TY - JOUR
AU1 - Bohn,, Jonas
AU2 - Halabian,, Reza
AU3 - Schrader,, Lukas
AU4 - Shabardina,, Victoria
AU5 - Steffen,, Raphael
AU6 - Suzuki,, Yutaka
AU7 - Ernst, Ulrich, R
AU8 - Gadau,, Jürgen
AU9 - Makałowski,, Wojciech
AB - Abstract The harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America. The California harvester ant Pogonomyrmex californicus is the most widely distributed Pogonomyrmex species in North America. Pogonomyrmex californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present a genome assembly and annotation of P. californicus. The size of the assembly is 241 Mb, which is in agreement with the previously estimated genome size. We were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness at a 95% level. The presented P. californicus genome assembly will pave the way for investigations of the genomic underpinnings of social polymorphism in the number of queens, regulation of aggression, and the evolution of adaptations to dry habitats. genome assembly, genome annotation, Nanopore sequencing, polygyny, social insect, Hymenoptera Introduction Ants (Hymenoptera: Formicidae) are important components of almost all terrestrial ecosystems and more than 16,000 species have been described so far (AntWeb, version 8.41, California Academy of Science, online at https://www.antweb.org; accessed on August 19, 2020). The majority of them, over 6900, belong to the highly diverse subfamily Myrmicinae ants (AntWeb, version 8.41, California Academy of Science, online at https://www.antweb.org; accessed on August 19, 2020). Currently, 40 assembled ant genomes are available at NCBI (Entrez “Genome” accessed on August 19, 2020). The harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America (Buckley 1867; Cole 1968; Snelling et al. 2009). This genus thrives in extremely dry habitats, e.g. Death Valley or Anza Borega, and evolved seed harvesting behavior independently from the Old World harvester ant genus Messor. Members of the genus Pogonomyrmex are a very conspicuous element of the deserts in the Southwest of the USA and have been studied extensively (De Vita 1979; Rissing et al. 2000; Lighton and Turner 2004; Clark and Fewell 2014; Helmkampf et al. 2016; Overson et al. 2016). Within this genus, several interesting traits have evolved, such as social parasitism, genetic caste determination, and social polymorphism in terms of the queen number (Cole 1968; Rissing et al. 2000; Julian et al. 2002). Arguably, the most widely distributed Pogonomyrmex species in North America is P. californicus (Johnson 2002). Pogonomyrmex californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny has evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies (Rissing et al. 2000; Johnson 2004; Shaffer et al. 2016). The Red Imported Fire Ant, Solenopsis invicta, and several other Formica ant species have a similar social polymorphism, which has been shown to be due to a supergene (Wang et al. 2013; Yan et al. 2020). This discovery was only possible by next-generation sequencing and the availability of genomic information for these species. Of approximately 70 described Pogonomyrmex species, only Pogonomyrmex barbatus (AntWeb, version 8.41, California Academy of Science, online at https://www.antweb.org; accessed on August 19, 2020) has its genome sequenced, assembled, and annotated (Smith et al. 2011). Five other species of this genus (Pogonomyrmex anergismus, Pogonomyrmex colei, Pogonomyrmex imberbiculus, Pogonomyrmex occidentalis, and Pogonomyrmex rugosus) have nuclear genomes partially sequenced but none have been so far processed and only raw reads are available in NCBI’s Sequence Reads Archive (SRA). Sequences of P. rugosus, P. anergismus, and P. colei have been aligned to the P. barbatus genome for a study of gene gains/losses in socially parasitic ants (Smith et al. 2015). The genome sequencing and annotation of P. californicus will result in a better understanding of genomic sequence and structural variations and evolution in Formicidae in general and in the myrmicine genus Pogonomyrmex in particular. It will also pave the way for investigations of the genomic underpinnings of social polymorphism in the queen number, regulation of aggression, and the evolution of adaptations to dry habitats in P. californicus. Materials and methods Samples and transcriptome data source The nuclear DNA was extracted from 13 haploid males from a single polygynous colony collected in 2016 from Pine Valley, CA, USA (32.819761, −116.521512; N32 49 11 – W116 31 17). Previously published transcriptome data based in parts on queens from the same population/area (Helmkampf et al. 2016) were downloaded from NCBI’s Sequence Read Archive (BioProject accession number PRJDB4319). In addition, Oxford Nanopore sequencing (MinION) was performed on RNA extracted from workers of five polygynous colonies also collected in 2016 from Pine Valley, CA, USA. These reads are accessible at NCBI with BioProject accession number PRJNA622899. Genome sequencing and assembling DNA from 13 male ants was isolated using Qiagen MagAttract HMW DNA Kit with the protocol for tissue DNA extraction according to the protocol from October 2017. DNA was extracted from the whole body and all individuals were pooled together. This resulted in 