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Evolutionary Biology
Maternal mRNA input of growth and stress-response-related genes in cichlids in relation to egg size and trophic specialization.
Dec 06, 2018   EvoDevo
Ahi EP, Singh P, Lecaudey LA, Gessl W, Sturmbauer C
Maternal mRNA input of growth and stress-response-related genes in cichlids in relation to egg size and trophic specialization.
Dec 06, 2018
EvoDevo
Background: Egg size represents an important form of maternal effect determined by a complex interplay of long-term adaptation and short-term plasticity balancing egg size with brood size. Haplochromine cichlids are maternal mouthbrooders showing differential parental investment in different species, manifested in great variation in egg size, brood size and duration of maternal care. Little is known about maternally determined molecular characters of eggs in fishes and their relation to egg size and trophic specialization. Here we investigate maternal mRNA inputs of selected growth- and stress-related genes in eggs of mouthbrooding cichlid fishes adapted to different trophic niches from Lake Tanganyika, Lake Malawi, Lake Victoria and compare them to their riverine allies. Results: We first identified two reference genes, atf7ip and mid1ip1, to be suitable for cross-species quantification of mRNA abundance via qRT-PCR in the cichlid eggs. Using these reference genes, we found substantial variation in maternal mRNA input for a set of candidate genes related to growth and stress response across species and lakes. We observed negative correlation of mRNA abundance between two of growth hormone receptor paralogs (ghr1 and ghr2) across all haplochromine cichlid species which also differentiate the species in the two younger lakes, Malawi and Lake Victoria, from those in Lake Tanganyika and ancestral riverine species. Furthermore, we found correlations between egg size and maternal mRNA abundance of two growth-related genes igf2 and ghr2 across the haplochromine cichlids as well as distinct clustering of the species based on their trophic specialization using maternal mRNA abundance of five genes (ghr1, ghr2, igf2, gr and sgk1). Conclusions: These findings indicate that variations in egg size in closely related cichlid species can be linked to differences in maternal RNA deposition of key growth-related genes. In addition, the cichlid species with contrasting trophic specialization deposit different levels of maternal mRNAs in their eggs for particular growth-related genes; however, it is unclear whether such differences contribute to differential morphogenesis at later stages of development. Our results provide first insights into this aspect of gene activation, as a basis for future studies targeting their role during ecomorphological specialization and adaptive radiation.
Wild African Drosophila melanogaster Are Seasonal Specialists on Marula Fruit.
Dec 11, 2018   Current Biology : CB
Mansourian S, Enjin A, Jirle EV, Ramesh V, Rehermann G, Becher PG, Pool JE, Stensmyr MC
Wild African Drosophila melanogaster Are Seasonal Specialists on Marula Fruit.
Dec 11, 2018
Current Biology : CB
Although the vinegar fly Drosophila melanogaster is arguably the most studied organism on the planet, fundamental aspects of this species' natural ecology have remained enigmatic [1]. We have here investigated a wild population of D. melanogaster from a mopane forest in Zimbabwe. We find that these flies are closely associated with marula fruit (Sclerocarya birrea) and propose that this seasonally abundant and predominantly Southern African fruit is a key ancestral host of D. melanogaster. Moreover, when fruiting, marula is nearly exclusively used by D. melanogaster, suggesting that these forest-dwelling D. melanogaster are seasonal specialists, in a similar manner to, e.g., Drosophila erecta on screw pine cones [2]. We further demonstrate that the main chemicals released by marula activate odorant receptors that mediate species-specific host choice (Or22a) [3, 4] and oviposition site selection (Or19a) [5]. The Or22a-expressing neurons-ab3A-respond strongly to the marula ester ethyl isovalerate, a volatile rarely encountered in high amounts in other fruit. We also show that Or22a differs among African populations sampled from a wide range of habitats, in line with a function associated with host fruit usage. Flies from Southern Africa, most of which carry a distinct allele at the Or22a/Or22b locus, have ab3A neurons that are more sensitive to ethyl isovalerate than, e.g., European flies. Finally, we discuss the possibility that marula, which is also a culturally and nutritionally important resource to humans, may have helped the transition to commensalism in D. melanogaster.
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.
Dec 11, 2018   Molecular Ecology
Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.
Dec 11, 2018
Molecular Ecology
Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients. This article is protected by copyright. All rights reserved.
The diversity of population responses to environmental change.
