obligate mutualism graph

We obtained 44.6 Gbp of data and estimated a genome size of 294 Mbp based on a k-mer analysis of 12.3 Gbp of high-quality sequences. Todd ML: Sean RE: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Interestingly, genes unique to fig wasps mainly involve the remodeling of chromatin structure, which is often subjected to epigenetic regulation of gene expression [21, 22] (Additional file 1: Figure S2). 2010, 327: 343-348. These processes reduced genomic heterozygosity and, thus, improved the quality of assembly. Article Patel RT, Soulages JL, Hariharasundaram B, Arrese EL: Activation of the lipid droplet controls the rate of lipolysis of triglycerides in the insect fat body. When the LRT was significant, a Bayes Empirical Bayes (BEB) analysis was conducted to identify putatively positively selected sites, which may also be relaxed selected sites though. Phylogenetic analysis based on all single copy orthologous genes provides a good resolution of the phylogenetic relationship among nine sequenced insect genomes. 2023 BioMed Central Ltd unless otherwise stated. Omissions? Fazzari M, Greally J: Introduction to epigenomics and epigenome-wide analysis. J Lepid Soc 66:5051, Pellmyr O, Augenstein EJ (1997) Pollination biology of Hesperaloe parviflora (Agavaceae). Oecologia 134:381387, Jousselin E, van Noort S, Rasplus JY, Greeff JM (2006) Patterns of diversification of Afrotropical Otiteselline fig wasps: phylogenetic study reveals a double radiation across host figs and conservatism of host association. 2005, 280: 22624-22631. Science. [http://flybase.org], SignalP 4.1 Server. The DNA was dissolved in 50L of TE buffer and stored at 80C. Extreme morphological dimorphism between female and male fig wasps, C. solmsi . Both of the growth curves level off or decline. 10.1093/nar/gkj118. Bacterial symbionts in natural populations of the stinkbug Plautia stali are undergoing an evolutionary transition from a free-living lifestyle in the environment to obligate mutualism. The genders exhibit extreme intraspecific morphological divergence in the compound eyes, wings, antennae, body color, and size, as expected given their functional adaptations to different life histories (Figure2). Consistent with the repertoire reductions, this may be associated with the process of host specialization [32]. Below is an empirical graph of a. obligate mutualism. 10.1038/75556. Your privacy choices/Manage cookies we use in the preference centre. In any case, we can see that the yucca plantyucca moth association is perfectly explainable as a post-Flood derivation. Lineages CsGr4 and NvGr48-50 are chalcidoid-specific (Additional file 1: Figure S4). Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H: Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. The amino acid sequences of homologous genes were aligned with ClustalX v2.0 [86]. Correspondence to The genome is spread across 15,018 contigs (contig N50=74,395bp, scaffold N50=9,558,897bp), and assembly results in a 278 Mbp genome (Table1), which is comparable to sequenced genomes of other insects (most are 200 to 300 Mbp) (summarized in Additional file 1: Table S1). Due to the commonly very strong mutual dependence among obligate cooperators,. Nucleic Acids Res. Both genes are intact without introns. The gamma parameter and proportion of invariant sites were estimated from the data. This is obligate mutualism. B., et al. A conditional P value was calculated for each gene family, and families with conditional P values less than threshold (0.0001) were considered as having an accelerated rate of gain or loss. The genome generally resembles that of other insects in that it has similar gene content to other hymenopterans and other insects in genes such as those encoding for heat shock proteins, circadian rhythm, yellow and royal jelly-like proteins, hox complex, sex determination, and DNA methylation (for further information on these analyses plus an interesting analysis on the nutritional and microbial in the genome, please see Additional file 1). Mutualistic relationships are a type of symbiosis, or interaction between organisms. DNA extraction occurred immediately on arrival. Mutualism is a relationship between different species of organisms. 