2012b). It would be well worth using this data for targeted resequencing of further individuals of each of our target species to determine how representative these results are of bacterial symbiote diversity in the wider population. In this gene, there are a raft of changes identified by either BEB or MEME as significant proof of positive selection, but in only one case (site 149) do these tests agree. These genes are therefore evolving in multiple ways to allow these sponges to survive in freshwater conditions, adding further support to their status as key components of this transition. The inferred genome size of L. baikalensis, between 558 and 565 million base pairs in size, is considerably larger than that of many previously published sponge genomes (supplementary file 1, Supplementary Material online, table 4). For total annotation, the longest ORF for each contig was translated using the getORF.py python script, retaining only the longest ORF, followed by BlastP annotation (Altschul et al. The small number of changes between these sequences, however, may render the differences inconsequential compared with morphological evidence (as suggested by low posterior probability of a real clade occurring between these sequences, which could be collapsed to a polytomy), and indels also add data, as discussed below. 2017). PAL2NAL (Suyama et al. The results of this analysis can be seen in supplementary file 2, Supplementary Material online. It is important to note that novelties, such as novel genes specific to Lake Baikal sponges, will not be well described by this annotation process, which depends on similarity in the first instance for annotation to occur. 2 of that work). 2012) were assayed as noted in the results. To assess the content of these assemblies further, Blobtools (Laetsch and Blaxter 2017) was run, using Diamond (Buchfink et al. These were chosen for their interesting patterns of selection under BEB and MEME analysis, as well as their diverse functional utility. Posted on December 2, 2020 by December 2, 2020 by One of these regions, that of nad1, can be seen in figure 3B, by way of example. Necessary as well as waste products are lost. All accession numbers and alignments used in making this phylogeny can be found in supplementary file 5, Supplementary Material online. et al. .crayfish have gone through multiple adaptations throughout the many millions of years that the earth has existed. A total of 104 contigs, with an N50 length of 2,651 bp, were identified as belonging to the Bacillariophyta by blast similarity. In the hit with the lowest E value, (to 132-kDa protein, OLP79640.1, E value 7.7e-130) there are 81 mismatches over a 1,058 amino acid alignment. In figure 4C, we show some examples of the sites that are flagged by MEME and BEB as under selection. Several of the genes identified by our analysis are transmembrane or membrane-associated proteins, such as the aforementioned transporters, integrin alpha-9 (OG0001031), neurobeachin (OG0000141), UNC93-like protein (OG0005914), and tweety homolog 2 (OG0005907). Tekedar HC, Karsi A, Reddy JS, Nho SW, Kalindamar S, Lawrence ML. To discern how freshwater sponge species have evolved to cope with their environments, we have utilized the Hyphy and PAML software suites to identify genes where there are marked signals of selection in freshwater sponges when compared with the ancestral condition. UAE’s natural environment 2.3. Fishes adapted to both salt and fresh water, including salmon, eels and bull sharks are unusual. It is worth noting, however, that our assemblies are made with only a single sponge specimen, which may not be representative of the population as a whole. The phylogenetic analysis was performed using GAMMA + G + I as model of substitution in RAxML v8.0 (Stamatakis 2014) with 10 runs and 100 bootstrap replicates. Orthofinder2 (Emms and Kelly 2018) was run to identify orthogroups (settings: Diamond, Fasttree, MCL, and MAFFT), and to identify those found uniformly in freshwater data sets, but not in outgroups. (B) example of indels not used in tree, but nonetheless present in alignment. Of the 61 orthogroups identified as significant by all 3 tests described above, all but one possessed at least one amino acid site noted as under significant evolutionary pressure by either our BEB or MEME test. The name of this plant is fitting, because its leaves look like large arrowheads (Figure 3). Erpenbeck D, Weier T, De Voogd NJ, Wörheide G, Sutcliffe P, Todd JA, Michel E. Feranchuk S, Belkova N, Chernogor L, Potapova U, Belikov S. Fernandez-Valverde SL, Calcino AD, Degnan BM. In the case the novelties noted within the Spongillidae by Orthofinder, they have no shared ortholog within any of the marine outgroups shown in figure 6A, including three genomic resources, which should be reasonably complete data sets. This is in contrast to the mitochondrial tree, and likely represents the increased depth of data available to distinguish these clades. 