4575 ng of DNA of which 1.2 ng was used for a 10x Genomics Chromium sequencing approach. The sequencing library was prepared according to the Chromium™ Genome Library Kit standard protocol (Manual Part Number CG00022) and the Illumina HiSeq 3000 system was used to sequence the library. The quality of the produced reads was checked using FastQC software, version 0.11.5 (Andrews 2010). We performed neither filtering nor trimming on these linked-reads to avoid losing any information. We used the de novo assembler Supernova, version 2.1 (Weisenfeld et al. 2017), with the following parameters: –maxreads = 156111200 and –accept-extreme-coverage. The maximum number of reads was set to a 75× effective coverage of the genome, which was chosen based on a set of Supernova runs with different coverages to obtain optimal parameters as a trade-off between genome size, BUSCO assessment (see below), and N50 coverage (see Figure 1) and assuming P. californicus has a genome size of 244.5 Mb (http://www.genomesize.com). Subsequently, the resulting genome assembly was polished by three rounds of Pilon, version 1.23, processing (Walker et al. 2014). For this step, 678,988,626 one-hundred bp reads from an independent Illumina sequencing run from the same initial DNA extraction were added to the 269,953,173 linked-reads used for the genome assembly, bringing the number of reads used in the polishing step to almost 1 billion. For this additional sequencing standard, an Illumina protocol was used to prepare a sequencing library, which was sequenced using the Illumina HiSeq 3000 system. Figure 1 Open in new tabDownload slide Overview of the annotation workflow. The workflow includes a construction of the transcript assembly (upper part) and a pipeline for the genome annotation (lower part). The transcript assembly and annotations from related species are providing evidence for the annotation of PCGs. Figure 1 Open in new tabDownload slide Overview of the annotation workflow. The workflow includes a construction of the transcript assembly (upper part) and a pipeline for the genome annotation (lower part). The transcript assembly and annotations from related species are providing evidence for the annotation of PCGs. Transcript sequencing and assembling For transcriptome analysis, MinION long-read RNA sequencing of the entire bodies of worker ants from a laboratory colony (pleometrotic colony from Pine Valley, NJ, USA) was performed. We extracted RNA using Monarch® Total RNA Miniprep Kit (New England BioLabs GmbH, Frankfurt, D, E2010). Material was grounded in Mixer Mill 200 (Retsch GmbH, Haan, D) in a protection reagent. A quality check was performed with Bioanalyser, Nanophotometer, and Qubit. The library was prepared from 5 µg of the total RNA using cDNA-PCR sequencing kit SQK_PCS_9035_v108_revD_26.6.17 (Oxford Nanopore Technologies, Oxford, UK). The library was sequenced using MinION and the flow cell FLO-MIN107 R9 (Oxford Nanopore Technologies, Oxford, UK). ONT’s albacor software, version 2.3.1 with standard parameters, was used for base calling and only sequences that passed a standard quality check (placed in “pass” folder by basecaller) were used for further analyses. RNA Illumina reads from Helmkampf et al. (2016) were aligned employing Hisat, version 2.1.0 (Kim et al. 2015), for a genome-guided assembly. A genome-independent transcript assembly was done using Trinity, version 2.8.4 (Grabherr et al. 2011), on the next generation sequencing (NGS) RNA-Seq data, using the Trinity assembly provided by Helmkampf et al. (2016). In addition, minimap2, version 2.17 within FLAIR pipeline version 1.4, was used for aligning nanopore long reads and the Trinity assemblies to the genome. Finally, StringTie2, version 2.0.1 (Kovaka et al. 2019), was employed in order to link the different transcript assemblies filtered by a minimum FPKM of 0.14, as also performed by Helmkampf et al. (2016). Repeat annotation We used two independent pipelines for de novo repeats discovery, namely RepeatModeler, version 1.0.11 (http://repeatmasker.org/RepeatModeler/), and REPET, version 2.5 (Flutre et al. 2011). The obtained libraries were merged with Hymenoptera-specific repeats from RepBase, version 22.07 (Bao et al. 2015). TEclass software, version 2.1.3 (Abrusán et al. 2009), was used for classification of consensus sequences lacking TE-family assignment. Finally, we removed sequences sharing more than 90% identity by employing CD-HIT, version 4.7 (Fu et al. 2012). This resulted in the library consisting of 2595 consensus sequences, which were used to annotate repeats in the P. californicus genome using RepeatMasker, version 4.0.7 (Smit et al. 2013). Protein-coding gene annotation The identification of protein-coding genes (PCGs) in the newly assembled genome of P. californicus was carried out by GeneModelMapper (GeMoMa), version 1.6.1 (Keilwagen et al. 2018), followed by MAKER2, version 2.31.10 (Holt and Yandell 2011) (see Figure 1). We used annotation of four insect species (P. barbatus, S. invicta, Camponotus floridanus, and A. mellifera) to run GeMoMa. These annotations were downloaded from NCBI (see Supplementary Table S1). GeMoMa was run for each reference species separately and the results were merged using the GeMoMa annotation