- Genomic analysis of the four ecologically distinct cactus host populations of. - Drosophila mojavensis. - Background: Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. - This study examines the rate of molecular evolution at protein-coding genes throughout the genome in response to host adaptation in the cactophilic Drosophila mojavensis. - By examining changes in the genetic code both at the level of individual genes and at the whole-genome level it is possible to gain a better understanding of how local ecological conditions can shape the pattern of variation within and between ecologic- ally distinct populations [1, 2]. - Yet, an examination of the genomic di- vergence of ecologically distinct populations can yield valuable insight into the adaptation process especially when the genomic data is placed in an ecological context [5]. - Furthermore, a conse- quence of the fixation of ecologically-relevant variants has been implicated in the evolution of barriers to gene flow and potentially the origins of reproductively isolated popu- lations, i.e. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article. - Host preferences and performance in this system facili- tates the genetic and genomic isolation observed between the host populations, as each prefers a different microenvir- onment and likely does not interact and hybridize with members of the other population [11, 12].. - Genes involved in the immune system, gam- ete development, sensory perception, metabolism, cell motility, and genes involved with cancer were those found to have signatures of positive selection. - mojavensis, a fly endemic to the southwestern United States and northwestern Mexico that has become a model for the understanding of the genetics of adaptation [27]. - Individuals from all four populations can interbreed with each other and produce viable fertile off- spring, and no postzygotic incompatibilities appear to exist, although some evidence indicate low levels of prezygotic isolation between some of the populations [29]. - 1 Distribution of the four cactus host populations of D.. - In addition to the nutritional differences of the ne- croses that exist between the distinct cactus species, the rots contain a number of compounds that have toxic prop- erties which can affect the performance and viability of non-resident cactophilic Drosophila [39–41]. - This selective pressure has resulted in the fixation of variants that facili- tate the survival of D. - Among the loci that are differen- tially expressed or constitutively fixed between populations many are involved in detoxification, metabolism, chemo- sensory perception and behavior, supporting the role of the local necrotic cactus conditions in shaping transcriptional variation [43–45]. - Of the 14,680 loci annotated in the reference genome the vast majority were also present in our template- based assemblies of the other three populations. - 2 Boxplot of log 2 ω values for loci located in each of the D.. - mojavensis populations to their respective ecological condi- tions we examined loci with ω values in the top 10% of the distribution, hereafter referred to as TOP10 loci. - A similar pattern of ω values was observed for the TOP10 loci, where a significant excess of the smaller gene group (<. - 1 Kb) was com- posed of TOP10 loci, and a significantly fewer were observed in the greater than 4 Kb bin (Additional file 2: Figure S5). - Among the TOP10 loci, there was a significant representation of them in the male-biased group of genes and a significant underrepresentation in the female-biased genes (Fig. - After removing both the female- and male-biased genes, we observed that of the 5101 remaining loci those in the lowest expression category showed the greatest ω values (Additional file 2: Figure S12, Table S6). - categories of the PAML-FDR loci (Additional file 2: Fig- ures S13 and S14).. - We compare rates of molecular evolution of loci that are differentially expressed in response to cactus host utilization [44] as well as those loci who exhibit fixed significant expression differences between the four host populations in the ab- sence of cactus compounds (i.e. - Of our 9087 genes in our filtered dataset, approximately genes did not have orthologous calls back to loci in the D. - Of the remaining set of genes with D. - melanogaster orthologs, less than half of the genes (3649) had at least one gene ontology (GO) term.. - melanogaster ortholo- gous in the TOP10 and PAML-FDR genes was greater (40 and 23%, respectively). - A network analysis of the same set of loci indi- cates similar functional networks as well as those associated with defense and chromatin regulation and remodeling (Fig. - Among molecular functions, in the TOP10 dataset, serine endo- peptidase activity appeared to be overrepresented (Add- itional file 2: Table S8).. - In this study we sequenced, assembled and analyzed the genomes of each of the four cactus host populations of D. - mojavensis for the purpose of assessing the genomic consequences of the adaptation to local ecological. - mojavensis we observed the highest rate of molecular evolution in the small F element, followed by elements B and E, and then the remaining autosomal elements and the X chromosome (Fig. - A subsequent gen- omic analysis of the X chromosome across more distant Drosophila species (D. - 5 Functional clustering of Biological Process GO terms of the TOP10 loci. - The greatest ω values were present in the dot chromosome which in D. - One possible explanation for the elevated rates of molecular evolution in these chro- mosomes is the distinct karyotypes of the sequenced lines (Additional file 2: Table S9). - A more detailed analysis of the consequence of chromosomal inversion on the evolutionary trajector- ies of associated loci will be performed in future analyses of de novo assemblies of D. - Genes across the genome as well as those with evidence of positive selection or in the top 10% of ω values were assessed for a number of characteristics. - This indicates that although the phylogenetic scale of the present study is limited (within D. - 6 Network clustering of Biological Process GO terms of the TOP10 loci. - 0.001), but explains very little of the variation in K s (r Additional file 2: Figure S21). - Therefore, it is difficult to infer the ef- fect of the association between K s and protein length, and the lack of positive correlation might be a func- tion of the close relationship between the genomes studied here. - The negative association between intron number and rate of molecular evolution has been pre- viously suggested to be due to the presence of exonic splice site enhancers which help in the correct re- moval of introns from the transcription sequence. - The correlation between gene length and rate of molecular evolution could also be explained as a re- sult of the increased level of interactions between sites of larger exons [61]. - Given our coarse transcription data we were not able to tease apart which of the above-mentioned