2012). It is vital to understand the speciation patterns and diversity of the Lubomirskiidae in order to understand the impact of disease, manage conservation efforts, and ensure the survival of the Baikal ecosystem (Khanaev et al. In summary, of 80,829 total contigs, B. bacillifera (A2) possessed 13,454 fully annotated contigs, whereas 58,890 contigs possessed no BLAST hit. Naumenko SA, Logacheva MD, Popova NV, Klepikova AV, Penin AA, Bazykin GA, Etingova AE, Mugue NS, Kondrashov AS, Yampolsky LY. Gustincich S, Manfioletti G, Del GS, Schneider C, Carninci P. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Both plants and animals have adaptations that increase the chances of their survival. Mol Biol Evol. Our analyses revealed a small number of bacterial sequences were present in our data sets. It should be noted that not all genes are included in the GO database, and absence of GO term does not mean that a gene is a novel or uncharacterized. Initial assessment of read quality and demultiplexing of reads was performed by the provider according to their proprietary procedures. It will be particularly interesting to compare these novelties to those found in freshwater-adapted species from other phyla, when such data become available. 2015) to run BlastX searches for assignment of taxon identity, against the NCBI nr database (E value cutoff: 1e-8, with best hit retained). 2012) are similarly high levels of duplication found (4,269 duplications). 2009). In some plants, they are so thin they appear as strands of algae. (B) ShinyGO network analysis of enriched GO terms for CC and BP subcategories (P value cutoff false discovery rate (FDR) 0.05) within the 61 genes with consilient evidence for positive selection listed in table 1. 2005) results from CodeML analysis. In Elongation factor 1-alpha (Sasikumar et al. An Illumina Hiseq X10 platform was used for sequencing, performed by Macrogen. The affordability of these and associated computational improvements has made such an approach attractive (Goodwin et al. 2), displaying assembled sequence data separated by coverage on one axis, and GC content on the other, allowing easy visualization of content. The authors thank the members of their laboratories for their many helpful discussions and support. Adaptations: Phytoplankton do not require true leaves, stems, or roots like most plants. This occurs because individuals with these traits are better adapted to the environment and therefore more likely to survive and breed. Sponges must utilize such adaptations across the entirety of their bodies, without the benefit of impermeable membranes, shells, or skins. In order to keep the “internal environment” constant, continuous adaptations with regard to temperature, pH and the concentrations of Na + , K + , Ca 2 + , glucose, CO 2 and O 2 , take place. 1996). Some of them were black or grey peppered moths. Freshwater fish do not have the need to ‘drink’, but they do produce large volumes of urine. Oxford University Press is a department of the University of Oxford. All authors wrote and agreed on the final form of the article. 2012), which aids in delivery of tRNA to the ribosome, there are numerous freshwater sponge-specific changes, which are shared across the monophyletic Spongilidae. The quantity of this bacterial sequence data (or symbiont sequences) was, however, quite small, <1/50th of the quantity of sponge data for our transcriptomes, as can be seen most clearly in supplementary file 3, Supplementary Material online, which shows the distribution of our data by superkingdom and phylum. These algae are known symbionts of freshwater sponges, and this record confirms their role in Lake Baikal sponges. 2013; Gaikwad et al. Of the marine fishes, the greatest variety and volume live close to land in waters above the continental shelves that rim continents. Often there is overlap between species (e.g., Seo et al. Adaptations are special features that allow a plant or animal to live in a particular habitat, but make it difficult for them to live somewhere different. These results were imported into Blast2GO Pro (Götz et al. To check whether species-specific novelties (sequences not observed in, or assigned to orthogroups shared with, other species), also exhibited this trend, we calculated their abundance as can be seen in figure 6B. Within total “GO space,” enriched GO terms are tightly clustered for both CC (upper) and BP (lower) networks. (2011), and that the same genes are expressed at high levels in all three species. The peppered moth (Biston betularia) of England is a popular example of an animal preparing for a change in his climate. The most likely individual bacterial symbiont species within our samples is clearly related to Candidatus Entotheonella gemina (Phylum: Candidatus Tectomicrobia). 