filter (GAF). Next, four runs of MAKER2 were used to refine genome annotation. MAKER2 was used with the following data: GeMoMa predictions, transcript assembly, transcript and protein annotations from relative species, and RepeatMasker annotation (see above). AUGUSTUS (Stanke and Morgenstern 2005), which is a part of the MAKER2 pipeline, was trained on the AUGUSTUS reference model from Nasonia for the first run and trained on the created P. californicus reference model by applying BUSCO, version 3.0.2 (Waterhouse et al. 2018), for the third run. In addition, SNAP (Korf 2004) was performed for the last three MAKER2 runs and trained on Hidden Markov Model (HMM) reference models from gene predictions of the previous run with a minimum length of 50 amino acids and a maximum annotation edit distance of 0.25. Redundant identical transcripts and proteins within the final predictions of MAKER2 were filtered with CD-Hit, version 4.7 (Fu et al. 2012). Functional classification of PCGs The functional classification of the unique PCGs was based on sequence similarity. NCBI’s non-redundant (nr) protein database was searched using BLASTP, version 2.2.31 (Altschul et al. 1990), with default settings except e-value set to 1e−6 and coverage threshold as described below. We considered three possibilities for query and reference sequences overlap. First, the exact matches of the BLAST alignment cover more than 70% to the reference protein and the query protein. In this case, the query protein is similar to the reference protein. Second, if the query protein is just a part of the reference protein, the BLAST matches will cover more than 70% of the query sequence but less than 70% of the reference sequence. Lastly, the reference sequence might be included in the query protein. In this case, the BLAST matches are covering more than 70% of the reference protein but less than 70% of the query protein. This allowed addition of the functional description from the reference protein (annotated protein in the nr database) to the protein query (P. californicus protein predicted by MAKER2 annotation). Further downstream analysis was done with Interproscan, version 5.30 (Jones et al. 2014), for deletion of protein domain residues in classified and non-classified proteins. This analysis includes several pipelines including PANTHER, Pfam, Gene3D, SUPERFAMILY, MobiDBLite, ProSiteProfiles, SMART, CDD, Coils, PRINTS, TIGRFAM, PIRSF, Hamap, ProDom, and SFLD. Odorant receptor annotation We annotated odorant receptors (ORs) for the genomes of P. californicus and P. barbatus using manually curated OR gene models from three other ant species: Acromyrmex echinatior, Atta cephalotes, and S. invicta (McKenzie et al. 2016). Initial OR gene models were annotated with exonerate, version 2.4.0, and GeMoMa, version 1.4, and combined with Evidence Modeler, version 1.1.1 (Haas et al. 2008). All models were screened for the 7tm_6 protein domain typical for insect OR proteins with PfamScan, version 1.5. All genes were further assigned to different OR protein subfamilies by aligning the protein sequence against a set of OR subfamily reference sequences (S. McKenzie, personal communication). Protein alignment was calculated with MAFFT (Katoh et al. 2002) using the following parameters: −globalpair = T, −keeporder = T, −maxiterate = 16. The resulting alignment was trimmed employing trimal with the parameters: −keepheader = T −strictall = T (Capella-Gutiérrez et al. 2009). The phylogenetic tree of all predicted OR gene models in both ant species was inferred with FastTreeMP (Price et al. 2010) with the following settings: −pseudo −lg −gamma. Annotation of non-PCGs In addition to the PCGs, non-coding genes were annotated as well. Genes for tRNAs have been annotated with tRNAscan-SE, version 2.0.3 (Chan et al. 2019). Other types of ncRNAs, including rRNAs, snRNAs, snoRNAs, miRNAs, and lncRNAs, were predicted by Infernal, version 1.1.2 (Nawrocki and Eddy 2013). To this end, we downloaded the Rfam library, release 14.1, of the covariance models along with the Rfam clan file (https://rfam.xfam.org). Afterwards, cmscan, a built-in Infernal program, was used to annotate the RNAs represented in the Rfam library in the genome under study. Eventually, the lower-scoring overlaps were removed and the final results were used to generate the gff file containing the annotation of non-coding RNA genes. In addition, we searched for homologs of lncRNA genes from P. barbatus (based on the annotation of assembly from Supplementary Table S1) in P. californicus using Splign, version 2.1.0 (Kapustin et al. 2008). Genes where the exons detected by Splign cover more than 90% of P. barbatus lncRNA genes were classified as lncRNA genes in the P. californicus genome assembly. Comparative genomic analysis The LAST aligner, version 909, was used for whole-genome alignments (Kiełbasa et al. 2011). The P. californicus and P. barbatus genome assemblies were aligned in order to find cognate genes and to search for conserved synteny. We used BEDTools intersect, version 2.27.1 (Quinlan and Hall 2010), to compare the genome annotations and estimate the proportion of shared genes. Assembly and annotation quality assessment The nucleotide-level quality of final assembly was evaluated