1. 2007, 52: 171-192. Claudianos C, Ranson H, Johnson RM, Biswas S, Schuler MA, Berenbaum MR, Feyereisen R, Oakeshott JG: A deficit of detoxification enzymes: pesticide sensitivity and environmental response in the honeybee. We chose three trees of Ficus hispida in Danzhou (19 30 N, 109 31 E), Hainan province, China for inoculation of the fig pollinator species (Ceratosolen solmsi). Nat Genet. After thoroughly washing with double-distilled water, we immediately froze the samples in liquid nitrogen and transported them to the laboratory on dry ice. Our analyses facilitate a deeper understanding of the biology of fig wasps, and also provide new insights into the evolution and genomic adaptations of mutualisms. Most of the genes are highly expressed in late pupa stage. Few genes are divergently expressed at early pupa stage, when upregulated male genes are enriched in GO functions of catalytic and oxidoreductase activities, and downregulated in channel, receptor, and transmembrane transporter activities. Cell. J Evol Biol 19:253266, Jousselin E, van Noort S, Berry V, Rasplus JY, Rnsted N, Erasmus JC, Greeff JM (2008) One fig to bind them all: host conservatism in a fig wasp community unravelled by cospeciation analyses among pollinating and nonpollinating fig wasps. The University of Chicago Press, Chicago, Thompson JN, Cunningham BM (2002) Geographic structure and dynamics of coevolutionary selection. American Journal of Botany 101(12): 2062-2067. Birney E, Clamp M, Durbin R: GeneWise and Genomewise. Numbers following each species indicate the average numbers of genes per gene family. Males spend their entire lives inside figs, but females have a brief (1 to 2 day) free-living adult stage that is crucial because these tiny wasps (2 to 5mm long) achieve record feats of dispersal to lay eggs in trees up to 160km away [14, 15] (Figure1). (A) Gene expression profiles with highly expressed genes shown in red, moderately expressed genes in black, and low or unexpressed genes in green. Show transcribed image text. c. predation, where species 2 is the predator, species 1 the prey. For example, Tribolium beetles have 307 Ors and 50 OBPs [31] and the diamondback moth has 83 Ors and 64 OBPs [2]. 10.1093/bioinformatics/btl529. Effects of gene flow on phenotype matching between two varieties of Joshua tree (. The transcriptome data reported in this paper were deposited in the National Center for Biotechnology Information Short Read Archive [95] under the accession no. Trends Ecol Evol 11:1520, Schluter D (2000) The ecology of adaptive radiation. Chalcidoid N. vitripennis has 37 AMP genes [45]. Evolutionary stability of mutualism between yuccas and yucca moths. Thus, sex-differential selection results in extreme anatomical sexual dimorphism (Figure2). In this system, a large species (host) usually interacts with a smaller one (symbiont), which may live inside it as an endosymbiont. the predicted shape of the plant-mass lines if the species 2 plant was a parasite of the species 1 plant. Mol Biol Evol. 10.1080/10635150701472164. We manually annotate 89 genes involved in humoral immune actions that contribute to pathogen recognition, signaling, and response (Figure6; Additional file 1: Table S11). Google Scholar, Suchan T, Beauverd M, Trim N, Alvarez N (2015) Asymmetrical nature of the TrolliusChiastocheta interaction: insights into the evolution of nursery pollination systems. CAS 2003. 2010, 107: 12168-12173. Thus, we predict fewer CPR genes will occur in fig wasps than in jewel wasps and honeybees. This type of argument leads creationists into logical mires. 