- Research article
- Open Access
Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis
BMC Genomics volume 16, Article number: 193 (2015)
Insertion sequences (ISs) are approximately 1 kbp long “jumping” genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I (“cut-and-paste”) Mobile Genetic Elements. ISs are proposed to be involved in the reductive evolution of symbiotic prokaryotes. Our previous sequencing of the genome of the cyanobacterium ‘Nostoc azollae’ 0708, living in a tight perpetual symbiotic association with a plant (the water fern Azolla), revealed the presence of an eroding genome, with a high number of insertion sequences (ISs) together with an unprecedented large proportion of pseudogenes. To investigate the role of ISs in the reductive evolution of ‘Nostoc azollae’ 0708, and potentially in the formation of pseudogenes, a bioinformatic investigation of the IS identities and positions in 47 cyanobacterial genomes was conducted. To widen the scope, the IS contents were analysed qualitatively and quantitatively in 20 other genomes representing both free-living and symbiotic bacteria.
Insertion Sequences were not randomly distributed in the bacterial genomes and were found to transpose short distances from their original location (“local hopping”) and pseudogenes were enriched in the vicinity of IS elements. In general, symbiotic organisms showed higher densities of IS elements and pseudogenes than non-symbiotic bacteria. A total of 1108 distinct repeated sequences over 500 bp were identified in the 67 genomes investigated. In the genome of ‘Nostoc azollae’ 0708, IS elements were apparent at 970 locations (14.3%), with 428 being full-length. Morphologically complex cyanobacteria with large genomes showed higher frequencies of IS elements, irrespective of life style.
The apparent co-location of IS elements and pseudogenes found in prokaryotic genomes implies earlier IS transpositions into genes. As transpositions tend to be local rather than genome wide this likely explains the proximity between IS elements and pseudogenes. These findings suggest that ISs facilitate the reductive evolution in for instance in the symbiotic cyanobacterium ‘Nostoc azollae’ 0708 and in other obligate prokaryotic symbionts.
Insertion Sequences (ISs) are defined as genomic sequences of “cut-and-paste” mobile DNA, typically 800-1300 bp in length, which encode the protein Transposase. The Transposase protein consists of a DNA binding domain and a catalytic site with the ability to excise and to reinsert the IS DNA sequence into another position, thus moving an IS from one location in the genome to another [1,2]. In some situations e.g. during replication, duplications of IS elements occur, i.e. “copy-and-paste” rather than “cut-and-paste”, allowing the IS elements to multiply and proliferate in the genome . As incidents of cut-and-paste events are more difficult to detect than are copy-and-paste incidents, cut-and-paste transpositions are more frequent than implied by the sheer number of IS elements observed in a genome. IS transpositions commonly leave traces in the form of small, difficult to recognize, 2-20 nt direct repeats at the excision site. Insertion sequences accumulate in genomes when the evolutionary pressure is low and when decreases in population size result in genetic drift. They are known to influence the evolution of an organism e.g. through gene activation and inactivation, repression, deletions, rearrangements, recombinations, and gene transfers . ISs are considered important for driving reductive evolution in host restricted symbiont microbes [4,5]. For instance, clusters of ISs in genomic “hot spots” have been shown to be correlated with areas of gene loss and genomic recombinations in the gram positive bacterium Frankia, strains of which form mutualistic symbioses with plants [6,7]. The same phenomenon has been observed in the intracellular gram-negative bacterium Shigella flexneri  and in the eukaryotic Tetraodon nigroviridis (puffer fish) . In “recent” obligate bacterial symbionts the genome reduction is usually small, while the number of insertion sequences tends to be high. In contrast, in ancient symbiosis the norm is bacterial symbionts with small genomes and few or no ISs .
In the small floating fern Azolla  (Figure 1), the symbiotic association with the filamentous cyanobacterium ‘Nostoc azollae’ 0708 (from now on abbreviated NoAz) has developed into an extraordinary tight degree [12-14]. During leaf development in Azolla, an extracellular cavity is formed in the leaf. These cavities are in nature always occupied by filaments of NoAz. The Azolla-NoAz symbiosis is obligate for the bacterial symbiont, as NoAz is unable to grow outside the plant  and thus spends its entire life cycle within the plant. Transfer of the cyanobiont (cyanobacterial symbiont) to new plant generations is facilitated by a unique vertical transfer mechanism. Upon formation of the Azolla megasporocarp, the female seed-like reproductive structure of Azolla, filaments of NoAz are attracted to and enter into a specific ‘chamber’ in this structure, where they reside in a dormant form until germination . When the megasporocarp germinates and develops into new plantlets, the bacterial inoculum differentiates into mobile cells that colonize developing leaf cavities. Inside the cavities, they differentiate again, forming the nitrogen-fixing cell type termed Heterocysts that deliver fixed nitrogen to the plant, thereby satisfying the nitrogen need of the plant.