using Merqury software (Rhie et al. 2020). We assessed the completeness of our assembly and annotation using BUSCO, version 3.0.2 (Waterhouse et al. 2018), and DOGMA web server (Dohmen et al. 2016; Kemena et al. 2019). For BUSCO analyses, we used the Hymenoptera-specific single-copy orthologous genes from OrthoDB, version 9 (Zdobnov et al. 2017). For DOGMA, we employed the insect domain core set from Pfam, version 32. Data availability All analyses, including the assembly and the annotation pipeline, are available at http://www.bioinformatics.uni-muenster.de/publication_data/P.californicus_annotation/index.hbi. The raw sequencing data are available at the NCBI Sequence Read Archive under accession number PRJNA622899 (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA622899). Supplementary Material is available at figshare https://doi.org/10.25387/g3.13259183. Results and discussion Sequencing results We performed two rounds of NGS genomic sequencing and transcriptome sequencing using nanopore long reads technology. We obtained 339,494,313 of 100 bp (about 34 Gb) pair-end reads after standard Illumina sequencing and 269,953,173 of 150 bp (about 40.5 Gb) linked-reads using a 10x Genomics technology. Only the latter reads were used for the genome assembly. Additionally, MinION transcriptome sequencing resulted in 394,085 reads ranging between 49 and 6182 bp. N50 of the set was 660 bp and the total size of 241.6 Mb with a median read Phred had a quality score of 7.8, which translates to about 85% accuracy. Genome assembly and evaluation We assembled a draft P. californicus genome using a linked-read 10x Genomics approach and the Supernova assembler. Assuming 244.5 Mb as the genome size of P. californicus (http://www.genomesize.com), our 10x Genomics data coverage was 162×. Supernova was originally designed for de novo assemblies of human genomes (Weisenfeld et al. 2017). Nevertheless, recently it has been successfully used for non-human genome assemblies (Ozerov et al. 2018; Wang et al. 2019; Lu et al. 2020). For human genomes, a 56× coverage is recommended. However, since there is not much information on the optimal coverage for non-model genomes, we performed a series of assemblies. We resampled our sequencing data to obtain coverages ranging from 47× to 162× (see Figure 2). In order to minimize the number of artificially duplicated and missing BUSCO genes, we decided that a coverage of 75× is optimal for the assembly of the P. californicus genome (see Figure 2). Based on this assembly (75× coverage), the P. californicus draft genome consisted of 6793 contigs totaling in 240,287,203 bp with about 13 undetermined nucleotides (Ns) per 1 kb. The Supernova assembly was followed by three rounds of polishing by Pilon. This resulted in further improvement of the assembly, with a final assembly of 241,081,918 bp and a reduced number of N characters (see Supplementary Table S2). The nucleotide-level quality value of the final assembly evaluated by Merqury (Rhie et al. 2020) was 45.56, which corresponds to 99.99% accuracy (error rate = 2.78e−05). Figure 2 Open in new tabDownload slide Raw read coverage effect on assembly size and quality. Please note that assembly size is provided in mega base pairs. Figure 2 Open in new tabDownload slide Raw read coverage effect on assembly size and quality. Please note that assembly size is provided in mega base pairs. By comparing the genome assemblies of relative ants used in the annotation pipeline, our genome assembly seems to have a very small N character coverage. This means that we have shorter regions between contigs within scaffolds and less portions of input sequencing reads contain N characters (see Table 1). This impact is very much noticeable by comparing assemblies of the congeners (P. californicus and P. barbatus) in our set of insects. The N50 of the scaffolds is five times higher because of the about six times higher N character coverage in the P. barbatus assembly. Additionally, by considering the assembly size difference of 5 Mb between these two ants, we believe that we present a more complete assembly and consequently a better annotation of the P. californicus genome in comparison to the P. barbatus one. Moreover, because of a more fragmented genome assembly, the latter may include more erroneous transcript models. Table 1 Comparison of genome assemblies of related insect species Parameter . P. californicus . P. barbatus . S. invicta . C. floridanus . A. mellifera . Assembly size 241 Mb 236 Mb 399 Mb 284 Mb 250 Mb Scaffold N50 208,871 bp 819,605 bp 621,039 bp 1,585,631 bp 997,192 bp Scaffold N90 16,229 bp 117,988 bp 1,950 bp 211,219 bp 147,519 bp Number of scaffolds 6,793 4,645 66,904 657 5,644 Percent of N characters in the assembly 1.15 6.60 8.31 0.62 8.45 GC content 36.7 36.5 36.2 34.3 32.7 RefSeq assembly ID n/a GCF_000187915.1 GCF_000188075.2 GCF_003227725.1 GCF_000002195.4 Parameter . P. californicus . P. barbatus . S. invicta . C. floridanus . A. mellifera . Assembly size 241 Mb 236 Mb 399 Mb 284 Mb 250 Mb Scaffold N50 208,871 bp 819,605 bp 621,039 bp 1,585,631 bp 997,192 bp Scaffold N90 16,229 bp 117,988 bp 1,950 bp 211,219 bp 147,519 bp Number of scaffolds 6,793 4,645 66,904 657 5,644 Percent of N characters in the assembly 1.15 