Dec 11, 2018   Ecology Letters
Colchero F, Jones OR, Conde DA, Hodgson D, Zajitschek F,   . . . . . .   , While GM, Baudisch A, Flatt T, Coulson T, Gaillard JM
The diversity of population responses to environmental change.
Dec 11, 2018
Ecology Letters
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and when ages are reduced to stages. We find that stage- vs. age-based models can produce markedly divergent stochastic population growth rates. The differences are most pronounced when there are survival-fecundity-trade-offs, which reduce the variance in the population growth rate. Finally, the expected value and variance of the stochastic growth rates of populations with different age-specific demographic rates can diverge to the extent that, while some populations may thrive, others will inevitably go extinct.
Delegating sex: differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction.
Dec 11, 2018   Genome Biology And Evolution
Álvarez-Campos P, Kenny NJ, Verdes A, Fernández R, Novo M, Giribet G, Riesgo A
Delegating sex: differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction.
Dec 11, 2018
Genome Biology And Evolution
Stolonization in syllid annelids is a unique mode of reproduction among animals. During the breeding season, a structure resembling the adult but containing only gametes, called stolon, is formed generally at the posterior end of the animal. When stolons mature, they detach from the adult and gametes are released into the water column. The process is synchronized within each species, and it has been reported to be under environmental and endogenous control, probably via endocrine regulation. To further understand reproduction in syllids and to elucidate the molecular toolkit underlying stolonization, we generated Illumina RNA-seq data from different tissues of reproductive and non-reproductive individuals of Syllis magdalena, and characterized gene expression during the stolonization process. Several genes involved in gametogenesis (ovochymase, vitellogenin, testis-specific serine/threonine-kinase), immune response (complement receptor 2), neuronal development (tyrosine-protein kinase Src42A), cell proliferation (alpha-1D adrenergic receptor), and steroid metabolism (hydroxysteroid dehydrogenase 2) were found differentially expressed in the different tissues and conditions analyzed. In addition, our findings suggest that several neurohormones, such as methyl farnesoate, dopamine and serotonin, might trigger stolon formation, the correct maturation of gametes and the detachment of stolons when gametogenesis ends. The process seems to be under circadian control, as indicated by the expression patterns of r-opsins. Overall, our results shed light into the genes that orchestrate the onset of gamete formation, and improve our understanding of how some hormones, previously reported to be involved in reproduction and metamorphosis processes in other invertebrates, seem to also regulate reproduction via stolonization.
Erratum to: Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.
Dec 11, 2018   GigaScience
Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S,   . . . . . .   , Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP
Evolution of the yeast recombination landscape.
Dec 11, 2018   Molecular Biology And Evolution
Liu H, Maclean CJ, Zhang J
Evolution of the yeast recombination landscape.
Dec 11, 2018
Molecular Biology And Evolution
Meiotic recombination comprises crossovers and non-crossovers. Recombination, crossover in particular, shuffles mutations and impacts both the level of genetic polymorphism and the speed of adaptation. In many species, the recombination rate varies across the genome with hot- and cold-spots. The hotspot paradox hypothesis asserts that recombination hotspots are evolutionarily unstable due to self-destruction. However, the genomic landscape of double-strand breaks (DSBs), which initiate recombination, is evolutionarily conserved among divergent yeast species, casting doubt on the hotspot paradox hypothesis. Nonetheless, because only a subset of DSBs are associated with crossovers, the evolutionary conservation of the crossover landscape could differ from that of DSBs. Here we investigate this possibility by generating a high-resolution recombination map of the budding yeast Saccharomyces paradoxus through whole-genome sequencing of fifty meiotic tetrads and by comparing this recombination map with that of S. cerevisiae. We observe a 40% lower recombination rate in S. paradoxus than in S. cerevisiae. Compared with the DSB landscape, the crossover landscape is even more conserved. Further analyses indicate that the elevated conservation of the crossover landscape is explained by a near-subtelomeric crossover preference in both yeasts, which we find to be attributable at least in part to crossover interference. We conclude that the yeast crossover landscape is highly conserved and that the evolutionary conservation of this landscape can differ from that of the DSB landscape.
Sex-specific dominance reversal of genetic variation for fitness.
Dec 11, 2018   PLoS Biology
Grieshop K, Arnqvist G
Sex-specific dominance reversal of genetic variation for fitness.
