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Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster
Chimeric genes form through the combination of portions of existing coding sequences to create a new open reading frame. These new genes can create novel protein structures that are likely to serve as a strong source of novelty upon which selection can act. We have identified 14 chimeric genes that formed through DNA-level mutations in Drosophila melanogaster, and we investigate expression profiles, domain structures, and population genetics for each of these genes to examine their potential to effect adaptive evolution. We find that chimeric gene formation commonly produces mid-domain breaks and unites portions of wholly unrelated peptides, creating novel protein structures that are entirely distinct from other constructs in the genome. These new genes are often involved in selective sweeps. We further find a disparity between chimeric genes that have recently formed and swept to fixation versus chimeric genes that have been preserved over long periods of time, suggesting that preservation and adaptation are distinct processes. Finally, we demonstrate that chimeric gene formation can produce qualitative expression changes that are difficult to mimic through duplicate gene formation, and that extremely young chimeric genes (d S < 0.03) are more likely to be associated with selective sweeps than duplicate genes of the same age. Hence, chimeric genes can serve as an exceptional source of genetic novelty that can have a profound influence on adaptive evolution in D. melanogaster.Organismic and Evolutionary Biolog
Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster group
Here, we provide revised gene models for D. ananassae, D. yakuba, and D.
simulans, which include UTRs and empirically verified intron-exon boundaries,
as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast
comparison. Using these revised annotations, we perform differential expression
testing using the cufflinks suite to provide a broad overview of differential
expression between reproductive tissues and the carcass. We identify thousands
of genes that are differentially expressed across tissues in D. yakuba and D.
simulans, with roughly 60% agreement in expression patterns of orthologs in D.
yakuba and D. simulans. We identify several cases of putative polycistronic
transcripts, pointing to a combination of transcriptional read-through in the
genome as well as putative gene fusion and fission events across taxa. We
furthermore identify hundreds of lineage specific genes in each species with no
blast hits among transcripts of any other Drosophila species, which are
candidates for neofunctionalized proteins and a potential source of genetic
novelty.Comment: Revised manuscript, also available online preprint at G3: Genes,
Genomes, Genetics. Gene models, ortholog calls, and tissue specific
expression results are available at http://github.com/ThorntonLab/GFF or the
UCSC browser on the Thornton Lab public track hub at http://genome.ucsc.ed
Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater Bivalve \u3ci\u3eMegalonaias nervosa\u3c/i\u3e
Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, harvesting, and changes in fish–host prevalence. Currently, over 70% of species in North America are threatened, endangered or extinct. To characterize the genetic response to recent selective pressures, we collected population genetic data for one successful bivalve species, Megalonaias nervosa. We identify megabase-sized regions that are nearly monomorphic across the population, signals of strong, recent selection reshaping diversity across 73 Mb total. These signatures of selection are greater than is commonly seen in population genetic models. We observe 102 duplicate genes with high dN/dS on terminal branches among regions with sweeps, suggesting that gene duplication is a causative mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect functional classes important for Unionid survival, including anticoagulation genes important for fish host parasitization, detox genes, mitochondria management, and shell formation. We identify sweeps in regions with no known functional impacts, suggesting mechanisms of adaptation that deserve greater attention in future work on species survival. In contrast, polymorphic transposable elements (TEs) appear to be detrimental and underrepresented among regions with sweeps. TE site frequency spectra are skewed toward singleton variants, and TEs among regions with sweeps are present at low frequency. Our work suggests that duplicate genes are an essential source of genetic novelty that has helped this species succeed in environments where others have struggled. These results suggest that gene duplications deserve greater attention in non-model population genomics, especially in species that have recently faced sudden environmental challenges
Strong, recent selective sweeps reshape genetic diversity in freshwater bivalve Megalonaias nervosa
Freshwater Unionid bivalves have recently faced ecological upheaval through
pollution, barriers to dispersal, human harvesting, and changes in fish-host
prevalence. Currently, over 70% of species are threatened, endangered or
extinct. To characterize the genetic response to these recent selective
pressures, we collected population genetic data for one successful bivalve
species, Megalonaias nervosa. We identify megabase sized regions that are
nearly monomorphic across the population, a signal of strong, recent selection
reshaping genetic diversity. These signatures of selection encompass a total of
73Mb, greater response to selection than is commonly seen in population genetic
models. We observe 102 duplicate genes with high dN/dS on terminal branches
among regions with sweeps, suggesting that gene duplication is a causative
mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect
functional classes known to be important for Unionid survival, including
anticoagulation genes important for fish host parasitization, detox genes,
mitochondria management, and shell formation. We identify selective sweeps in
regions with no known functional impacts, suggesting mechanisms of adaptation
that deserve greater attention in future work on species survival. In contrast,
polymorphic transposable element insertions appear to be detrimental and
underrepresented among regions with sweeps. TE site frequency spectra are
skewed toward singleton variants, and TEs among regions with sweeps are present
only at low frequency. Our work suggests that duplicate genes are an essential
source of genetic novelty that has helped this successful species succeed in
environments where others have struggled. These results suggest that gene
duplications deserve greater attention in non-model population genomics,
especially in species that have recently faced sudden environmental challenges.Comment: 6 figures, 4 supplementary tables, 31 pages tota
Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans
We have used whole genome paired-end Illumina sequence data to identify
tandem duplications in 20 isofemale lines of D. yakuba, and 20 isofemale lines
of D. simulans and performed genome wide validation with PacBio long molecule
sequencing. We identify 1,415 tandem duplications that are segregating in D.