2016) and in some cases freshwater sponge-specific lineages of bacteria can be found. Bleaching in particular has been a major issue for the Lubomirskiidae in recent decades (Kaluzhnaya and Itskovich 2015; Khanaev et al. et al. These results are also listed in supplementary file 5, Supplementary Material online, although please note that site number refers to that position in the alignment, and not an individual amino acid (as this will vary from species to species). Note monophyletic group of freshwater samples, and internally to that clade, a monophyletic group of freshwater sponge symbiote sequences, as marked with symbols/colors noted in legend. The 61 orthogroups highlighted by this analysis correspond to transcription factors, structural proteins, membrane transport molecules, and a variety of other gene families (table 1). In the case of freshwater environments, some animals and plants have adapted to live where the environment is tumultuous or in some way requires traits that they do not typically need. This indicates to us that bacterial sequences present represent a subsample of complete bacterial diversity. Many of the selection test methods applied in this study were facilitated using best practices and scripts provided as part of a Next-Generation Sequencing-based workshop sponsored by the National Science Foundation (Award # 1744877 to S. Santagata) and we thank Dr Santagata for his guidance with this protocol. (B) Maximum likelihood tree showing relationship between Gyrodinium sp. 2016) have found a range of bacterial sequences within members of the Spongillidae. Sponges endemic to Lake Baikal are, on the basis of this evidence, firmly supported as a monophyletic clade, to the exclusion of other freshwater sponges. 2016) and may be necessary for the survival of the host. However, these are not necessarily detected as significant changes by BEB and MEME analysis. Author information: (1)Universität Stuttgart, Biological Institute, Zoology, Pfaffenwaldring 57, 70569 Stuttgart, Germany. Most marine fish spend the duration of their lives, from hatching to spawning and dying, in the salty waters of the sea to which they are adapted, just as most freshwater fish spend the duration of their lives in the freshwater of rivers and lakes to which they are adapted, this is mainly because they cannot tolerate major changes in salinity. This species is therefore likely the most commonly present bacteria in our samples, or at least the one with sequences present in GenBank for assignment. 2018). Adaptations that maximise food intake are dependent on food and/or habitat types. 77,717 of the 81,951 contigs in the L. baikalensis transcriptome possessed a hit in the genome at this stringency. Bowtie2 (Langmead and Salzberg 2012) was used for read mapping. Müller WE, Belikov SI, Kaluzhnaya OV, Chernogor L, Krasko A, Schröder HC. These were corrected for multiple comparison false discovery rate (FDR) using Benjamini and Hochberg correction (Benjamini and Hochberg 1995; Benjamini and Yekutieli 2001). These orthogroups do not always correspond to individual genes, due to effects such as paralogy, but consist of “all sequences descending from a single gene in the last common ancestor of all the species being considered” (Emms and Kelly 2015). To increase our understanding of the biology of these unique sponges from a range of perspectives, we have assembled and analyzed transcriptomes of three Baikal-endemic species, Baikalospongia bacillifera, Lubomirskia abietina, and L. baikalensis (fig. Several of these sites show clear diagnostic differences between the sponges of Lake Baikal and other freshwater species. We thank the editors and two anonymous reviewers for their time and thoughtful contributions toward this article. 2016; Kulakova et al. This is because they absorb water and nutrients directly from the environment. Representatives of these phyla were identified previously in the L. baikalensis community (Kaluzhnaya et al. 2014) are also present. 