Dec 11, 2018
PLoS Biology
The maintenance of genetic variance in fitness represents one of the most longstanding enigmas in evolutionary biology. Sexually antagonistic (SA) selection may contribute substantially to maintaining genetic variance in fitness by maintaining alternative alleles with opposite fitness effects in the two sexes. This is especially likely if such SA loci exhibit sex-specific dominance reversal (SSDR)-wherein the allele that benefits a given sex is also dominant in that sex-which would generate balancing selection and maintain stable SA polymorphisms for fitness. However, direct empirical tests of SSDR for fitness are currently lacking. Here, we performed a full diallel cross among isogenic strains derived from a natural population of the seed beetle Callosobruchus maculatus that is known to exhibit SA genetic variance in fitness. We measured sex-specific competitive lifetime reproductive success (i.e., fitness) in >500 sex-by-genotype F1 combinations and found that segregating genetic variation in fitness exhibited pronounced contributions from dominance variance and sex-specific dominance variance. A closer inspection of the nature of dominance variance revealed that the fixed allelic variation captured within each strain tended to be dominant in one sex but recessive in the other, revealing genome-wide SSDR for SA polymorphisms underlying fitness. Our findings suggest that SA balancing selection could play an underappreciated role in maintaining fitness variance in natural populations.
Fall webworm genomes yield insights into rapid adaptation of invasive species.
Dec 11, 2018   Nature Ecology & Evolution
Wu N, Zhang S, Li X, Cao Y, Liu X, Wang Q, Liu Q, Liu H, Hu X, Zhou XJ, James AA, Zhang Z, Huang Y, Zhan S
Fall webworm genomes yield insights into rapid adaptation of invasive species.
Dec 11, 2018
Nature Ecology & Evolution
Invasive species cause considerable ecological and economic damage. Despite decades of broad impacts of invasives on diversity and agriculture, the genetic adaptations and near-term evolution of invading populations are poorly understood. The fall webworm, Hyphantria cunea, a highly successful invasive species that originated in North America, spread throughout the Northern Hemisphere during the past 80 years. Here, we use whole-genome sequencing of invasive populations and transcriptome profiling to probe the underlying genetic bases for the rapid adaptation of this species to new environments and host plants. We find substantial reductions in genomic diversity consistent with founder effects. Genes and pathways associated with carbohydrate metabolism and gustatory receptors are substantially expanded in the webworm genome and show strong signatures of functional polymorphisms in the invasive population. We also find that silk-yielding-associated genes maintained a relatively low level of functional diversity, and identify candidate genes that may regulate the development of silk glands in fall webworms. These data suggest that the fall webworm's ability to colonize novel hosts, mediated by plasticity in their gustatory capabilities along with an increased ability to utilize novel nutrition sources and substrates, has facilitated the rapid and successful adaptation of the species throughout its range.
Mechanistic insights revealed by a UBE2A mutation linked to intellectual disability.
Dec 11, 2018   Nature Chemical Biology Add nature.com free-link Cancel
de Oliveira JF, do Prado PFV, da Costa SS, Sforça ML, Canateli C, Ranzani AT, Maschietto M, de Oliveira PSL, Otto PA, Klevit RE, Krepischi ACV, Rosenberg C, Franchini KG
Mechanistic insights revealed by a UBE2A mutation linked to intellectual disability.
Dec 11, 2018
Nature Chemical Biology
Ubiquitin-conjugating enzymes (E2) enable protein ubiquitination by conjugating ubiquitin to their catalytic cysteine for subsequent transfer to a target lysine side chain. Deprotonation of the incoming lysine enables its nucleophilicity, but determinants of lysine activation remain poorly understood. We report a novel pathogenic mutation in the E2 UBE2A, identified in two brothers with mild intellectual disability. The pathogenic Q93E mutation yields UBE2A with impaired aminolysis activity but no loss of the ability to be conjugated with ubiquitin. Importantly, the low intrinsic reactivity of UBE2A Q93E was not overcome by a cognate ubiquitin E3 ligase, RAD18, with the UBE2A target PCNA. However, UBE2A Q93E was reactive at high pH or with a low-pKa amine as the nucleophile, thus providing the first evidence of reversion of a defective UBE2A mutation. We propose that Q93E substitution perturbs the UBE2A catalytic microenvironment essential for lysine deprotonation during ubiquitin transfer, thus generating an enzyme that is disabled but not dead.