yakuba as well as 975 duplications in D. simulans, indicating greater variation
in D. yakuba. Additionally, we observe high rates of secondary deletions at
duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites
in D. yakuba modified with deletions. These secondary deletions are consistent
with the action of the large loop mismatch repair system acting to remove
polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in
duplicated alleles and a richer substrate of genetic novelty than has been
previously reported. Most duplications are present in only single strains,
suggesting deleterious impacts are common. D. simulans shows larger numbers of
whole gene duplications in comparison to larger proportions of gene fragments
in D. yakuba. D. simulans displays an excess of high frequency variants on the
X chromosome, consistent with adaptive evolution through duplications on the D.
simulans X or demographic forces driving duplicates to high frequency. We
identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans,
as well as 143 cases of recruited non-coding sequence in D. yakuba and 96 in D.
simulans, in agreement with rates of chimeric gene origination in D.
melanogaster. Together, these results suggest that tandem duplications often
result in complex variation beyond whole gene duplications that offers a rich
substrate of standing variation that is likely to contribute both to
detrimental phenotypes and disease, as well as to adaptive evolutionary change.Comment: Revised Version- Accepted at Molecular Biology and Evolutio
Transcriptome Complexities Across Eukaryotes
Genomic complexity is a growing field of evolution, with case studies for
comparative evolutionary analyses in model and emerging non-model systems.
Understanding complexity and the functional components of the genome is an
untapped wealth of knowledge ripe for exploration. With the "remarkable lack of
correspondence" between genome size and complexity, there needs to be a way to
quantify complexity across organisms. In this study we use a set of complexity
metrics that allow for evaluation of changes in complexity using TranD. We
ascertain if complexity is increasing or decreasing across transcriptomes and
at what structural level, as complexity is varied. We define three metrics --
TpG, EpT, and EpG in this study to quantify the complexity of the transcriptome
that encapsulate the dynamics of alternative splicing. Here we compare
complexity metrics across 1) whole genome annotations, 2) a filtered subset of
orthologs, and 3) novel genes to elucidate the impacts of ortholog and novel
genes in transcriptome analysis. We also derive a metric from Hong et al.,
2006, Effective Exon Number (EEN), to compare the distribution of exon sizes
within transcripts against random expectations of uniform exon placement. EEN
accounts for differences in exon size, which is important because novel genes
differences in complexity for orthologs and whole transcriptome analyses are
biased towards low complexity genes with few exons and few alternative
transcripts. With our metric analyses, we are able to implement changes in
complexity across diverse lineages with greater precision and accuracy than
previous cross-species comparisons under ortholog conditioning. These analyses
represent a step forward toward whole transcriptome analysis in the emerging
field of non-model evolutionary genomics, with key insights for evolutionary
inference of complexity changes on deep timescales across the tree of life. We
suggest a means to quantify biases generated in ortholog calling and correct
complexity analysis for lineage-specific effects. With these metrics, we
directly assay the quantitative properties of newly formed lineage-specific
genes as they lower complexity in transcriptomes.Comment: 33 pages main text; 6 main figures; 25 pages of supplement; 1
supplementary table; 24 Supp Figures; 58 pages tota
Gene content and distribution in the nuclear genome of Fragaria vesca
Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.EEA BalcarceFil: Pontaroli, Ana Clara. Instituto Nacional de TecnologÃa Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. University of Georgia. Department of Genetics; Estados UnidosFil: Rogers, Rebekah L. Harvard University. Department of Organismic and Evolutionary Biology; Estados Unidos. University of Georgia. Department of Genetics; Estados UnidosFil: Qian, Zhang. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Shields, Melanie E. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Davis, Thomas M. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Folta, Kevin M. University of Florida. Horticultural Sciences Department; Estados UnidosFil: SanMiguel, Phillip. Purdue University. Department of Horticulture and Landscape Architecture; Estados UnidosFil: Bennetzen, Jeffrey L. University of Georgia. Department of Genetics; Estados Unido
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