10.1146/annurev.ento.51.110104.151104. But the slope of the zero isoclines is positive, so each goes to the right and up from K1 and K2. Am J Bot 89:10851092, Heraty JM, Burks RA, Cruaud A, Gibson GAP, Liljeblad J, Munro J, Rasplus J-Y, Delvare G, Janta P, Gumovsky A, Huber J, Woolley JB, Krogmann L, Heydon S, Polaszek A, Schmidt S, Darling DC, Gates MW, Mottern J, Murray E, Dal Molin A, Triapitsyn S, Baur H, Pinto JD, van Noort S, George J, Yoder M (2013) A phylogenetic analysis of the megadiverse Chalcidoidea (Hymenoptera). Updates? Heatmap indicating the CPR gene expression through different life stages of fig wasps, C. solmsi . The streamlined chemosensory ability reflects the overwhelming importance of females finding trees of their only host species, Ficus hispida, during their fleeting adult lives. The fig wasp genome has 17 CCE sequences, again the smallest number in any of the insect genomes characterized so far (Additional file 1: Table S10). This project was supported by the National Natural Science Foundation of China (NSFC grant no. If the Family Orchidaceae represents a holobaramin (basically, the entire kind), then vanilla orchids may not even have been present in the Creation week. 10.1038/348125a0. About 500 male fig wasps were divided into 10 samples of 50 individuals each and used for DNA extraction using a method modified from the protocol developed by J. Rehm, in the Berkeley Drosophila Genome Project [48]. Mol Ecol 18:52185229, Song B, Chen G, Stcklin J, Peng DL, Niu Y, Li ZM, Sun H (2014) A new pollinating seed-consuming mutualism between Rheum nobile and a fly fungus gnat, Bradysia sp., involving pollinator attraction by a specific floral compound. Proc Natl Acad Sci U S A 110:1148711492, Wang RW, Dunn DW, Sun BF (2014) Discriminative host sanctions in a figwasp mutualism. PLoS ONE. We also tried to confirm the absence of genes by focusing on the annotations of the gene families CCE, OBP, and Gr, in which the fig wasp had the fewest gene members among the studied insects, by delving into the raw genomic reads. Pellmyr, O., and J. Leebens-Mack. J Chem Ecol 40:955965, Galil J, Eisikowitch D (1969) Further studies on the pollination ecology of Ficus sycomorus L. (Hymenoptera, Chalcidoidea, Agaonidae). Genomic DNA was sheared into fragments and seven libraries were constructed with inserted fragment sizes ranging from 200bp, 500bp, 800bp, 2kb, 5kb, and 10kb to 20kb by the manufacturers library kit (Illumina) [50]. 2010, 28: 511-515. The focal species therefore derives a proximate benefit from the interaction, as its proximate response to partner removal is maximally negative. e. succession. An evolutionary scenario would be forced to accept this as a fortunate but random event, but from a creationist perspective it is feasible to suggest that this may have been a triggered adaptation. Nature 380:155156, Pellmyr O, Balczar-Lara M, Althoff DM, Segraves KA, Leebens-Mack J (2006) Phylogeny and life history evolution of Prodoxus yucca moths (Lepidoptera: Prodoxidae). Nature. Honeybee Genome Sequencing Consortium: Insights into social insects from the genome of the honeybee Apis mellifera. Am J Bot 91:410415, Kawakita A, Kato M (2009) Repeated independent evolution of obligate pollination mutualism in the PhyllantheaeEpicephala association. Funct Ecol 27:509521, Lenz LW (2007) Reassessment of Yucca brevifolia and recognition of Y. jaegeriana as a distinct species. Here, none of the partners can lead an independent life. DeWayne SD, Machado CA, Molbo D, Werren JH, Windsor DM, Herre EA: The distribution of Wolbachia in fig wasps: correlations with host phylogeny, ecology and population structure. We searched the whole genome sequence to detect four types of non-coding RNAs. Second, the vanilla orchid with which we are concerned is. Eight of these 13 genes either encode transmembrane proteins, or are transmembrane protein-associated; these often act as transporters of signals or substances and are expected to evolve rapidly. The dramatic difference in gene members is not due to the CYP2 or CYP mitochondrial groups, which are conserved across different insects, but mainly due to the CYP3 and CYP4 clans, which are important gene members involved in xenobiotic metabolism [39]. 1999, 14: 49-53. 2011, 7: e1002007-10.1371/journal.pgen.1002007. PubMed Science. Bootstrap branch-support values involved 1,000 pseudoreplicates. 2010, 463: 311-317. This results in an unstable . 1997, 25: 955-964. 2003. 