6.60 8.31 0.62 8.45 GC content 36.7 36.5 36.2 34.3 32.7 RefSeq assembly ID n/a GCF_000187915.1 GCF_000188075.2 GCF_003227725.1 GCF_000002195.4 With the exception of P. californicus, the data were taken from NCBI. Open in new tab Table 1 Comparison of genome assemblies of related insect species Parameter . P. californicus . P. barbatus . S. invicta . C. floridanus . A. mellifera . Assembly size 241 Mb 236 Mb 399 Mb 284 Mb 250 Mb Scaffold N50 208,871 bp 819,605 bp 621,039 bp 1,585,631 bp 997,192 bp Scaffold N90 16,229 bp 117,988 bp 1,950 bp 211,219 bp 147,519 bp Number of scaffolds 6,793 4,645 66,904 657 5,644 Percent of N characters in the assembly 1.15 6.60 8.31 0.62 8.45 GC content 36.7 36.5 36.2 34.3 32.7 RefSeq assembly ID n/a GCF_000187915.1 GCF_000188075.2 GCF_003227725.1 GCF_000002195.4 Parameter . P. californicus . P. barbatus . S. invicta . C. floridanus . A. mellifera . Assembly size 241 Mb 236 Mb 399 Mb 284 Mb 250 Mb Scaffold N50 208,871 bp 819,605 bp 621,039 bp 1,585,631 bp 997,192 bp Scaffold N90 16,229 bp 117,988 bp 1,950 bp 211,219 bp 147,519 bp Number of scaffolds 6,793 4,645 66,904 657 5,644 Percent of N characters in the assembly 1.15 6.60 8.31 0.62 8.45 GC content 36.7 36.5 36.2 34.3 32.7 RefSeq assembly ID n/a GCF_000187915.1 GCF_000188075.2 GCF_003227725.1 GCF_000002195.4 With the exception of P. californicus, the data were taken from NCBI. Open in new tab Annotation of repetitive sequences Annotation of repetitive sequences was performed in two stages. First, we built a library of repetitive elements, which was later used to annotate individual repeats and mask the genome for annotation of different gene types. We used two different de novo pipelines to compile consensus sequences of P. californicus repetitive sequences, namely RepeatModeler (http://repeatmasker.org/RepeatModeler/) and REPET (Flutre et al. 2011). After adding 1240 Hymenoptera-specific repeats from RepBase, our library consisted of 3156 sequences, which were subjected to redundancy filtering using CD-HIT with the cutoff level set at 90%. The final library contained 2595 sequences ranging from 42 to 28,331 bp (median equal to 988 bp). Three hundred forty-five sequences in this dataset were unclassified and TEclass was employed to classify these sequences. We were able to classify most of them and only 71 sequences in our TE library remained unclassified. This library was used as a TE-reference set for a RepeatMasker run. In total, 20.25% of the genome was occupied by repetitive elements, including simple repeats and low complexity regions, 3.98% and 0.53% of the genome, respectively. Not surprisingly, most of the repeats are of TE-origin and all major groups of TEs are represented in the P. californicus genome. DNA elements are most common, followed by LTR retroposons and LINEs (see Table 2). Interestingly, SINEs are very rare in the genome. However, it is possible that most of unclassified interspersed repeats are actually SINEs. Table 2 Transposable elements present in the P. californius genome TE-class . Number of elements . Fraction of the genome . LTR 15,391 4.38% LINE 9,525 1.42% SINE 596 0.03% DNA 72,737 8.69% Unclassified 13,610 1.37% TE-class . Number of elements . Fraction of the genome . LTR 15,391 4.38% LINE 9,525 1.42% SINE 596 0.03% DNA 72,737 8.69% Unclassified 13,610 1.37% Open in new tab Table 2 Transposable elements present in the P. californius genome TE-class . Number of elements . Fraction of the genome . LTR 15,391 4.38% LINE 9,525 1.42% SINE 596 0.03% DNA 72,737 8.69% Unclassified 13,610 1.37% TE-class . Number of elements . Fraction of the genome . LTR 15,391 4.38% LINE 9,525 1.42% SINE 596 0.03% DNA 72,737 8.69% Unclassified 13,610 1.37% Open in new tab Annotation of PCGs A homology-based GeMoMa annotation followed by four runs of MAKER2 resulted in 15,688 PCGs, which included 170 exact duplicates of potential transcripts. All following downstream analyses were based on a non-redundant set of 15,518 transcripts and translated proteins of this set were referred to as being unique. Additionally, 2288 unique isoforms were annotated by our pipeline based on RNA-seq data. Detailed information on the number of predicted genes at different stages is provided in Supplementary Figure S1. The missing gene numbers presented in this figure come from a BUSCO assessment on unique P. californicus transcripts. Isoforms from the MAKER annotation are referred as alternative transcripts with different intron/exon decomposition (Campbell et al. 2014). For an annotation with MAKER, it is recommended to run it at least three times. There is a drastic increase of annotation in the second MAKER run, based on the training used SNAP from filtered annotations of the first MAKER run. The high reduction of annotations in the third MAKER run is based on the training of Augustus on the P. californicus genome using BUSCO and forcing detection of start and stop codons in order to predict complete genes. The functional classification of predicted genes was done employing BLASTp against NCBI’s nr protein database. We distinguish three categories of functional annotation: (1) 8807 predicted genes were similar to a protein present in nr database with the alignment coverage on query and target of at least 70% of