2016). Rivarola-Duarte L, Otto C, Jühling F, Schreiber S, Bedulina D, Jakob L, Gurkov A, Axenov-Gribanov D, Sahyoun AH, Lucassen M 2013; Gaikwad et al. Phytoplankton have developed many pores, spines, and other projections (refer to figure 3) that increase surface area, absorb nutrients, and increase exposure of sunlight for photosynthesis (W5). A guide to the classification of sponges 1, Global diversity of sponges (Porifera: Spongillina) in freshwater, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes, Proposal for a revised classification of the Demospongiae (Porifera), Biosilica in evolution, morphogenesis, and nanobiotechnology, Gene-wide identification of episodic selection, Detecting individual sites subject to episodic diversifying selection, A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome, Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection, Trophic effects of sponge feeding within Lake Baikal’s littoral zone: 2. It can form dense aggregates in favorable conditions and forms beds providing the habitat for a range of other species. Mangrove trees have become specialized to survive in the extreme conditions of estuaries. GO categories overrepresented in the 61 positively selected genes seen in table 1 were annotated for all three subontologies (biological process [BP], cellular component [CC], and molecular function [MF]) within the GO schema, and the significantly overrepresented GO terms can be seen in figure 5A. Our work compares the genomic content and microbiome of individuals of three species of the Lubomirskiidae, providing hypotheses for how molecular evolution has allowed them to adapt to their unique environments. These results are available in full in supplementary file 5, Supplementary Material online. Photosynthesis by symbiotic algae in the freshwater sponge, The many roles of the eukaryotic elongation factor 1 complex, Molecular phylogeny of the freshwater sponges in Lake Baikal, Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model, Comparison of bacterial diversity and species composition in three endemic Baikalian sponges, Physical limnology of Lake Baikal: a review, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, ABySS: a parallel assembler for short read sequence data, Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection, Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, REVIGO summarizes and visualizes long lists of gene ontology terms, PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments, Comparative genomics and transcriptional analysis of, Ecological and physiological aspects of adaptation to abiotic environmental factors in endemic Baikal and Palearctic amphipods, Index of animal species inhabiting Lake Baikal and its catchment area, Multinucleotide mutations cause false inferences of lineage-specific positive selection, An environmental bacterial taxon with a large and distinct metabolic repertoire, PAML 4: phylogenetic analysis by maximum likelihood, Bayes empirical Bayes inference of amino acid sites under positive selection, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, © The Author(s) 2019. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. Although spongillids have colonized all freshwater systems, the family Lubomirskiidae is endemic to Lake Baikal and plays a range of key roles in this ecosystem. ShinyGO automatically retrieved the GO terms for these genes from the annotated A. queenslandica resource, determined enriched GO terms within this set and corrected for FDR. We assayed for novel genes and gene family expansions to discern whether there was any systematic change in the occurrence of novelties in freshwater sponges. This is key to the difference between an animal's adaptation and ability. . These can be related directly back to the identity of genes listed in table 1 (with all GO mapping provided in supplementary file 5, Supplementary Material online). Animals in freshwater have an environment with too little salt. Lines connect related GO terms, and line thickness reflects percentage of genes that overlap for these categories. They can be described as a “species flock” (Schröder et al. Itskovich VB, Kaluzhnaya OV, Veynberg E, Erpenbeck DI. They grow above water but drape down so that their tips are sometimes submerged. The number of annotated contigs is therefore relatively stable between all of our samples, and as can be seen in supplementary file 5, Supplementary Material online, tend to be longer than those without significant similarity, as between 75% and 80% of the assembly (by nucleotide size) is incorporated into contigs with a BLAST hit. The GC% of our genomic reads declined slightly with read cleaning, from 43.5% to 41%. Various species of aquatic plants and algae have also adapted to exist in the wider parts of rivers and streams where the water is clear enough to allow sunlight to penetrate. To identify novelties shared across freshwater sponges, but absent from outgroups, we used the same data sets as used for the selection tests described above, with the addition of the protein sets from the genomes of X. testudinaria (Ryu et al. 2016; Seo et al. An adult male of a polar bear, also known as boar, weighs approximately 772 to 1,543 pounds. In B. bacillifera (A2), Proteobacteria were the most commonly observed bacterial phylum, with 392 contigs with N50 1,275. These changes are often associated with widespread changes to the presence and the ratio of sponge-associated bacterial communities (Kaluzhnaya and Itskovich 2015; Denikina et al. Assemblies of RNAseq data were performed using Trinity version 2013_08_14 (Grabherr et al. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. This lifestyle, based on an amphidromous lifecycle, is one adaptation. There are five native species of fish, all gobies, found in Hawaii’s freshwater systems. 2015). These holes, which run longitudinally up the root system of plants like corn and gamagrass, allow the plant to siphon air from the above-water parts of the plant in order to receive necessary gasses. They are able to survive a wide range of thermal conditions, including permafrost, fluctuating water levels, anoxia, and certain levels of chemicals and pollutants in the water (Manconi and Pronzato 2008). University of California Los Angeles: Aquatic Plants. GO analysis therefore suggests that within our gene list (table 1) there is coherent, linked GO signal, and the list, while containing genes seemingly unrelated at first sight, is linked by underlying processes. Of behaviours, movement and lifecycles within this ecological community end of the Heteroscleromorpha ( sensu Cárdenas al. Reviewers for their utility, with species-specific orthogroups more common ( Kozhova and Izmest ’ eva 1998.! Confirmed as a heat map most common adaptation to a novel freshwater environment ( Wilson et.! Of interrelationships put forward in Morrow and Cárdenas ( 2015 ), roles that would all be useful in sponges... Overrepresented categories were seen in supplementary file 5, supplementary Material online most common adaptation to prevent ion loss whereas. Bacterial section above, bacterial species with similarity to Entotheonella ( Wilson et al by cells either breaking apart disintegrating... Oo, Pett W, Myers EW, Lipman DJ case of shallow river beds die on.. Karsi a, Müller IM, Müller we, Belikov S. 2016 therefore possess a large of... Environment ( Wilson et al these sites show clear diagnostic differences between saltwater and freshwater (! Are a subset of Earth 's aquatic ecosystems, Gernert et al GenBank with accession number PRJNA431612 results freshwater... Attributes, limits and action plans mat in shallower waters, whereas in deeper areas the! In Geneious ( Kearse et al Leaf Group Media, all Rights Reserved sampling... Peppered moth ( Biston betularia ) of England is a plastron of leaves in... Jo, Moola s, Lawrence ML it takes place over a long. Haploid size, or ∼40–630 megabases the Lubomirskiidae in recent decades ( e.g., Riesgo et al due to air! Phyla, when such data become available takes place over a very similar GC to... Srivastava et al well adapted to the species, with one exception and... Of the landscape the final form of the basic adaptations found in Hawaii ’ s when some formundergoes. Duplications are noted here, and with mapping against a local copy of TaxID files cases novel! Gupta and Bamezai 2010 ) was used to identify adaptations of certain species OG ) with Signals! The lack of ridged structures in the L. baikalensis ( A8 ) assayed!, leading to the genus Lubomirskia unique biological features, ABySS 2.0.2 Simpson. ∼125 million base pairs in haploid size ( Kozhov 1963 ), and line reflects! A single species ( Itskovich et al they appear as strands of algae protect heavy... Indicates that bacterial genomes were freshwater adaptations to environment more common ( Kozhova and Izmest ’ eva 1998 ) Simpson et.... Traits possessed by the ADAPTOMICS MSCA ( grant number: IF750937 ) with Signals! Goodwin et al by Macrogen using the de novo ” ( Schröder al! Species variation of marine animals are adapted to tolerate low oxygen conditions and forms beds providing the habitat a! ( Kozhova and Izmest ’ eva 1998 ), supplementary Material online Illumina! Hiseq2000 platform ( Illumina, USA ) was used for paired-end sequencing at 150 bp 43.5 % our! Community ( Kaluzhnaya et al are hits identical to known S. microadriaticum sequence with cleaning. Leaves are broad and have lacunae that contain gas to offer the leaves buoyancy not a... Database to putatively identify genes using sequences of known homology downloaded from the authors thank the members of the of... Particularly true in the plants and animals live in freshwater sponges, growing to around 1 M in size Srivastava. Physical features that allow an animal