Indirect reciprocity with optional games and monitoring of interactions between defectors.
Dec 11, 2018   Mathematical Biosciences
Ghang W, Olejarz J, Nowak MA
Indirect reciprocity with optional games and monitoring of interactions between defectors.
Dec 11, 2018
Mathematical Biosciences
We study evolution of cooperation by indirect reciprocity with optional interactions. There are repeated interactions between two types of players, cooperators and defectors, in a population of finite size. Previously, we considered the scenario where an encounter between a cooperator and a defector results in the defector's identity being revealed with some probability, while an encounter between two defectors does not reveal their identities. Here, we study a generalization of this model: an encounter between a cooperator and a defector results in the defector's identity being revealed with probability QC; an encounter between two defectors results in each of those defectors' identities being revealed independently with probability QD. We find that larger values of QD can significantly increase both the average payoffs for cooperators and, in a dynamical setting, the basin of attraction for cooperation. Moreover, if QC is sufficiently small and QD is sufficiently large, then we find a new behavior over the previous model in which cooperators and defectors can stably coexist. We also study hesitation to cooperate with unknown individuals and defectors refusing interactions with known defectors to preserve their own unknown status.
Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species.
Dec 11, 2018   International Journal Of Biological Macromolecules
Liu J, Yu J, Zhou M, Yang J
Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species.
Dec 11, 2018
International Journal Of Biological Macromolecules
Japalura flaviceps is a subarboreal species, which is endemically distributed in China. Here, we determined the complete mitogenome of J. flaviceps. This mitogenome was a typical circular molecule of 17,140 bp in size, containing 13 protein-coding genes, 22 transfer-RNA-coding genes, two ribosomal-RNA-coding genes, and one control region. Our phylogenetic result using 15 genes divided all Agamidae lizards into six subfamilies and showed (((((Agaminae, Draconinae), Amphibolurinae), Hydrosaurinae), Uromastycinae), Leiolepinae), which was different from the previous studies. J. flaviceps had a closer relationship to Pseudocalotes species than Acanthosaura species, and they formed a well-supported lineage of Draconinae subfamily. There were nine mitochondrial gene rearrangement types among the 27 Agamidae species, and six of them were found in the Agaminae group. The trnP gene of J. flaviceps mitogenome was encoded on the heavy strand instead of its typical light strand position, providing an example of gene inversion in vertebrate mitogenomes. J. flaviceps shared the same gene arrangement type (inverted trnP gene) with other Draconinae species, strongly implying a single occurrence of the trnP inversion in the ancestral draconine lineage. Our study helps to understand mitogenome evolution and phylogenetic relationship of Agamidae species.
Ecosystem Traits Linking Functional Traits to Macroecology.
Dec 11, 2018   Trends In Ecology & Evolution
He N, Liu C, Piao S, Sack L, Xu L,   . . . . . .   , Sun W, Niu S, Li S, Zhang J, Yu G
Ecosystem Traits Linking Functional Traits to Macroecology.
Dec 11, 2018
Trends In Ecology & Evolution
As the range of studies on macroecology and functional traits expands, integration of traits into higher-level approaches offers new opportunities to improve clarification of larger-scale patterns and their mechanisms and predictions using models. Here, we propose a framework for quantifying 'ecosystem traits' and means to address the challenges of broadening the applicability of functional traits to macroecology. Ecosystem traits are traits or quantitative characteristics of organisms (plants, animals, and microbes) at the community level expressed as the intensity (or density) normalized per unit land area. Ecosystem traits can inter-relate and integrate data from field trait surveys, eddy-flux observation, remote sensing, and ecological models, and thereby provide new resolution of the responses and feedback at regional to global scale.
Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot.
Dec 06, 2018   Ecology And Evolution
DiBattista JD, Alfaro ME, Sorenson L, Choat JH, Hobbs JA, Sinclair-Taylor TH, Rocha LA, Chang J, Luiz OJ, Cowman PF, Friedman M, Berumen ML
Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot.
Dec 06, 2018
Ecology And Evolution
For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (
The Genetic Ancestry of Modern Indus Valley Populations from Northwest India.
Dec 11, 2018   American Journal Of Human Genetics
Pathak AK, Kadian A, Kushniarevich A, Montinaro F, Mondal M,   . . . . . .   , Pagani L, Kivisild T, Metspalu M, Chaubey G, Villems R
The Genetic Ancestry of Modern Indus Valley Populations from Northwest India.