Due to these intriguing characters we recently sequenced the NoAz genome . Analysis of the genome revealed characteristics of a genome in severe reduction, such as a large number of pseudogenes (1670 out of 5380 genes, or 31% of all genes), a low GC content (38.4%) and genomic streamlining around functions generating critical services for the NoAz-Azolla symbiosis, such as those related to nitrogen fixation. We thus proposed that NoAz is forced into an irreversible path of reductive evolution, as also observed in other obligate bacteria-eukaryote symbioses , likely to end in a severely reduced genome as seen in ancient symbionts. The cyanobiont will eventually loose autonomy, thereby starting to resemble organelles, such as chloroplasts, that once originated from cyanobacteria . Presently, it is unknown if any NoAz genes has been transferred to the plant nucleus as was the case for chloroplasts. Secreted vesicles containing DNA has been observed in the Azolla leaf cavity,  and extant chloroplasts may have evolved from a filamentous nitrogen-fixing heterocystous cyanobacterium of the same type as NoAz [17-19], which suggests that DNA transfer is possible.
More than 600 locations with repeated sequences classified as Insertion Sequences were observed in the NoAz genome . Here we define a particular DNA sequence encoding a transposase as an “Insertion Sequence” (IS). An IS is usually present in multiple copies in a genome. We term these copies “IS elements”. Hence, IS elements are the physical copies containing the IS DNA sequence, which in turn may have accumulated mutations leading to changes in sequence and length.
IS element abundance in genomes is proposed to be linked to the high number of pseudogenes observed in some IS rich organisms [20,21]. This pseudogenization may in turn make a symbiont dependent on the host organism and thereby promote the intimacy of the symbiosis.
To further our understanding of events that shaped the eroding genome of NoAz, and the role of the ISs discovered, we examined the identity and distribution of ISs in the NoAz genome in relation to the distribution of pseudogenes. To gain perspective, the IS and pseudogene distribution in the genome of NoAz was compared to 46 other sequenced free-living and symbiotic cyanobacteria. Moreover, nine symbiotic bacteria from a wide range of eukaryotic hosts, were also included in our analysis: Wolbachia , Yersinia pestis , Frankia , Candidatus Amoebophilus asiaticus , Bordetella pertussis , Orientia tsutsugamushi , Shigella flexneri , Mycoplasma mycoides , and Onion yellows phytoplasma  (Table 1, Additional file 1).
The results show that NoAz has a high portion of its genome occupied by IS elements: 14.3%, which is just below the proportion in O. tsutsugamushi (14.7%), but higher than in any of the other symbiotic organism investigated. Still, some non-symbiotic cyanobacteria had higher or equal IS contents to that of NoAz, e.g. the unicellular Crocosphaera watsonii (23.1%) and Microcystis aeruginosa (14.3%), pointing to multiple roles and consequences of IS elements in free-living and symbiotic bacteria. The observed co-location of IS elements and pseudogenes, as well as the tendency for some IS elements to perform “local hopping” suggests a model for the role of ISs in reductive evolution which is discussed.
Using the repeat identification software, BLAST and in-house python scripts, a total of 1108 different repeated sequences of a length above 500 bp (Additional file 2 and Additional 3) were identified in the totally 67 bacterial genomes investigated (Figure 2). These 1108 repeated sequences comprised 19841 copies or fragments in the genomes. Of the 1108 repeated sequences, about half or 578 sequences (comprising 4489 copies) belonged to previously annotated ISs identified and catalogued on the ISfinder website . Of the remaining 539 sequences, the majority or 419 sequences (11794 copies) showed similarities to known IS sequences. Of the total number of repeats, fifty sequences (926 copies) appeared to be of phage origin. These were found almost exclusively in Wolbachia, O. tsutsugamushi and ‘Onion yellows phytoplasma’, with phage contents of 2-6% of the genomes. ‘Onion yellows phytoplasma’ with the smallest genome, 0.85 Mbp, still diverted 7.7% of its genome to be occupied by IS elements and phages, and was the only organism with more phage remains than IS elements.
Sixty-one sequences (2632 copies) were putatively self-replicating because of their high copy numbers and/or similarities to genes with functions related to gene replication or transposition, e.g. endonucleases, RNA directed DNA polymerases and helicases. Each group of repeats contributed to the total amount as illustrated in Figure 3A. Repeats with IS characteristics were predominant both in diversity (number of different nucleotide sequences) and abundance (copy number).
The repeats showed considerable fragmentation: of the total number of IS elements in the 67 genomes examined 31% showed a length over 95% of its reference sequence, and 37% of the repeats were less than 15% of the sequence length (Figure 3B).
