No evidence that sex and transposable elements drive genome size variation in evening primroses

No evidence that sex and transposable elements drive genome size variation in evening primroses
J Arvid Agren, Stephan Greiner, Marc TJ Johnson, Stephen I Wright

Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sexual reproduction can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements. Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and transposable element content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry from 30 Oenothera species of varying reproductive system and find that variation in sexual/asexual reproduction cannot explain the almost two-fold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with transposable element abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and transposable element evolution in particular, it does not appear to have played a major role in the evening primroses.

Mitochondrial Genomes of Domestic Animals Need Scrutiny

Mitochondrial Genomes of Domestic Animals Need Scrutiny

Ni-Ni Shi, Long Fan, Yong-Gang Yao, Min-Sheng Peng, Ya-Ping Zhang
(Submitted on 16 Jul 2014)

More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (i.e. cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives. Nevertheless, few efforts have been performed to evaluate the sequence data quality, which heavily impact the original conclusion. Herein, we conducted a phylogenetic survey of these complete or near-complete mtDNA sequences based on mtDNA haplogroup trees for the eight animals. We show that, errors due to artificial recombination, surplus of mutations, and phantom mutations, do exist in 14.5% (194/1342) of mtDNA sequences and shall be treated with wide caution. We propose some caveats for mtDNA studies of domestic animals in the future.

Chromosomal distribution of cyto-nuclear genes in a dioecious plant with sex chromosomes

Chromosomal distribution of cyto-nuclear genes in a dioecious plant with sex chromosomes
Josh Hough, J Arvid Agren, Spencer CH Barrett, Stephen I Wright

The coordination between nuclear and organellar genes is essential to many aspects of eukaryotic life, including basic metabolism, energy production, and ultimately, organismal fitness. Whereas nuclear genes are bi-parentally inherited, mitochondrial and chloroplast genes are almost exclusively maternally inherited, and this asymmetry may lead to a bias in the chromosomal distribution of nuclear genes whose products act in the mitochondria or chloroplasts. In particular, because X-linked genes have a higher probability of co-transmission with organellar genes (2/3) compared to autosomal genes (1/2), selection for co-adaptation has been predicted to lead to an over-representation of nuclear-mitochondrial (N-mt) or nuclear-chloroplast (N-cp) genes on the X chromosome relative to autosomes. In contrast, the occurrence of sexually antagonistic organellar mutations might lead to selection for movement of cyto-nuclear genes from the X chromosome to autosomes to reduce male mutation load. Recent broad-scale comparative studies of N-mt distributions in animals have found evidence for these hypotheses in some species, but not others. Here, we use transcriptome sequences to conduct the first study of the chromosomal distribution of cyto-nuclear interacting genes in a plant species with sex chromosomes (Rumex hastatulus; Polygonaceae). We found no evidence of under- or over-representation of either N-mt or N-cp genes on the X chromosome, and thus no support for either the co-adaptation or the sexual-conflict hypothesis. We discuss how our results from a species with recently evolved sex chromosomes fit into an emerging picture of the evolutionary forces governing the chromosomal distribution of N-mt and N-cp genes.

Conservation and losses of avian non-coding RNA loci

Conservation and losses of avian non-coding RNA loci
Paul P. Gardner, Mario Fasold, Sarah W. Burge, Maria Ninova, Jana Hertel, Stephanie Kehr, Tammy E. Steeves, Sam Griffiths-Jones, Peter F. Stadler
Comments: 17 pages, 1 figure
Subjects: Genomics (q-bio.GN)

Here we present the results of a large-scale bioinformatic annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We show that a number of lncRNA-associated loci are conserved between birds and mammals, including several intriguing cases where the reported mammalian lncRNA function is not conserved in birds. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous “losses” of several RNA families, and attribute these to genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling Avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.