Dec 11, 2018
American Journal Of Human Genetics
The Indus Valley has been the backdrop for several historic and prehistoric population movements between South Asia and West Eurasia. However, the genetic structure of present-day populations from Northwest India is poorly characterized. Here we report new genome-wide genotype data for 45 modern individuals from four Northwest Indian populations, including the Ror, whose long-term occupation of the region can be traced back to the early Vedic scriptures. Our results suggest that although the genetic architecture of most Northwest Indian populations fits well on the broader North-South Indian genetic cline, culturally distinct groups such as the Ror stand out by being genetically more akin to populations living west of India; such populations include prehistorical and early historical ancient individuals from the Swat Valley near the Indus Valley. We argue that this affinity is more likely a result of genetic continuity since the Bronze Age migrations from the Steppe Belt than a result of recent admixture. The observed patterns of genetic relationships both with modern and ancient West Eurasians suggest that the Ror can be used as a proxy for a population descended from the Ancestral North Indian (ANI) population. Collectively, our results show that the Indus Valley populations are characterized by considerable genetic heterogeneity that has persisted over thousands of years.
Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism.
Dec 11, 2018   ELife
Shalaeva DN, Cherepanov DA, Galperin MY, Golovin AV, Mulkidjanian AY
Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism.
Dec 11, 2018
ELife
The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine 'finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases.
Regulatory and sequence evolution in response to selection for improved associative learning ability in Nasonia vitripennis.
Dec 11, 2018   BMC Genomics
Kraaijeveld K, Oostra V, Liefting M, Wertheim B, de Meijer E, Ellers J
Regulatory and sequence evolution in response to selection for improved associative learning ability in Nasonia vitripennis.
Dec 11, 2018
BMC Genomics
BACKGROUND: Selection acts on the phenotype, yet only the genotype is inherited. While both the phenotypic and genotypic response to short-term selection can be measured, the link between these is a major unsolved problem in evolutionary biology, in particular for complex behavioural phenotypes. RESULTS: Here we characterize the genomic and the transcriptomic basis of associative learning ability in the parasitic wasp Nasonia vitripennis and use gene network analysis to link the two. We artificially selected for improved associative learning ability in four independent pairs of lines and identified signatures of selection across the genome. Allele frequency diverged consistently between the selected and control lines in 118 single nucleotide polymorphisms (SNPs), clustering in 51 distinct genomic regions containing 128 genes. The majority of SNPs were found in regulatory regions, suggesting a potential role for gene expression evolution. We therefore sequenced the transcriptomes of selected and control lines and identified 36 consistently differentially expressed transcripts with large changes in expression. None of the differentially expressed genes also showed sequence divergence as a result of selection. Instead, gene network analysis showed many of the genes with consistent allele frequency differences and all of the differentially expressed genes to cluster in a single co-expression network. At a functional level, both genomic and transcriptomic analyses implicated members of gene networks known to be involved in neural plasticity and cognitive processes. CONCLUSIONS: Taken together, our results reveal how specific cognitive abilities can readily respond to selection via a complex interplay between regulatory and sequence evolution.
Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles.
Dec 11, 2018   BMC Genomics
Fay JV, Watkins CJ, Shrestha RK, Litwiñiuk SL, Talavera Stefani LN, Rojas CA, Argüelles CF, Ferreras JA, Caccamo M, Miretti MM
Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles.
Dec 11, 2018
BMC Genomics
BACKGROUND: The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in > 90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles. RESULTS: In this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR. CONCLUSIONS: Our study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves' polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites.
Look Closely, the Beautiful May Be Small: Precursor-Derived Peptides in Plants.
Dec 11, 2018   Annual Review Of Plant Biology
Olsson V, Joos L, Zhu S, Gevaert K, Butenko MA, De Smet I
Look Closely, the Beautiful May Be Small: Precursor-Derived Peptides in Plants.
