Using Transposable Elements as Tools to Better Understand Evolution at the Genomic Level

Transposable elements (TEs), also known as jumping genes, are DNA sequences capable of mobilizing and replicating within the genome. In mammals, it is not uncommon for 50% of the genome to be derived from TEs, yet they remain an underutilized tool for tracking evolutionary change. With the increasing number of publicly funded genome projects and affordable access to next-generation sequencing platforms, it is important to demonstrate the role TEs may play in helping us understand evolutionary patterns. The research presented herein utilizes TEs to investigate such patterns at the genomic, specific, and generic levels in three distinct ways. First at the genomic level, an analysis of the historical TE activity within the thirteen-lined ground squirrel (Spermophilus tridecemlineatus) shows that non-LTR retrotransposon activity has been declining for the past ~26 million years and appears to have ceased ~5 million years ago. Since most mammals, and all other rodents studied to date, have active TEs the extinction event in S. tridecemlineatus makes it a valuable model for understanding the factors driving TE activity and extinction. Second, we examined TEs as factors impacting genomic and species diversity. We found that DNA transposon insertions in Eptesicus fuscus, appear to have been exapted as miRNAs. When placed within a phylogenetic context a burst of transposon-driven, miRNA origination and the vespertilionid species radiation occurred simultaneously ~30 million years ago. This observation implies that lineage specific TEs could generate lineage specific regulatory pathways, and consequently lineage specific phenotypic differences. Finally, we utilized TEs to investigate their phylogenetic potential at the level of genus. In particular a method was developed that identified, over 670 thousand Ves SINE insertions in seven species of Myotis for use in future phylogenetic studies. Our method was able to accurately identify insertions in taxa for which no reference genome was available and was confirmed using traditional PCR and Sanger sequencing methods. By identifying polymorphic Ves insertions, it may be possible to resolve the phylogeny of one of the largest species radiations in mammals

Marsupials and monotremes sort genome treasures from junk

A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals (including humans) and more distant vertebrate species

Computational Analysis of Papionini Evolution Using Alu Insertions

Alu elements are primate specific retrotransposons that have remained active throughout the course of primate evolution. As a result of this sustained mobilization. Alu elements are present in greater copy number in primate genomes than any other transposable element. An average of over one million Alu elements has been identified in every sequenced haplorrhine genome to date. These characteristics qualify Alu elements as ideal characters for studying evolutionary relationship among primates. The increasing availability of whole genome sequencing data presents novel challenges and opportunities for comparative genomic analyses. Genomic data is now publicly available for most primate species. Such an abundance of resources allows researchers to re-examine previously unresolved or unexplored evolutionary relationships applying a comprehensive whole genome approach. The implications of such research models for studying human biology and evolution. Historically, the Old World monkey primate models has been a popular choice for investigating the human condition. More specifically, no catarrhine taxon has been exploited more extensively than those belonging to the Papionini tribe. This dissertation describes an innovation computational method suitable for examining complex phylogenetic relationships among primates. Furthermore, it utilizes a quickly expanding database of publicly available whole genome sequencing data to perform phylogenetic and population genetic analyses. Through an integrative approach, the reported algorithm can identify Alu insertions indicative of hybridization and admixture. In addition, this method can be used to construct fully resolved cladograms despite well-documented histories of admixture and hybridization

Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

<p>Abstract</p> <p>Background</p> <p>Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish.</p> <p>Results</p> <p>Ten BAC clones of a spiny pufferfish <it>Diodon holocanthus </it>were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the <it>D. holocanthus </it>genome were identified, and 77 distinct genes were predicted. In the sequenced <it>D. holocanthus </it>genome, 364 kb is homologous with 265 kb of the <it>Takifugu rubripes </it>genome, and 223 kb is homologous with 148 kb of the <it>Tetraodon nigroviridis </it>genome. The repetitive DNA accounts for 8% of the sequenced <it>D. holocanthus </it>genome, which is higher than that in the <it>T. rubripes </it>genome (6.89%) and that in the <it>Te. nigroviridis </it>genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced <it>D. holocanthus </it>genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in <it>D. holocanthus </it>genome increased to 10.6% compared with <it>T. rubripes </it>and increased to 9.19% compared with <it>Te. nigroviridis</it>. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in <it>D. holocanthus </it>genome is significantly longer than that in the smooth pufferfish genome (435 bp).</p> <p>Conclusion</p> <p>Compared with the smooth pufferfish, <it>D. holocanthus </it>has a low gene density and repeat elements rich genome. Genome size variation between <it>D. holocanthus </it>and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. The length difference of intron is consistent with the genome size variation between <it>D. holocanthus </it>and the smooth pufferfish. Different transposable element accumulation is responsible for genome size variation between <it>D. holocanthus </it>and the smooth pufferfish.</p

Genome Desertification in Eutherians: Can Gene Deserts Explain the Uneven Distribution of Genes in Placental Mammalian Genomes?