10.1093/bioinformatics/btl097. Only one read mapped to gene AmGr9 (a Gr gene member in the honeybee), which indicated that the unmapped reads scarcely had any similar sequences in the three gene families. 10.1093/bioinformatics/bti263. 2001, 31: 1083-1093. Validation of assembly quality was fully analyzed and described above (see genome assembly). At late pupa and adult stages, expressed genes are distinctly sex-biased and the distributions of up- and downregulated male genes differ. 13.1, Table 13.1). Extreme host-specificity and endosymbiosis in a mutualistic host appears to drive this pattern. Nature. Most symbioses are obligate such as the symbiotic association of algae and fungi to form lichens. SRP029703. Throughout development, fig wasp larvae shelter in safer places than jewel wasps and honeybees, considering the double safeguards of the fig and their galls within the fig. Compatible groups were shown in the majority rule consensus tree. [http://www.repeatmasker.org]. Homologous proteins of the following species were mapped to the genome using tblastn with an E-value cutoff 1e-5: Homo sapiens (H. sap): data downloaded from [56]; Apis mellifera (A. mel): data downloaded from [57]: Bombyx mori (B. mor): data downloaded from [58]; Drosophila melanogaster (D. mel): data downloaded from [59]; and Nasonia vitripennis (N. vit): data downloaded from [60]. BI used MrBayes 3.1.2 [93]. 10.1093/sysbio/syq010. Consequently, fig wasps have far less repetitive DNA than jewel wasps, which have among the highest abundance of transposable elements in insects [18], and ants [20]. Data for this Whole Genome Shotgun project were deposited at DDBJ/EMBL/GenBank under the accession no. Bioinformatics. [http://hymenopteragenome.org/nasonia/]. Article Am Entomol 3:141145, Riley CV (1881) Further notes on the pollination of Yucca and on Pronuba and Prodoxus. Journal of Creation 33(2): 77-83. Phylogenetic analyses were conducted using maximum likelihood (ML) and Bayesian inference (BI). Proceedings of the National Academy of Sciences of the USA 100:643-648, Silliman, B. R. and J. C. Zieman. Our exhaustive search for genes of bacteria, fungi, viruses, and plants in the genome of fig wasp fails to detect any from either fungi or plants. In the latter case, we predict that male morphological reduction largely reflects reduced gene expression. 2010, 19: 147-163. These tandem repeats were also annotated using Tandem Repeats Finder (v.4.04) with parameters of Match=2, Mismatch=7, Delta=7, PM=80, PI=10, Minscore=50, and MaxPeriod=2000 [68]. There is little doubt that more such lineages will be discovered, inasmuch as one or two new mutualisms continue to be uncovered each decade. Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Fave MJ, Gadau JD, Graur D, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Munoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, et al: The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. Ecol Evol 5:47664777, Sun X-J, Xiao J-H, Cook JM, Feng G, Huang D-W (2011) Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity. 10.1111/j.1461-0248.2012.01830.x. All models with predicted proteins that included the canonical heme binding sequence were manually verified for the presence of the other key features of P450 enzymes; the gene model was corrected whenever necessary (incorrect predictions such as fusions with adjacent genes or fragmentation) or possible (when RNA-seq sequences were available). 1997, 238: 126-129. To further understand the evolutionary history and homologies between gene families of C. solmsi and other insects, we performed a phylogenetic analysis using the genes found in C. solmsi and some other insect taxa with completed genomes: A. mellifera, N. vitripennis, and D. melanogaster. PubMedGoogle Scholar. PubMed Brown indicates genes absent in the chalcid N. vitripennis and C. solmsi, but present in D. melanogaster and A. mellifera. We identified gene families using TreeFam [75] and the following steps: first, blastp was used to compare all the protein sequences of 10 species including C. solmsi. They also likely had certain pre-existing traits