Dec 11, 2018
Annual Review Of Plant Biology
During the past decade, a flurry of research focusing on the role of peptides as short- and long-distance signaling molecules in plant cell communication has been undertaken. Here,we focus on peptides derived from nonfunctional precursors, and we address several key questions regarding peptide signaling. We provide an overview of the regulatory steps involved in producing a biologically active peptide ligand that can bind its corresponding receptor(s) and discuss how this binding and subsequent activation lead to specific cellular outputs. We discuss different experimental approaches that can be used to match peptide ligands with their receptors. Lastly, we explore how peptides evolved from basic signaling units regulating essential processes in plants to more complex signaling systems as new adaptive traits developed and how nonplant organisms exploit this signaling machinery by producing peptide mimics. Expected final online publication date for the Annual Review of Plant Biology Volume 70 is April 29, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
RAD-seq data reveal a cryptic Viburnum species on the North American Coastal Plain.
Dec 06, 2018   Systematic Biology
Spriggs EL, Eaton DAR, Sweeney PW, Schlutius C, Edwards EJ, Donoghue MJ
RAD-seq data reveal a cryptic Viburnum species on the North American Coastal Plain.
Dec 06, 2018
Systematic Biology
Species are the starting point for most studies of ecology and evolution, but the proper circumscription of species can be extremely difficult in morphologically variable lineages, and there are still few convincing examples of molecularly-informed species delimitation in plants. We focus here on the Viburnum nudum complex, a highly variable clade that is widely distributed in eastern North America. Taxonomic treatments have mostly divided this complex into northern (V. nudum var. cassinoides) and southern (V. nudum var. nudum) entities, but additional names have been proposed. We used multiple lines of evidence, including RADseq, morphological, and geographic data, to test how many independently evolving lineages exist within the V. nudum complex. Genetic clustering and phylogenetic methods revealed three distinct groups-one lineage that is highly divergent, and two others that are recently diverged and morphologically similar. A combination of evidence that includes reciprocal monophyly, lack of introgression, and discrete rather than continuous patterns of variation supports the recognition of all three lineages as separate species. These results identify a surprising case of cryptic diversity in which two broadly sympatric species have consistently been lumped in taxonomic treatments. The clarity of our findings is directly related to the dense sampling and high quality genetic data in this study. We argue that there is a critical need for carefully sampled and integrative species delimitation studies to clarify species boundaries even in well-known plant lineages. Studies following the model that we have developed here are likely to identify many more cryptic lineages and will fundamentally improve our understanding of plant speciation and patterns of species richness.
Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach.
Dec 06, 2018   Molecular Biology And Evolution
Beaulieu JM, O'Meara BC, Zaretzki R, Landerer C, Chai J, Gilchrist MA
Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach.
Dec 06, 2018
Molecular Biology And Evolution
We present a new phylogenetic approach SelAC (Selection on Amino acids and Codons), whose substitution rates are based on a nested model linking protein expression to population genetics. Unlike simpler codon models which assume a single substitution matrix for all sites, our model more realistically represents the evolution of protein coding DNA under the assumption of consistent, stabilizing selection using cost-benefit approach. This cost-benefit approach allows us generate a set of 20 optimal amino acid specific matrix families using just a handful of parameters and naturally links the strength of stabilizing selection to protein synthesis levels, which we can estimate. Using a yeast dataset of 100 orthologs for 6 taxa, we find SelAC fits the data much better than popular models by 104-105 AICc units. Our results also indicated that nested, mechanistic models better predict observed data patterns highlighting the improvement in biological realism in amino acid sequence evolution that our model provides. Additional parameters estimated by SelAC indicate that a large amount of non-phylogenetic, but biologically meaningful, information can be inferred from exisiting data. For example, SelAC prediction of gene specific protein synthesis rates correlates well with both empirical (r = 0.33-0.48) and other theoretical predictions (r=0.45-0.64) for multiple yeast species. SelAC also provides estimates of the optimal amino acid at each site. Finally, because SelAC is a nested approach based on clearly stated biological assumptions, future modifications, such as including shifts in the optimal amino acid sequence within or across lineages, are possible.
Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting.
Dec 06, 2018   Systematic Biology
Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P
Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting.