Insertion sequences in NoAz
In NoAz, a total of 907 IS elements occupied 14.3% of the total genome. These IS elements were in various states of preservation, but the majority had a length ≥ 95% of its corresponding IS sequence. At the same time, a total of 1670 genes were annotated as pseudogenes in the NoAz genome, almost double the amount annotated in any other bacterium examined here.
The size of the NoAz genome with all IS elements removed is 4.67 Mbps, which is considerably larger than the IS-free genome size of its two closest free-living cyanobacterial relatives Raphidiopsis brookii (3.16 Mbps) and Cylindrospermopsis raciborskii (3.69 Mbps). However, if the 1670 pseudogenes in NoAz (covering 1.5 Mbps), are also removed the sizes start to match.
Copies of the same IS tended to cluster together in the genome of NoAz, or to be absent from a large region (Figure 4). IS elements in close proximity to each other were also more similar in nucleotide identity than were IS elements distant from each other (Figure 5, Additional file 4). In some cases, the most proximal ISs on the chromosome were also closest in terms of sequence identity (uncorrected p-distance) (Figure 4, NoAz_R_21).
As seen in the graphical representations of IS element and pseudogene positions in the NoAz genome these are frequently located in proximity to each other (Figure 1D). This is to some degree due to the tendency for IS elements, many of which are pseudogenes, to cluster (together) in the genome. However, it is apparent that both other IS elements and regular genes are pseudogenized in the vicinity of IS elements (Figure 6A-D). Exceptions are genes that are presumably critical to symbiotic functions, which are maintained intact despite their proximity to presumably active IS elements (Figure 6E).
Insertion sequences in other cyanobacteria
The high IS concentration in NoAz (14.3%) is unique among the seven multicellular and highly differentiated heterocyst-forming cyanobacteria investigated (Figure 7). In fact, NoAz contains more than three times more IS elements than these close relatives, whether symbiotic or free-living. In contrast, some more distantly related and less differentiated (non-heterocystous) relatives showed IS contents equal to or exceeding that of NoAz. The IS content of the single-celled Microcystis aeruginosa and Crocosphaera watsonii were 14.3% and 23.1%, respectively. C. watsonii is an abundant oceanic nitrogen-fixer , while M. aeruginosa is a widespread toxin producing freshwater species unable to fix nitrogen. Moreover, in some cases, closely related cyanobacteria show extreme differences in IS content. This is the case within the genus Arthrospira, with the halophilic A. maxima having an IS density of 9.2%, versus the freshwater Arthrospira platensis with merely a 0.7% IS density and also in C. watsonii (23.1%) versus the recently discovered nitrogen-fixing but symbiotic cyanobacterium UCYN-A  (lacking ISs). This is also the case for NoAz and its two close relatives C. raciborskii and R. brookii, with the former showing 133 IS hits per Mbp, comparable to 177 IS hits per Mbp in NoAz. On the other hand, the C. raciborskii fragments are truncated to a larger extent (Figure 8), making the fraction of the IS occupied genome significantly smaller (3.3%) than in NoAz. While the two Arthrospira species occupy widely different habitats (saline/freshwater) the differences in IS abundance in the two fresh-water species C. raciborskii and R. brookii cannot be attributed to different life styles.
Notably, the IS abundance in cyanobacteria does not correlate with either symbiotic state, morphology or phylogeny, ISs rather appear to be particularly prevalent in the clade comprising complex cyanobacteria with large genomes ((Figure 7, Clade 1 ). Clade 2, which consists exclusively of single-celled species with small cell size and streamlined genomes, such as marine Prochlorococcus and Synechococcus, are almost completely devoid of IS elements or DNA repeats of any kind (Figure 7).
Insertion sequences in non-cyanobacterial species
Symbiotic bacteria outside the cyanobacterial phylum showed a wide range of IS densities, 0.8-14.7%, with a median of 5.7% (Figure 2). As in cyanobacteria, genomes with a high IS frequency also tended to have a large proportion of full length IS elements. Most symbiotic bacteria also contained a high proportion of pseudogenes in their genomes, 6-12%, i.e. a considerably higher frequency than in cyanobacteria (0-5%, except for NoAz and T. erythraeum). Bacteria belonging to the gram positive genus Frankia in general contained low densities of IS elements, 1-2%, and few pseudogenes, except for the symbiont of Datisca with 5% IS elements and 7% pseudogenes.
