perfect record of all information regarding the evolutionary history. Such information includes all genomic sequences at each generation, which allows for an empirical model of substitution, a detailed characterization of homoplasious characters, etc.
Unlike computational simulation, digital evolution maintains a greater degree of biological realism. There are many elements important to the evolving system that are not set a priori by the investigator. For example, since Avida exhibits natural selection inherently (rather than being simulated) there is a distribution of mutational effects and very complex epistatic interactions that change dynamically along with the evolving system. In addition, population processes such as genetic drift, hitchhiking, etc are all innate components.
The results presented here are a mere scratch on the surface of possibilities. The application of digital experimental evolution to phylogenetic methodological design and evaluation has the potential to be substantial.
For questions, ideas, collaborations, etc please email kohncory@msu.edu
Apollo - A webinar for the Phascolarctos cinereus research communityMonica Munoz-Torres
Web Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Web Apollo. It is addressed to the members of the Phascolarctos cinereus research community.
This is the first presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on different levels.
Thanks to Klaas Vandepoele of the PSB department.
Slides from a Comparative Genomics and Visualisation course (part 1) presented at the University of Dundee, 7th March 2014. Other materials are available at GitHub (https://github.com/widdowquinn/Teaching)
This is an introduction to conducting manual annotation efforts using Apollo. This webinar was offered to members of the i5K Research community on 2015-10-07.
Genome to pangenome : A doorway into crops genome explorationKiranKm11
This seminar underpins the significance and need of formulating pan-genome oriented crop improvement strategies over single reference genome based studies. Pangenome graphs uncovers large repository of genetic variation which could we useful for planning and executing strategic crop improvement programmed
'Genomics' is nothing but the study of entire genetic compliment of an organism. Plant genomics is study of plant genome. This is my topic of M.Sc. course 'Plant biotechnology'.
2. But first...a teaching interlude
●
Teaching half time for Duke Bio 202 (genetics and
evolution)
●
Responsible for one lab section, lab development,
and lecturing
●
Interesting integration of Duke course with Coursera
next semester
3. Overview
1. Transposable elements as a model system
2. Genomic contributions to life history evolution in
Asparagales
3. TEs and aging in Drosophila
4. What is in a genome?
●
The first step in analyzing genomes is usually to mask or filter repetitive
sequences, which often comprise a large portion of the nuclear genome
●
Repetitive sequences include satellites, telomeres, and other “junk” DNA
elements
●
“Selfish” DNA (or mobile genetic elements) is a category of repetitive
sequences representing transposable elements (parasitic self-replicating
derived from viruses)
●
Growing evidence (including ENCODE) supports that “junk” DNA
contains essential function and provides material for evolutionary
innovation
Class I: Retrotransposons Class II: DNA transposons
LTR TIR
LINE Crypton
SINE Helitron
ERV Maverick
SVA
www.virtualsciencefair.org
TEs Asparagales Drosophila
5. TEs directly affect organisms as they move throughout a genome
●
TEs interact with genes
●
TE insertion within a gene disrupts function
●
Exaptation of TEs into genes: Alu elements contributed to
evolution of three color vision (Dulai, 1999)
●
Gene expression and regulatory changes
●
TEs affect molecular evolution
●
Indels
●
increased recombination (chromosomal restructuring)
●
Links between TEs and adaptation/speciation
TEs
Kate Hertweck, Genomic effects of repetitive DNA DNA
NESCent, Genomic effects of junk
Asparagales Drosophila
6. TEs indirectly affect organisms through changes in genome size
Changes in overall genome size
Physical-mechanical effects of nuclear size and mass
Many historical hypotheses about relationships between genome size
and life history (complexity, mean generation time, ecology, growth
form)
TEs Asparagales Drosophila
7. Research questions and goals
●
What are patterns of genome expansion and contraction
throughout the evolutionary history of organisms?
●
Patterns in genome size change
●
Proliferation of TEs within lineages
Evolutionnews.org
TEs Asparagales Drosophila
8. Research questions and goals
●
What are patterns of genome expansion and contraction
throughout the evolutionary history of organisms?
●
Patterns in genome size change
●
Proliferation of TEs within lineages
●
Do genomic patterns correlate with changes in
life history?