Dec 06, 2018
Systematic Biology
Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements. We found two contrasting hypotheses of gymnotiform evolutionary relationships depending on whether phylogenetic inferences were based on concatenation or coalescent methods. In the first case, all analyses inferred a previously-and commonly-proposed hypothesis, where the family Apteronotidae was found as the sister group to all other gymnotiform families. In contrast, coalescent-based analyses suggested a novel hypothesis where families producing pulse-type (viz., Gymnotidae, Hypopomidae and Rhamphichthyidae) and wave-type electric signals (viz., Apteronotidae, Sternopygidae) were reciprocally monophyletic. Nodal support for this second hypothesis increased when analyzing loci with the highest phylogenetic information content and further increased when data were pruned using targeted filtering methods that maximized phylogenetic informativeness at the deepest nodes of the Gymnotiformes. Bayesian concordance analyses and topology tests of individual gene genealogies demonstrated that the difficulty of resolving this radiation was likely due to high gene-tree incongruences that resulted from incomplete lineage sorting. We show that data filtering reduces gene tree heterogeneity and increases nodal support and consistency of species trees using coalescent methods; however, we failed to observe the same effect when using concatenation methods. Furthermore, the targeted filtering strategies applied here support the use of "gene data interrogation" rather than "gene genealogy interrogation" approaches in phylogenomic analyses, to extract phylogenetic signal from intractable portions of the Tree of Life.
Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function.
Dec 06, 2018   ELife
Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, Lovell JT, McKay JK
Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function.
Dec 06, 2018
ELife
Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses 7 times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops.
Disruption of sex-specific doublesex exons results in male- and female-specific defects in the black cutworm, Agrotis ipsilon.
Dec 06, 2018   Pest Management Science
Chen X, Cao Y, Zhan S, Tan A, Palli SR, Huang Y
Disruption of sex-specific doublesex exons results in male- and female-specific defects in the black cutworm, Agrotis ipsilon.
Dec 06, 2018
Pest Management Science
BACKGROUND: Doublesex (dsx), the downstream gene in the insect sex determination pathway, is a key regulator of sexually dimorphic development and behavior across a variety of insects. Manipulating the expression of dsx could be a useful method in genetic control of insects. However, information on the sex-specific function of dsx in non-model insects is lacking. RESULTS: In this work, we isolated a dsx homolog, which is alternatively spliced into six female-specific and one male-specific isoforms, from an important agricultural pest, the black cutworm, Agrotis ipsilon. Studies on the expression of sex-specific Aidsx mRNA during embryonic development showed that the 6th hour post oviposition is the key stage for sex determination in A. ipsilon. Functional analysis of Aidsx was conducted using CRISPR/Cas9 system targeting female-specific and male-specific Aidsx exons. Disruptions of sex-specific exons of Aidsx resulted in corresponding sex-specific, sexually dimorphic defects in external genitals, gonads and antennae, and expression of sex-specific genes as well as production of offspring in both sexes. CONCLUSION: Our results not only demonstrate that dsx is a key player determining A. ipsilon sexually dimorphic traits, but also provide a potential method for genetic control of this pest. This article is protected by copyright. All rights reserved.
Homeostatic maintenance of non-structural carbohydrates during the 2015-2016 El Niño drought across a tropical forest precipitation gradient.
Dec 11, 2018   Plant, Cell & Environment
Dickman LT, McDowell NG, Grossiord C, Collins AD, Wolfe BT,   . . . . . .   , Ely KS, Michaletz ST, Xu C, Kueppers L, Chambers JQ
Homeostatic maintenance of non-structural carbohydrates during the 2015-2016 El Niño drought across a tropical forest precipitation gradient.
Dec 11, 2018
Plant, Cell & Environment
Non-structural carbohydrates (NSCs) are essential for maintenance of plant metabolism, and may be sensitive to both short- and long-term climatic variation. NSC variation in moist tropical forests has rarely been studied, so regulation of NSCs in these systems is poorly understood. We measured foliar and branch NSC content in 23 tree species at three sites located across a large precipitation gradient in Panama during the 2015-2016 El Niño to examine how short- and long-term climatic variation impact carbohydrate dynamics. Across all sites, leaf NSCs increased over diurnal time-periods. There was no significant difference in total NSCs as the drought progressed (leaf p=0.32, branch p=0.30), nor across the rainfall gradient (leaf p=0.91, branch p=0.96). Foliar soluble sugars decreased while starch increased over the duration of the dry period, suggesting greater partitioning of NSCs to storage than metabolism or transport as drought progressed. There was large variation across species at all sites, but total foliar NSCs were positively correlated with leaf mass per area, while branch sugars were positively related to leaf temperature and negatively correlated with daily photosynthesis and wood density. The NSC homeostasis across a wide range of conditions suggests that NSCs are an allocation priority in moist tropical forests.

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