the protein length; (2) 3129 predicted genes were similar to an nr-protein with an alignment coverage of query or target with less than 70% of the protein length, and (3) 2047 predicted proteins where neither the query nor the target fulfill the 70% alignment coverage threshold. These predictions show some similarity to proteins but may be novel proteins as they are not clearly classified. About 1535 predicted proteins did not have any cognate protein in nr database. Therefore, in total, we classified about 90% of all predicted proteins. These include also 54 proteins that consist of multiple domains potentially representing individual proteins. This may be the result of protein fusion or erroneous gene prediction. Interestingly, from these 1535 potential orphan genes from P. californicus, 544 are apparently present in the P. barbatus genome; however, they are missing from the current P. barbatus annotation. The number of orphan genes or TSG/LSG (taxon-specific/lineage-specific genes) in P. californicus is what would be expected for two relatively closely related ant species but is much lower than what has been shown in leaf cutter ants (Wissler et al. 2013). In comparison to other relative insect genomes, we have annotated more PCGs (see Table 3). This may suggest that our pipeline resulted in some false-positive predictions. Interestingly but not surprisingly, non-classified proteins are on average significantly shorter than classified proteins: non-classified proteins are on average 108 amino acid long versus a 536 amino acid average length for classified proteins (see Supplementary Figure S2). Table 3 Comparison of P. californicus genome annotation with selected Hymenopteran genomes Species . Assembly size . Protein coding . tRNA . lncRNA . Other RNA . Total . Assembly version . Annotation version . Acromyrmex echinatior 296 Mb 11,219 159 1,210 449 13,037 Aech_3.9 100 Camponotus floridanus 233 Mb 12,512 208 1,243 696 14,659 Cflo_v7.5 102 Dinoponera quadriceps 260 Mb 11,048 212 570 493 12,323 ASM131382v1 100 Harpegnathos saltator 335 Mb 12,654 230 1,385 928 15,197 Hsal_v8.5 102 Linepithema humile 220 Mb 11,610 178 1,411 655 13,854 Lhum_UMD_V04 100 Monomorium pharaonis 326 Mb 14,019 186 3,126 1,318 18,649 ASM1337386v2 102 Ooceraea biroi 224 Mb 11,907 202 1571 970 14,650 Obir_v5.4 100 Pogonomyrmex barbatus 236 Mb 11,348 201 1,138 406 13,093 Pbar_UMD_V03 101 Pogonomyrmex californicus 241 Mb 15,688 1,180 931 79 17,878 n/a n/a Pseudomyrmex gracilis 283 Mb 11,572 193 935 558 13,258 ASM200609v1 100 Solenopsis invicta 399 Mb 14,820 227 1,376 691 17,114 Si_gnH 103 Apis mellifera 225 Mb 9,935 218 3,146 1,295 14,594 Amel_HAv3.1 104 Species . Assembly size . Protein coding . tRNA . lncRNA . Other RNA . Total . Assembly version . Annotation version . Acromyrmex echinatior 296 Mb 11,219 159 1,210 449 13,037 Aech_3.9 100 Camponotus floridanus 233 Mb 12,512 208 1,243 696 14,659 Cflo_v7.5 102 Dinoponera quadriceps 260 Mb 11,048 212 570 493 12,323 ASM131382v1 100 Harpegnathos saltator 335 Mb 12,654 230 1,385 928 15,197 Hsal_v8.5 102 Linepithema humile 220 Mb 11,610 178 1,411 655 13,854 Lhum_UMD_V04 100 Monomorium pharaonis 326 Mb 14,019 186 3,126 1,318 18,649 ASM1337386v2 102 Ooceraea biroi 224 Mb 11,907 202 1571 970 14,650 Obir_v5.4 100 Pogonomyrmex barbatus 236 Mb 11,348 201 1,138 406 13,093 Pbar_UMD_V03 101 Pogonomyrmex californicus 241 Mb 15,688 1,180 931 79 17,878 n/a n/a Pseudomyrmex gracilis 283 Mb 11,572 193 935 558 13,258 ASM200609v1 100 Solenopsis invicta 399 Mb 14,820 227 1,376 691 17,114 Si_gnH 103 Apis mellifera 225 Mb 9,935 218 3,146 1,295 14,594 Amel_HAv3.1 104 All the data are taken from NCBI’s genome database except P. californicus. Open in new tab Table 3 Comparison of P. californicus genome annotation with selected Hymenopteran genomes Species . Assembly size . Protein coding . tRNA . lncRNA . Other RNA . Total . Assembly version . Annotation version . Acromyrmex echinatior 296 Mb 11,219 159 1,210 449 13,037 Aech_3.9 100 Camponotus floridanus 233 Mb 12,512 208 1,243 696 14,659 Cflo_v7.5 102 Dinoponera quadriceps 260 Mb 11,048 212 570 493 12,323 ASM131382v1 100 Harpegnathos saltator 335 Mb 12,654 230 1,385 928 15,197 Hsal_v8.5 102 Linepithema humile 220 Mb 11,610 178 1,411 655 13,854 Lhum_UMD_V04 100 Monomorium pharaonis 326 Mb 14,019 186 3,126 1,318 18,649 ASM1337386v2 102 Ooceraea biroi 224 Mb 11,907 202 1571 970 14,650 Obir_v5.4 100 Pogonomyrmex barbatus 236 Mb 11,348 201 1,138 406 13,093 Pbar_UMD_V03 101 Pogonomyrmex californicus 241 Mb 15,688 1,180 931 79 17,878 n/a n/a Pseudomyrmex gracilis 283 Mb 11,572 193 935 558 13,258 ASM200609v1 100 Solenopsis invicta 399 Mb 14,820 227 1,376 691 17,114 Si_gnH 103 Apis mellifera 225 Mb 9,935 218 3,146 1,295 14,594 Amel_HAv3.1 104 Species . Assembly size . Protein coding . tRNA . lncRNA . Other RNA . Total . Assembly version . Annotation version . Acromyrmex echinatior 296 Mb 11,219 159 1,210 449 13,037 Aech_3.9 100 Camponotus floridanus 233 Mb 12,512 208 1,243 696 14,659 Cflo_v7.5 102 Dinoponera quadriceps 260 Mb 11,048 212 570 493 12,323 ASM131382v1 100 Harpegnathos saltator 335 Mb 12,654 230 1,385 928 15,197 Hsal_v8.5 102 Linepithema humile 220 Mb 11,610 178 1,411 655 13,854 Lhum_UMD_V04 100 Monomorium pharaonis 326 Mb 14,019 186 3,126 