The evolution of genome size as well as structure and organization of genomes belongs among the key questions of genome biology. Here we show, based on a comparative analysis of 30 genomes, that there is generally a tight correlation between the number of genes per chromosome and the length of the respective chromosome in eukaryotic genomes. The surprising exceptions to this pattern are placental mammalian genomes. We identify the number and, more importantly, the uneven distribution of gene deserts among chromosomes, i.e., long (>500 kb) stretches of DNA that do not encode for genes, as the main contributing factor for the observed anomaly of eutherian genomes. Gene-rich placental mammalian chromosomes have smaller proportions of gene deserts and vice versa. We show that the uneven distribution of gene deserts is a derived character state of eutherians. The functional and evolutionary significance of this particular feature of eutherian genomes remains to be explained

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

<p>Abstract</p> <p>Background</p> <p>Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined.</p> <p>Results</p> <p>To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, <it>Macropus eugenii</it>, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements.</p> <p>Conclusion</p> <p>Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials and eutherians that may have predisposed these genomic regions to large-scale chromosomal instability.</p

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages

Jumping the fine line between species: horizontal transfer and evolution of repetitive elements in eukaryotic species

Transposable elements (TEs) are mobile DNA sequences, colloquially known as ‘jumping genes’ because of their ability to replicate to new genomic locations. Active TEs have the potential to transform genome structure by inserting into regulatory regions or accumulating within the genome. Mammals are particularly susceptible to TE expansion; TEs account for significant proportions of all eukaryotic genomes we see today. Horizontal transfer (HT) is the transmission of genetic material between non-mating species. HT is frequently observed in prokaryotes but rarely occurs in multicellular eukaryotes. As TEs are autonomous elements, they have the capability to move into another genome and immediately commence replicating, making them the perfect candidate for eukaryotic HT. Growing evidence indicates that this phenomenon is more widespread than current literature suggests, although questions still remain concerning the frequency of HT and whether all TEs are capable of moving between species. In this thesis, I describe large-scale phylogenomic analyses of eukaryotic species in order to identify and characterise TEs, particularly BovB and L1 (predominantly found in mammals). Past studies on this topic were limited by the scarce availability of genome sequences, which were mainly model organisms. I addressed this limitation by comprehensively screening more than 500 species, demonstrating the remarkable and overlooked diversity of L1s across the eukaryotic tree of life. The rapid explosion of L1s in mammals provides a striking contrast to the diverged L1 lineages found in other metazoans and plants. Even within individual genomes there are marked differences between ancient, degraded L1s and young, intact L1s that are potentially still active. L1s are only believed to vertically inherited; with my plethora of data, I challenged this perception by mining for L1 HT candidates. For comparison, I used BovB retrotransposons as an exemplar of obvious and rampant eukaryotic HT. I extended the current BovB paradigm to include more species, find new vectors of transfer, and refine the estimated times of insertion. Similarities between the distributions of L1 and BovB led me to postulate that the presence of L1s in therian mammals is due to an ancient HT event. Similar L1 HT events can be observed in plants. Given the extent of L1 colonisation in today’s mammals, the idea that L1s were initially introduced as foreign DNA has wide-reaching implications for our perception of genome evolution. Repetitive elements are often discarded from analyses because they are deemed ‘junk’ DNA. However, a genome’s junk is a bioinformatician’s treasure. Chapter 4 details a novel method for resolving species differences by using the repetitive intervals in a genome to identify binary variance (presence versus absence). We were able to infer the evolutionary relationships of 21 modern and ancient elephants and compare the results to an established phylogeny from single nucleotide polymorphisms (SNP). Repeats can thus be used as informative genetic markers, particularly useful for datasets with no known SNP variants. Altogether, this thesis presents in silico approaches for handling large and highly repetitive datasets. By characterising millions of repetitive elements from 503 eukaryotic species, we provide evidence of their impact and importance in eukaryotic evolution.Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Biological Sciences, 2017

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Background Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics.Results We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived similar to 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads.Conclusions We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes

Short interspersed nuclear element (SINE) sequences in the genome of the human pathogenic fungus Aspergillus fumigatus Af293.

Copyright: © 2016 The Authors. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Citation: Kanhayuwa L, Coutts RHA (2016) Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293. PLoS ONE 11(10): e0163215. https://doi.org/10.1371/journal.pone.0163215.Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4-14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140-493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3'-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50-65% and 60-75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259-343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.Peer reviewedFinal Published versio