Hsp90 promotes kinase evolution

Hsp90 promotes kinase evolution

Jennifer Lachowiec, Tzitziki Lemus, Elhanan Borenstein, Christine Queitsch

Heat-shock protein 90 (Hsp90) promotes the maturation and stability of its client proteins, including many kinases. In doing so, Hsp90 may allow its clients to accumulate mutations as previously proposed by the capacitor hypothesis. If true, Hsp90 clients should show increased evolutionary rate compared to non-clients; however, other factors, such as gene expression and protein connectivity, may confound or obscure the chaperone?s putative contribution. Here, we compared the evolutionary rates of many Hsp90 clients and non-clients in the human protein kinase superfamily. We show that Hsp90 client status promotes evolutionary rate independently of, but in a similar magnitude to, gene expression and protein connectivity. Hsp90?s effect on kinase evolutionary rate was detected across mammals and increased with time of divergence. Hsp90 clients also showed increased nucleotide diversity and harbored more damaging variation than non-client kinases across humans. These results are consistent with the central argument of the capacitor hypothesis that interaction with the chaperone allows its clients to harbor genetic variation. Hsp90 client status is thought to be highly dynamic with as few as one amino acid change rendering a protein dependent on the chaperone. Contrary to this expectation, we found that across protein kinase phylogeny Hsp90 client status tends to be gained, maintained, and shared among closely related kinases. We also infer that the ancestral protein kinase was not an Hsp90 client. Taken together, our results suggest that Hsp90 played an important role in shaping the kinase superfamily.

Restriction and recruitment – gene duplication and the origin and evolution of snake venom toxins

Restriction and recruitment – gene duplication and the origin and evolution of snake venom toxins

Adam D Hargreaves, Martin T Swain, Matthew J Hegarty, Darren W Logan, John F Mulley

The genetic and genomic mechanisms underlying evolutionary innovations are of fundamental importance to our understanding of animal evolution. Snake venom represents one such innovation and has been hypothesised to have originated and diversified via a process that involves duplication of genes encoding body proteins and subsequent recruitment of the copy to the venom gland where natural selection can act to develop or increase toxicity. However, gene duplication is known to be a rare event in vertebrate genomes and the recruitment of duplicated genes to a novel expression domain (neofunctionalisation) is an even rarer process that requires the evolution of novel combinations of transcription factor binding sites in upstream regulatory regions. This hypothesis concerning the evolution of snake venom is therefore very unlikely. Nonetheless, it is often assumed to be established fact and this has hampered research into the true origins of snake venom toxins. We have generated transcriptomic data for a diversity of body tissues and salivary and venom glands from venomous and non-venomous reptiles, which has allowed us to critically evaluate this hypothesis. Our comparative transcriptomic analysis of venom and salivary glands and body tissues in five species of reptile reveals that snake venom does not evolve via the hypothesised process of duplication and recruitment of body proteins. Indeed, our results show that many proposed venom toxins are in fact expressed in a wide variety of body tissues, including the salivary gland of non-venomous reptiles and have therefore been restricted to the venom gland following duplication, not recruited. Thus snake venom evolves via the duplication and subfunctionalisation of genes encoding existing salivary proteins. These results highlight the danger of the “just-so story: in evolutionary biology, where an elegant and intuitive idea is repeated so often that it assumes the mantle of established fact, to the detriment of the field as a whole.

Complete plastid genome assembly of invasive plant, Centaurea diffusa

Complete plastid genome assembly of invasive plant, Centaurea diffusa

Kathryn G Turner, Christopher J Grassa

Invasive plants present both problems and possibilities for discovery, which may be addressed utilizing new genomic tools. Here we present the completed plastome assembly for the problematic invasive weed, Centaurea diffusa. This new tool represents a significant contribution to future studies of the ecological genomics of invasive plants, particularly this weedy genus, and studies of the Asteraceae in general.

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Brant C. Faircloth, Michael G. Branstetter, Noor D. White, Seán G. Brady
(Submitted on 2 Jun 2014)

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci collected across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g., exons). However, molecular techniques requiring RNA as a template are limited to using very high quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n=1510) of ultraconserved elements (UCE) shared among the insect order Hymenoptera. We use in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled Hymenoptera, and we design a set of baits for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We use our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 MYA) to very young (≥1 MYA) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support.