1,318 18,649 ASM1337386v2 102 Ooceraea biroi 224 Mb 11,907 202 1571 970 14,650 Obir_v5.4 100 Pogonomyrmex barbatus 236 Mb 11,348 201 1,138 406 13,093 Pbar_UMD_V03 101 Pogonomyrmex californicus 241 Mb 15,688 1,180 931 79 17,878 n/a n/a Pseudomyrmex gracilis 283 Mb 11,572 193 935 558 13,258 ASM200609v1 100 Solenopsis invicta 399 Mb 14,820 227 1,376 691 17,114 Si_gnH 103 Apis mellifera 225 Mb 9,935 218 3,146 1,295 14,594 Amel_HAv3.1 104 All the data are taken from NCBI’s genome database except P. californicus. Open in new tab In addition to the sequence similarity classification, we also performed further protein domain analysis with Interproscan. Ninety-one percent of classified proteins include predictions from Interproscan (see Supplementary Figure S3), while only 24% of non-classified proteins show some Interproscan predictions (see Supplementary Figure S4). The Interproscan results from classified predictions include mostly predictions from PANTHER (Protein ANalysis THrough Evolutionary Relationships), which is a protein classification system (Thomas et al. 2003) and Pfam, which is a large collection of protein domains (El-Gebali et al. 2019). These predictions promote the evidence of the classified proteins. Most predictions of the non-classified proteins are coming from MobiDBLite, which is included in the Interpro database and is used for detection of long intrinsically disordered regions (Necci et al. 2017). Based on Intrinsic disorder (ID) and missing Domains in the Pfam database, at least 10% of the human proteome are missing protein domain detections (Mistry et al. 2013). This suggests that these proteins are non-classified based on ID and/or incomplete databases. Based on the length of the non-classified proteins (see Supplementary Figure S2), they seem to include several small proteins which are very much of biological importance but not annotated by most annotation pipelines (Su et al. 2013). Odorant receptors Chemical communication and perception of olfactory cues via ORs is essential for the performance of many tasks in ant colonies (Trible et al. 2017; Yan et al. 2017). Given the biological significance of this gene family in ants, we generated in-depth annotations of OR genes in the two closely related Pogonomyrmex species, P. californicus and P. barbatus, for which assembled genomes are available. Our custom pipeline predicted 417 OR gene models in the P. californicus genome and 454 OR gene models in the P. barbatus genome. Of these, 303 gene models were complete in P. californicus and 342 were complete in P. barbatus (see Figure 3, Supplementary Table S3). This nearly doubles the number of originally predicted OR gene models (274) published for P. barbatus (Smith et al. 2011). Classifying our gene models by known OR gene families showed that most of them fall into the 9-exon (9E) family, with the next biggest families being L, V, E, and U in both P. barbatus and P. californicus (see Supplementary Table S4). This is in line with previous studies about OR genes in ants (Engsontia et al. 2015; McKenzie and Kronauer 2018). A phylogenetic analysis of Pogonomyrmex ORs showed that most ORs can be considered as single-copy orthologs, as expected when comparing two closely related species. Clusters in the gene phylogeny of multiple genes from the same species would indicate either very recent gene duplications or losses (i.e. after the species split) or could hint at assembly errors in either genome. The lack of extensive same-species clusters (largest cluster: seven genes, no other cluster exceeding four genes) thus suggests that the assemblies are of equally high quality, with few signs of gene duplication through assembly errors. Figure 3 Open in new tabDownload slide OR gene repertoires are similar between P. californicus (N = 417 genes) and P. barbatus (N = 453 genes). Most gene models have their closest relative in the other species. The gene tree shows no large clusters containing genes exclusively of one of the two species. This is evidence for a close relatedness between the species and an equally high quality of the two genome assemblies. Figure 3 Open in new tabDownload slide OR gene repertoires are similar between P. californicus (N = 417 genes) and P. barbatus (N = 453 genes). Most gene models have their closest relative in the other species. The gene tree shows no large clusters containing genes exclusively of one of the two species. This is evidence for a close relatedness between the species and an equally high quality of the two genome assemblies. Annotation of non-PCGs There are several categories of functional RNAs, including tRNAs, lncRNAs, rRNAs, snoRNAs, snRNAs, and rRNAs. Annotation of some of these is pretty straightforward thanks to the conserved secondary structure, e.g. tRNA or snRNA genes, and some are more difficult to annotate, e.g. lncRNA genes. Nevertheless, we were able to annotate more than 2000 such genes in the P. californicus genome (see Table 3). In general, numbers of non-PCGs detected in the P. californicus genome are similar to those in other insect genomes with the exception of tRNA genes exceeding more than five times the usual number of tRNA genes in insect genomes. Upon close inspection, it appeared that the excess of tRNA genes is due