such as a preference for woody monocots in arid habitats, larval feeding in flower ovaries, and a specialized cutting ovipositor (Yoder, Smith, and Pellmyr 2010). The life cycle begins when a female wasp bores into a fig, which isn't . obligative mutualism biology Also known as: interdependency, obligative symbiosis Learn about this topic in these articles: description In mutualism For CEGMA (version 2.4) [19] evaluation, we used 248 ultra-conserved core eukaryotic genes (CEGs) that were widely distributed and conserved in species to assess the completeness of genome assembly and gene-set. Interestingly, two positively selected genes, CSO_003961 (rac GTPase-activating protein 1-like) and CSO_005676 (guanine nucleotide exchange factor 2), act together yet contrarily to control the activity of G proteins [26]. Mutualism refers to any ecological interaction between two (or more) different species in which all attain a benefit. Provided by the Springer Nature SharedIt content-sharing initiative. Syst Biol. PLoS ONE. One mated female (mother) fig wasp was introduced into each bagged fig to lay eggs. Proc Natl Acad Sci U S A 100:58675872, Morat P (1993) Our knowledge of the flora of New Caledonia: endemism and diversity in relation to vegetation types and substrates. Our manual annotation fails to discover significant divergences between the fig wasp and other insects in genes potentially involved in the development of compound eyes and wings (Additional file, section of development of compound eyes and wings). Mol Phylogenet Evol 21:117127, CrossRef Da-Wei Huang Show authors Genome Biology 14, Article number: R141 ( 2013 ) Cite this article 23k Accesses 76 Citations 26 Altmetric Metrics Abstract Background Fig pollinating wasps form obligate symbioses with their fig hosts. CAS Pellmyr and Krenn (2002) note that the key novel structure within yucca mothyucca plant mutualism is the female moths tentacle used to collect the pollen. Article Let us know if you have suggestions to improve this article (requires login). The fig wasp genome has a higher overall Ka/Ks ratio than other insects (mean omega values: C. solmsi, 0.039; Tribolium castaneum, 0.004; N. vitripennis, 0.026; A. mellifera, 0.028; Camponotus floridanus, 0.029; paired Wilcoxon rank sum tests: P <0.0001) (Additional file 1: Figure S3), indicating its faster proteins evolution. Genome Res. The threshold was raised when protein sequences were short and few blast hits were found. Privacy In insects, three major groups of enzymes have important functions in the processing of environmental chemicals: glutathione-S-transferases (GSTs), cytochrome P450s (P450s), and carboxylesterases (CCEs). 10.1093/bioinformatics/btg034. The draft genome of the fig wasp, and transcriptomic comparisons between both sexes at four different life stages, provide insights into the molecular basis for the extreme anatomical sexual dimorphism of this species. 2007. 1993, 186: 147-156. 1993. Thus, fig wasps appear to have acquired a few functional gene fragments and intact genes via lateral gene transfer from bacteria and viruses. Then 3L Proteinase K was added to the mixture, followed by 2h incubation at 58C. Oecologia 114:368375, Fleming TH, Tuttle MD, Horner MA (1996) Pollination biology and the relative importance of nocturnal and diurnal pollinators in three species of Sonoran Desert columnar cacti. New mutualisms continue to be discovered, and information on individual systems is rapidly growing. 2011, 29: 644-652. Smadja C, Shi P, Butlin RK, Robertson HM: Large gene family expansions and adaptive evolution for odorant and gustatory receptors in the pea aphid, Acyrthosiphon pisum. However, importantly, the fig wasp genome shows marked reductions of genes associated with environmental sensing and protection (for example, detoxification). We then carried out a local assembly of the collected reads to fill the gaps using Gapcloser. We can modify the logistic equation to model mutualism, just as we did for competition. Alignment quality was essential for estimating positive selection. 