●
Improving methods for comparative genomics
across broad taxonomic levels
●
Application of phylogenetic comparative
methods to genomic data
Evolutionnews.org
TEs Asparagales Drosophila
9. Overview
1. Transposable elements as a model system
2. Genomic contributions to life history evolution in
Asparagales
3. TEs and aging in Drosophila
Collaborators:
J. Chris Pires and lab (U of Missouri)
Patrick Edger
Dustin Mayfield
10. Genomic evolution in Asparagales
●
Many edible species (onion, asparagus, agave) and ornamentals
(orchid, amaryllis, yucca)
●
Lots of variation in life history traits: physiology, growth habit,
habitat
●
Interesting patterns of genomic evolution
●
Wide variation genome size
●
Bimodal karyotypes
●
Despite possessing some of the largest angiosperm genomes, we
know little about the TEs in Asparagales
●
Possibility to test hypotheses of correlations between genomic
changes and life history traits
ag.arizona.edu Naturehills.com
TEs Asparagales Drosophila
15. Our data
●
Illumina (80-120 bp single end), 6 taxa per lane
●
GSS (Genome Survey Sequences): total genomic DNA!
●
Data originally collected for systematics
●
Assembled plastomes, mtDNA genes, and nrDNA genes from less than 10% of
data (Steele et al 2012)
●
Poaceae (family of grasses, model system)
●
Medium-sized genomes
●
Well-annotated library of repeats
●
Asparagales (order of petaloid monocots, non-model system)
●
Very large genomes
●
Discovery of novel repeats
TEs Asparagales Drosophila
16. Our data
●
Illumina (80-120 bp single end), 6 taxa per lane
●
GSS (Genome Survey Sequences): total genomic DNA!
●
Data originally collected for systematics
●
Assembled plastomes, mtDNA genes, and nrDNA genes from less than 10% of
data (Steele et al 2012)
●
Poaceae (family of grasses, model system)
●
Medium-sized genomes
●
Well-annotated library of repeats
●
Asparagales (order of petaloid monocots, non-model system)
●
Very large genomes
●
Discovery of novel repeats
●
Is there a way to characterize repeats when the genome
is a big black box?
TEs Asparagales Drosophila
17. Bioinformatics approach
●
Sequence assembly:
●
Ab initio repeat construction: use raw sequence reads to build
pseudomolecules or ancestral sequences
●
De novo sequence assembly: standard genome assembly
methods, screen resulting contigs
TEs Asparagales Drosophila
18. Bioinformatics approach
●
Sequence assembly:
●
Ab initio repeat construction: use raw sequence reads to build
pseudomolecules or ancestral sequences
●
De novo sequence assembly: standard genome assembly
methods, screen resulting contigs
●
Annotation method:
Motif searching
●
Reference library
TEs Asparagales Drosophila
19. Bioinformatics approach
●
Sequence assembly:
●
Ab initio repeat construction: use raw sequence reads to build
pseudomolecules or ancestral sequences
●
De novo sequence assembly: standard genome assembly
methods, screen resulting contigs
●
Annotation method:
Motif searching
●
Reference library
Sidenote: improving the ontology for transposable elements
(classification and annotation)
Sequence Ontology (SO)
Comparative Data Analysis Ontology (CDAO)
TEs Asparagales Drosophila
20. Pipeline
Scripts available on GitHub: Raw fastq files
AsparagalesTEscripts
De novo genome assembly (MSR-CA)
Filter out scaffolds that BLAST to reference organellar genomes
Run RepeatMasker to identify similarity to known repeats
(3110 repeats, 98.7% are from grasses )
Discard unknown scaffolds and “unimportant” repeats, categorize others by type
Map raw reads back to scaffolds to estimate relative proportion of TE
TEs Asparagales Drosophila
21. Pipeline
Scripts available on GitHub: Raw fastq files
AsparagalesTEscripts
De novo genome assembly (MSR-CA)
Filter out scaffolds that BLAST to reference organellar genomes
Run RepeatMasker to identify similarity to known repeats
(3110 repeats, 98.7% are from grasses )
Discard unknown scaffolds and “unimportant” repeats, categorize others by type
Map raw reads back to scaffolds to estimate relative proportion of TE
TEs Asparagales Drosophila
22. Quality control: Poaceae
●
Largest scaffolds with deepest coverage are from the chloroplast and
mitochondrial genomes, but are easily identified for exclusion
●
All relevant classes of repeats are present in scaffolds from a single genome
●
Even long repeats can be reconstructed into a single scaffold
●
Characterization of repeats is not dependent on sequence coverage
●
Estimates of quantity repeats are not very accurate-- but there is little
consensus of TE quantification in published literature!
●
Decision: use a dataset constructed from similar data and analyzed in the
same pipeline so any error is systematic and shared among all taxa
●
How well do these methods work for non-model systems?
TEs Asparagales Drosophila
23. Example: LTR from Hosta
●
Reads map across scaffold: assembly is reliable
●
Some divergence in reads: measure of diversity?