to unusual number of tRNAThr genes and in particular its GGT isotype. Moreover, these genes are identical to each other including 200-bp flanking regions, thus suggesting that they might be an artifact of faulty assembly and not a real biological phenomenon. Assembly and annotation quality assessment BUSCO and DOGMA programs were used for quality assessment. These programs work on different signatures in order to estimate the completeness of genome assemblies and the resulting annotation of transcripts and proteins. Duplicated transcripts and proteins within annotations of relative genomes were detected using cd-hit as it was done for the P. californicus annotation (see Table 4). In general, results from the two programs are in good agreement. The small differences are consequences of different methodology employed by the software; while BUSCO is searching for single-copy orthologous hymenopteran genes, DOGMA searches for Conserved Domain Arrangements (CDA) from an insect reference set. Our annotation of P. californicus is comparable to or exceeds annotation of published ant genomes. The only parameter that seems to be significantly different in our assembly is the level of genome duplication reported by BUSCO—over 2% comparing to less than 0.4% in other genomes. This is also reflected in the number of duplicated transcript but interestingly not in the number of duplicated proteins (see Table 4). However, at this point, it is difficult to evaluate if this phenomenon reflects the intrinsic biological feature of the P. californicus genome or results from a less-than-perfect assembly of the genome. Table 4 Comparison of completeness and quality of Hymenopteran insects used for the annotation of P. californicus Species . BUSCO genome completeness (%) . BUSCO genome duplication (%) . BUSCO transcript completeness (%) . DOGMA transcript completeness (%) . P. californicus 95.80 2.20 91.60 94.80 P. barbatus 94.20 0.10 95.80 97.60 S. invicta 85.70 0.30 94.10 96.50 C. floridanus 85.90 0.30 99.20 98.10 A. mellifera 97.10 0.20 98.60 98.30 Species . BUSCO genome completeness (%) . BUSCO genome duplication (%) . BUSCO transcript completeness (%) . DOGMA transcript completeness (%) . P. californicus 95.80 2.20 91.60 94.80 P. barbatus 94.20 0.10 95.80 97.60 S. invicta 85.70 0.30 94.10 96.50 C. floridanus 85.90 0.30 99.20 98.10 A. mellifera 97.10 0.20 98.60 98.30 BUSCO and DOGMA analyses are based on unique sets of transcripts without duplicated sequences and soft-masked genomes were used in BUSCO assessments. Open in new tab Table 4 Comparison of completeness and quality of Hymenopteran insects used for the annotation of P. californicus Species . BUSCO genome completeness (%) . BUSCO genome duplication (%) . BUSCO transcript completeness (%) . DOGMA transcript completeness (%) . P. californicus 95.80 2.20 91.60 94.80 P. barbatus 94.20 0.10 95.80 97.60 S. invicta 85.70 0.30 94.10 96.50 C. floridanus 85.90 0.30 99.20 98.10 A. mellifera 97.10 0.20 98.60 98.30 Species . BUSCO genome completeness (%) . BUSCO genome duplication (%) . BUSCO transcript completeness (%) . DOGMA transcript completeness (%) . P. californicus 95.80 2.20 91.60 94.80 P. barbatus 94.20 0.10 95.80 97.60 S. invicta 85.70 0.30 94.10 96.50 C. floridanus 85.90 0.30 99.20 98.10 A. mellifera 97.10 0.20 98.60 98.30 BUSCO and DOGMA analyses are based on unique sets of transcripts without duplicated sequences and soft-masked genomes were used in BUSCO assessments. Open in new tab Conclusions With the availability of a genome assembly and annotation for P. californicus, we can now start to analyze the genetic architecture of the intraspecific social polymorphism, differences in aggressive behavior of founding queens, and adaptations to desert life in this widely distributed harvester ant. This will also allow us to test whether a supergene, similar to other cases of intraspecific social polymorphism, is responsible for this trait variation. We should also be able to demonstrate that the evolution of OR genes in both Pogonomyrmex species proceeded at approximately the same rate without any obvious major gene losses or gains. Funding This research was partly funded by the German Research Foundation (DFG) as part of the SFB TRR 212 (NC³)—project numbers 316099922 and internal fund of the Institute of Bioinformatics. Conflicts of interest: None declared. Literature cited Abrusán G , Grundmann N, DeMester L, Makalowski W. 2009 . 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Nucleic Acids Res . 45 : D744 – D749 . Google Scholar Crossref Search ADS PubMed WorldCat Author notes †Present address: Division of Medical Informatics for Translational Oncology, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. ‡Present address: Institute of Evolutionary Biology, CSIC-University Pompeu Fabra, Marítim de la Barceloneta 39, 08003 Barcelona, Spain. © The Author(s) 2020. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
TI - Genome assembly and annotation of the California harvester ant Pogonomyrmex californicus
JF - G3: Genes|Genomes|Genetics
DO - 10.1093/g3journal/jkaa019
DA - 2021-01-18
UR - https://www.deepdyve.com/lp/oxford-university-press/genome-assembly-and-annotation-of-the-california-harvester-ant-Prbgh9N6to
VL - 11
IS - 1
DP - DeepDyve
ER -