forces might more strongly shape the rate of molecular evolution in these genomes. - These changes are likely a result of the distinct nutritional and xenobiotic environment the different D. - The chemical composition of the cacti and the species of yeast found in each rot varies [35–42] and thus the populations have likely needed to optimize the recognition, avoidance and processing of these necrosis- specific compounds through changes in metabolism, physiology and behavior.. - While the apparent positive selection on these genes could be due to a response to pesticides they might experience in the field, but more likely they may be evolving in response to the effects of the toxic or nu- tritional compounds found in cactus rots.. - Many of the previously identified proteins playing a role in detoxification in cactophiles (Glutathione S-transferases, Cytochrome P450s, Ester- ases and UDP-glycosyltransferase) have been associated with detoxification in a broad number of taxa [83–87].. - In fact, in recent comparative genomic analysis of the cactophilic D. - In the present genomic analysis of the D. - A population genetics analysis of GstD1 has indicated a pattern of adaptive amino acid evolution at this locus in the Sonora and Baja California populations [32]. - The location of the fixed residue fixed in the lineages leading to these two populations indicated potential functional consequences and a recent kinetic analysis of these proteins have sup- port this prediction (Matzkin, unpublished data).. - A number of the TOP10 loci in this study perform functions associated with sensory perception and be- havior (Fig. - Recent analysis of populations dif- ferentiation in odorant and gustatory receptors have shown that unlike what might be initially predicted a number of the changes in these receptors suggests that effects at the level of signal transduction in addition to odorant recognition [103]. - In addition to their role in xenobiotic metabolism, serine proteases have been shown to be involved in the network of proteins associated with reproductive interactions in sev- eral taxa. - Knockouts of serine proteases have been shown to interfere with the behavioral and physiological effects of the male-derived sex peptide [106].. - The pattern of positive selection and/or elevated rate of molecular evo- lution for proteases and reproductive loci in the present study may highlight the continuing genomic consequence of sexual selection in this species.. - In this first ever genome-wide analysis of the pattern of molecular evolution across the four ecologically distinct populations of D. - mojavensis, we have begun to describe the genomic consequences of the adapta- tion of these cactophilic Drosophila to their respective envi- ronments. - Furthermore, fast evolving loci also were more likely to be differentially expressed in response to cactus host use and have fixed inter-population expression differ- ences, indicating that both transcriptional and coding se- quence changes have been involved in the local ecological adaptation of D. - Summary of the karyo- type of each of the lines sequenced as well as the Cata- lina Island template genome stock can be found in Additional file 2: Table S9. - Gel electrophoresis was run on each sample to check the quality of the extraction. - Paired-end and mate pair Illumina reads were filtered and trimmed using step one of the A5 Pipeline [110].. - A5 was run on the Dense Memory Cluster of the Alabama Super Computer Center with four processing cores and 64 gigabytes of memory allocated for each run. - The refer- ence genome of the Catalina Island population of D.. - mojavensis was assembled as part of the Drosophila 12 Genomes Consortium [17]. - Version 1.04 of the reference genome was retrieved from FlyBase version FB . - Using Geneious 8.1 and its Map to Ref- erence feature the cleaned reads were assembled to each of the template scaffolds. - These annotations were transferred to each of the new genomes by aligning each assembled genome scaffold to the reference genome scaffold using Mauve Genome Alignment [116] with default settings except for selecting assume collinear genomes. - Sequence files for each gene were concatenated and then aligned using the de- fault settings of the aligner Muscle . - Files of aligned genes were converted to AXT format using the Perl script parseFastaIntoAXT.pl including in the package.. - Values for ω were calculated using codeml part of the PAML 4.9 package [47]. - to protein sequence with Transeq, part of the EMBOSS package [117] and any genes with internal stop codons were removed.. - Significance values were found by taking the differ- ence between the log likelihood values of the two out- puts and multiplying them by two. - This yielded a total of 9087 genes that were used in the analysis. - Histograms of a log 2 transformation of the ω values were produced using JMP 10. - A com- parison between the log 2 transformations of the NG Ka/. - Comparison of model 0 omega between FDR significant loci and non-significant loci was also done for differential expression between third-instar larva of the four host populations with ANOVA in JMP 10.. - mojavensis ortholog that was present in the unfiltered dataset as retrieved from FlyBase version FB . - mojavensis loci examined in the study.. - TOP10: Loci with ω values in the top 10% of the distribution. - CWA performed the assembly and analysis of the genomic data and was involved in the writing of the manuscript. - LMM conceived of and designed the study, was involved in the analysis and the writing of the manuscript. - Ecological genomics: understanding gene and genome function in the natural environment. - Host Fidelity is an effective premating barrier between sympatric races of the apple maggot Fly. - A scan for positively selected genes in the genomes of humans and chimpanzees.. - Natural selection on protein-coding genes in the human genome. - The mosaic ancestry of the Drosophila genetic reference panel and the D. - Analysis of the community structure of yeasts associated with the decaying stems of Cactus. - Analysis of the community structure of yeasts associated with the decaying stems of cactus. - Chemical interactions in the cactus- microorganism-Drosophila model system of the Sonoran Desert. - Cytological and phylogenetic relationships in the Repleta Group of the Genus Drosophila. - Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. - Evolution of the Mojavensis cluster of cactophilic Drosophila with descriptions of two new species. - Towards a more nuanced understanding of the relationship between sex-biased gene expression and rates of protein-coding sequence evolution. - Identification of a novel class of insect glutathione S- transferases involved in resistance to DDT in the malaria vector Anopheles gambiae. - Five Drosophila genomes reveal nonneutral evolution and the signature of host specialization in the chemoreceptor superfamily
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