TEs Asparagales Drosophila
24. REs in Core Asparagales
TEs Asparagales Drosophila
30. Developing genomic traits for comparative biology
●
Genomic traits can be treated just like any other phenotype
• Number of gene copies of a single family
• Genome size, intron size, GC content, number of chromosomes,
polyploidy, karyotype (sex chromosomes)
• Sometimes genomic traits evolve in such a way that models need to
be altered to accommodate their variation
●
We finally have enough information to be able to apply these methods
across robust phylogenies of organisms!
●
What about transposable elements?
TEs Asparagales Drosophila
31. So what?
●
You can peek into the black box of large plant genomes with even very
limited genomic sequence data
●
There is a great deal of variation in TE compliments among closely
related plant species
●
These methods can easily be applied to extant datasets to summarize
TEs
TEs Asparagales Drosophila
32. So what?
●
Data available for most plants are low coverage, with little known about
the TEs present and their direct effects on the genome and organism
●
Plant genomes tolerate more plasticity than animal genomes
• Polyploidy, chromosomal restructuring more common in plants
• Repetitive compliment comprises a higher proportion of plant
genomes
• Differences in gene silencing
●
Pretty plants are great, but what if we want a more applied approach?
TEs Asparagales Drosophila
33. Overview
1. Transposable elements as a model system
2. Genomic contributions to life history evolution in
Asparagales
3. TEs and aging in Drosophila
Collaborators:
Joseph Graves (UNCG, NC A&T)
Michael Rose (UC Irvine)
Mira Han (NESCent)
34. Genomics of aging
●
Aging as “detuning” of adaptation
●
Age-related genes and expression patterns
●
Does the movement of TEs throughout a genome correspond to how
long an organism lives?
●
Previously discussed life history traits only involve TE proliferation in
gametic tissue
●
Questions about aging involve changes in organisms throughout
lifespan, especially if results can be transferred to human research
TEs Asparagales Drosophila
35. Experimental data
●
Replicate populations of fruit flies selected for both short and long life
spans (Burke et al 2010)
●
Next-gen sequencing of pooled populations
●
SNP analysis indicates allele frequency changes at many loci, but
little evidence for selective sweeps
●
Extensive gene expression change
TEs Asparagales Drosophila
36. Experimental approach
●
Does the frequency of a TE differ between control and treatment
populations?
●
Are there patterns consistent with type of TE
●
T-lex: perl script for identifying presence and absence of annotated
transposable elements
●
2947 transposable elements from publicly available genome
sequence
Scripts available on GitHub: FB
flyTEscripts MITE
LINE
LTR
TIR
TEs Asparagales Drosophila
37. Preliminary results
●
Controls and populations selected for shorter lifespan
●
All population pairs are statistically the same (Kruskal-Wallis,
p=0.9414)
700
600
500
number of TEs
400 NA
0
300 100
final
200
100
0
1 2 3 4 5
population
TEs Asparagales Drosophila
38. Preliminary results
●
Controls and populations selected for shorter lifespan
●
153 TEs vary in one or more population
●
70 TEs vary in all five populations
●
some TE frequencies move to fixation
TEs Asparagales Drosophila
39. Finishing the job...
●
What are patterns from other population pairs (selection for longer
lifespan)?
●
Formal statistical testing for variation
●
Where are TEs of interest located in the genome? What genes are
located nearby?
●
T-lex de novo: searching for unannotated insertions
– Are there unique TE insertions related to longer life spans?
TEs Asparagales Drosophila
40. Conclusions
●
What are general patterns of TE evolution?
●
Different TEs contribute to genome size obesity.
●
We still need better methods to compare genomes.
●
Are there common patterns between TEs and life history trait evolution?
●
Yes, very specific insertions, at least in Drosophila.
●
How can comparative methods be appropriated for genomic
characeristics?
●
Does TE proliferation contribute to diversification or shifts in rates of
molecular evolution?
●
We are getting closer to possessing enough data to answer these
questions.
TEs Asparagales Drosophila
41. Conclusions
●
There are many interesting questions to be investigated using other
folks' genomic trash!
●
A little sequencing data can tell you a lot about a genome.
●
Many markers for systematic purposes
●
You can characterize major groups of repeats even in the absence
of a robust reference library for the species.
●
Informatics tools and resources abound!
TEs Asparagales Drosophila
42. Acknowledgements
NESCent (National Evolutionary Synthesis Center)
Allen Roderigo
Karen Cranston (and bioinformatics group!)
www.nescent.org
k8hert.blogspot.com
Find me:
Twitter @k8hert
Google+ k8hertweck@gmail.com
Kate Hertweck, TE ontology effects of junk DNA
Evolutionary