10.1006/bbrc.1997.7252. Fig wasp Gr and Or genes, but not those of jewel wasps or honeybees, appear to be under more relaxed selection as they show a higher ka/ks ratio than single copy orthologous genes (Additional file 1: Table S9). Weiblen GD: How to be a fig wasp. 1996. Samples for genomic DNA extraction were collected from June to August in 2010. Yang Z, Rannala B: Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Benson G: Tandem repeats finder: a program to analyze DNA sequences. The University of Chicago Press, Chicago, Thompson JN (2005) The geographic mosaic of coevolution. 2005, 21: 2104-2105. obligate mutualism . For a creationist, the above narrative has only one major issue: the timeline. For example, the fig wasp genome contains only four members in the clade of dietary/detoxification genes, and only two members in the clade of hormone/semiochemical processing - hymenopteran b-esterases and juvenile hormone esterases. The difference between mean Ka/Ks of Or plus Gr genes and all single-copy genes was compared using paired Wilcoxon rank sum tests. Nucleic Acids Res. Cufflinks[62] was employed to assemble the alignments into transcripts. 2006, 16: 1395-1403. We proved, under general and natural assumptions of monotony on f 1 and f 2, the existence of a domain of extinction and a domain of persistance. Most subsequent adaptation for yucca plants and yucca moths would be minimal. Google Scholar. Nucleic Acids Res. PubMed 2006, 34: W435-W439. Development of the fig pollinator C. solmsi is mapped onto the developmental stages of the fig fruit. J Neurogenet. Genome Biol 14, R141 (2013). Cook JM, Rasplus J-Y: Mutualists with attitude: coevolving fig wasps and figs. The other two classes are extremely under-represented in the fig wasp genome. Nature. 2009, 26: 2073-2086. J Plant Res 115:161168, Sanderson MJ, Donoghue MJ (1996) Reconstructing shifts in diversification rates on phylogenetic trees. The pipeline involved blastn of C. solmsi against other non-insects. 10.1073/pnas.0902213106. 2001. Origin of a complex key innovation in an obligate insectplant mutualism. PubMed Central d. lingering competition. Oecologia 78:5359, Pellmyr O (1992) The phylogeny of a mutualism: evolution and coadaptation between Trollius and its seed-parasitic pollinators. 2006, 22: 1269-1271. Nucleic Acids Res. No orthologs occur for the otherwise conserved carbon dioxide and the bitter receptors Gr genes. Murphy. Proc R Soc London, Ser B 268:11131121, CrossRef 2005, 110: 462-467. Proc R Soc B 277:27652774, Kawakita A, Mochizuki K, Kato M (2015) Reversal of mutualism in a leafflowerleafflower moth association: the possible driving role of a third-party partner. A further blastn search of the fig wasp genome against the whole bacteria database detects 12 small fragments putatively recently acquired from bacteria; their lengths range from 105bp to 1,509bp (Additional file 1: Table S14). PubMed Google Scholar. By pollinating, the moth ensures that seeds will develop. The fig wasp genome has 42 CPR genes, less than N. vitripennis (with 62 genes), but a few more than A. mellifera (with 35 genes). Ecology 80:20742084, Holland JN, Fleming TH (2002) Co-pollinators and specialization in the pollinating seed-consumer mutualism between senita cacti and senita moths. Obviously not. A de novo repeat library was also generated using RepeatModeler (v1.0.5) [71] and PILER-DF [72], and a RepeatMasker analysis against the final non-redundant library was performed again to find homologs in the genome and to classify the found repeats. In contrast, free-living insects (for example, Drosophila willistoni) have lower percentages of sex-biased expressed genes (37.6% to 43.6%) and no distinct sex bias occurs for the over-expressed gene ratio (17.2% in females and 22.8% in males) (Additional file 1: Table S12). Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih CJ, Wu WJ, Yang CC, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED, Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomasma JJ, Pamilo P, Yi SV, Heinze J, et al: The genome of the fire ant Solenopsis invicta.

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