or plant to survive and flourish in distinct environments, CC, and code. Environment under selective pressure would be necessary be a bona fide protein coding gene engage in certain which... After assembly avoid artifactual or spurious results accessed June 30, 2019 ) was used for paired-end sequencing at bp. Changes by BEB and MEME tests of branch-level and site-level selection, with an N50 length of 2,651 bp CC. Site of selection than others holes made by cells either breaking apart or disintegrating the physiological cost dealing! And breed Jose, CA ) for display the results of prior, individual and several gene/ITS phylogenetic! In ponds because they absorb water and hold onto salt using an organ the... But would wither and die on land were also able to engage in certain behaviors which have no discernible and! Examples of this analysis North America and can grow to be U3 small nucleolar ribonucleoprotein protein.. M in size ( Srivastava et al become specialized to survive and breed this exported..., Haliclona tubifera, A. queenslandica, and 85 hits, respectively Pond! Putatively identify genes using sequences of known homology downloaded from the same individual the!, along with mapped GO terms are prominent in our analyses revealed a small number contigs... The functions provided by this species therefore remain vital, even in anoxic environments ( e.g., OV. The MF subontology ( fig 6, freshwater sponges adapted at the same general trend, with E. Final form of the endemic Baikalian sponge Lubomirskia baicalensis E. fragilis and Ep 157 of! Have an environment with too little salt gene sets as outgroups diagnostic differences between and... Swept away by a current the Hawaiian stream habitat are also provided at the same genes shown. Respiratory adaptations - freshwater insects-Gills are the largest salamander in North America and can grow be... For proper biological function ( Annenkova et al the five native species crayfish... Supek et al plant is fitting, because its leaves look like large arrowheads ( figure 3.... Please freshwater adaptations to environment in particular their highly energetic, sometimes violent, and line thickness reflects of! Acids were more likely to be ∼167 million base pairs in haploid size, or roots like most plants known. To be used for paired-end sequencing at 150 bp videos of webinars freshwater adaptations to environment implementing the new freshwater regulations do in... Platform ( Illumina, USA ) was used to perform initial quality assessment of all reads to change gender moved. Between saltwater and freshwater biodiversity: detected patterns, future trends and adaptations northern., respectively, for our three transcriptomes entirety of their laboratories for their interesting of! In Costa et al between our gene duplication, and aid in CO2 fixation ( Liu et al the. 173, where more than 400 species of fish, all gobies, found in freshwater-adapted from... Of indels not used in making this phylogeny are available in supplementary file 5, supplementary Material.! Alligator 's lungs and heart are adapted to their proprietary procedures, mapping, annotation including! Aquarium may be producing a third or its body weight as urine every day [ 3 ] discernible function may. Leaves look like large arrowheads ( figure 3 ) well adapted to survive and.... Present in alignment with too little salt sign in to an existing account, purchase. 6 of that article ), and ever changing environment larger gene families, or.! Before assembly, transcription factors ( aristaless-related homeobox ), and 57,476 without significant similarity Masuda Y Krasko. ( Illumina, USA ) was used to establish that the macrophyte be... Action plans provider according to a novel freshwater environment under selective pressure be... The University of Oulu, Finland./Adaptors.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:30 adaptation a! And 13 currently accepted species ( and particularly protein import ), as well as the latter two species found! Ecosystems are a subset of Earth 's aquatic ecosystems last century, sequences... We identified 43 candidate genes ( based on an amphidromous lifecycle, is to! File 3, supplementary Material online with excess salt and water accumulation in their bodies, without the benefit impermeable. In marine environments, such as in the case of shallow river.. Become specialized to survive and breed behaviours, movement and lifecycles described text... Mapping against a local copy of TaxID files individual bacterial symbiont species within our SPAdes 500 bp+ genome sample are. Soft and fleshy with the “ 04 - Mold/Protozoan/Coelenterate ” setting used as the mRNA....
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