Author post: Tandem duplications and the limits of natural selection in Drosophila yakuba and Drosophila simulans

This guest post is by Rebekah Rogers (@evolscientist) on her paper with coauthors “Tandem duplications and the limits of natural selection in Drosophila yakuba and Drosophila simulans” arXived here.

Tandem duplications are widely recognized as a source of genetic novelty. Duplication of gene sequences can result in adaptive evolution through the development of novel functions or specialization in subsets of ancestral functions when ‘spare parts’ are relieved of evolutionary constraints. Additionally, tandem duplications have the potential to create entirely novel gene structures through chimeric gene formation and recruitment of formerly non-coding sequence. Here, we survey the limits of standing variation for tandem duplications in natural populations of D. yakuba and D. simulans, estimate the upper bound of mutation rates, and explore their role in rapid evolution.

Tandem duplicates on the X chromosome in D. simulans show an excess of high frequency variants consistent with adaptive evolution through tandem duplication. Furthermore, we identify an overrepresentation of genes involved in rapidly evolving phenotypes such as chorion development and oogenesis, drug and toxin metabolism, chitin cuticle formation, chemosensory processes, lipases and endopeptidases expressed in male reproduction, as well as immune response to pathogens in both D. yakuba and D. simulans. The enrichment of such rapidly evolving functional classes points to a role for tandem duplicates in Red Queen dynamics and responses to strong selective pressures.
In spite of the observed concordance across functional classes we observe few duplicated genes that are shared across species indicating that parallel recruitment of tandem duplications is rare. The span of duplicates in the population is quite limited, and we estimate that less than 15% of the genome is represented among the tandem duplications segregating in the entire population for the species. Moreover, many duplicates are present at low frequency and will have difficulty escaping the forces of drift during selective sweeps. This very limited standing variation combined with low mutation rates for tandem duplications results in severe limitations in the substrate of genetic novelty that is available for adaptation.

Thus, the limits of standing variation and the rate of new mutations are expected to play a vital role in defining evolutionary trajectories and the ability of organisms to adapt in the event of gross environmental change. Given the limited substrate of genetic novelty, we expect that if adaptation is dependent upon gene duplications, suboptimal outcomes in adaptive walks will be common, long wait times will occur for new phenotypic changes, and many multicellular eukaryotes will display limited ability to adapt to rapidly changing environments.

Diversity and evolution of centromere repeats in the maize genome

Diversity and evolution of centromere repeats in the maize genome

Paul Bilinski, Kevin Distor, Jose Gutierrez-Lopez, Gabriela Mendoza Mendoza, Jinghua Shi, R. Kelly Dawe, Jeffrey Ross-Ibarra

Centromere repeats are found in most eukaryotes and play a critical role in kinetochore formation. Though CentC repeats exhibit considerable diversity both within and among species, little is understood about the mechanisms that drive cen- tromere repeat evolution. Here, we use maize as a model to investigate how a complex history involving polyploidy, fractionation, and recent domestication has impacted the diversity of the maize CentC repeat. We first validate the existence of long tan- dem arrays of repeats in maize and other taxa in the genus Zea. Although we find considerable sequence diversity among CentC copies genome-wide, genetic similar- ity among repeats is highest within these arrays, suggesting that tandem duplica- tions are the primary mechanism for the generation of new copies. Genetic clustering analyses identify similar sequences among distant repeats, and simulations suggest that this pattern may be due to homoplasious mutation. Although the two ancestral subgenomes of maize have contributed nearly equal numbers of centromeres, our analysis shows that the vast majority of all CentC repeats derive from one of the parental genomes. Finally, by comparing maize with its wild progenitor teosinte, we find that the abundance of CentC has decreased through domestication while the peri- centromeric repeat Cent4 has drastically increased.