Among the bacteria with a relatively high repeat density (>3%), full-length IS elements were in majority (Figure 3, Figure 8). Bacteria with a low density of IS elements showed a larger proportion of fragmented IS elements, with lengths <50% of the reference sequence. The occurrence of intact IS elements in IS rich genomes is particularly obvious in NoAz, where over 40% of the IS elements being full-length. Yet another example is in the difference between A. Maxima, with 9.2% IS elements, out of which 30% is full-length and its closest relative A. platensis with only 0.7% IS elements, and 1.5% full-length IS elements.
New IS elements
Full length-copies of 210 previously annotated ISs were identified in our investigation. For example, IS895  and IS100kyp from Y. pestis, IS892  from the free-living cyanobacterium Nostoc PCC 7120 and ISNpu1 – ISNpu13 found in the symbiotically competent cyanobacterium N. punctiforme . Another 362 previously annotated ISs were found as fragments, being <95% of their full lengths.
In addition, a number of previously unannotated (<95% nucleotide similarity to annotated ISs) repeats were identified in the 67 genomes (Additional file 3). For instance, 24 previously unannotated putative ISs were found in NoAz, perhaps not surprising considering its high frequency of IS elements. The found sequences in NoAz varied widely as for previously identified ISs. For example, NoAz_R_22 is 86% identical to the nucleotide sequence of the previously annotated ISAva8, while NoAz_R_21 is a “hypothetical protein” where only a stretch of 100 amino acids are similar (77%) to known ISs. The IS repeats in NoAz were most similar to previously identified ISs from close relatives: N. punctiforme (Noaz_R_10, NoAz_R_19), Anabaena variabilis (NoAz_R_2, NoAz_R_22, NoAz_R_24), or from other IS-rich cyanobacteria: Acaryochloris marina (NoAz_R_17, NoAz_R_13, NoAz_R_14) and C. watsonii (NoAz_R_11, NoAz_R_18).
Unannotated putative ISs were also found previously annotated genomes. For instance, the sequence Npun_R_21 found in N. punctiforme was present in 28 full-length copies, and WolAna_R_20, a 538 long hypothetical protein, was found in 27 full-length copies in the Wolbachia genomes. The unicellular free-living cyanobacterium M. aeruginosa contained the highest frequency of unannotated ISs, with at least thirty sequences clearly of IS character. At least one IS in NoAz, NoAz_R_12, appeared spread among close relatives. This IS701 family IS, with 28 full-length repeats in NoAz, has well-preserved (blastn scores > 1300) copies in cyanobacteria such as N. punctiforme, Anabaena cylindrica, Calothrix sp. PCC 7507 and Calothrix sp. PCC 6303.
Insertion sequences display ‘local hopping’
It has previously been reported that some ISs in Escherichia coli transpose short distances rather than moving randomly across the genome . This appears to hold true for some of the ISs in NoAz as well (Figures 4 and 5). To determine whether these patterns exist in other bacteria, linear regression tests were performed on 100 of the most frequent ISs in the investigation. Uncorrected p-distances between two IS elements in the genomes were tested as a variable dependent on the length of nucleotides that separated them (see Methods). Seventeen of the 100 ISs investigated showed significant positive relationships between separation of the genome and p-distance. These 17 ISs tended to be less similar to each other the further they were separated. On average, the uncorrected p-distance between two IS elements decreased with 0.1-1 percentage unit per Mbp as their distance from each other increased. This means that 1-10 base pairs have mutated for every Mbp of separation (disregarding reversions). Tests searching for a negative correlation were not found. A tendency to perform “local hopping” is particularly apparent in NoAz. Ten IS species in NoAz, out of twenty investigated, showed a significant negative correlation between alignment similarity and genomic separation. When the 49 757 pairs of IS elements from the 100 ISs were tested together, an average change in uncorrected p-distance of -0.48 percentage units per Mbp of distance was found using linear regression, with a p-value of 2.35e-25.
Pseudogenes in proximity to insertion sequences
A graphical representations of the genome in NoAz illustrating the comparatively high numbers of IS elements and pseudogenes, revealed a pattern with pseudogenes appearing more frequently in the vicinity of IS elements. To test if this applied to other organisms, the average number of pseudogenes near IS elements was computed in the 67 genomes and compared to the average number of pseudogenes near regular genes. The test showed a significant positive correlation increase (Wilcoxon rank sum test) in the average number of pseudogenes close to IS elements, in comparison to the average number of pseudogenes in the vicinity of regular genes. In NoAz there appeared to be, on average, >30% more pseudogenes within 5 kbp of an IS element. This enrichment dropped to below 5% at a 200 kbp distance and became undetectable at 500 kbp distance (Figure 9). Similar patterns were apparent in the majority of the investigated organisms holding a sufficient number of IS elements and pseudogenes make statistical relevant (p < 0.05) differences (Wilcoxon test), such as N. punctiforme, all Frankia species except Frankia ACN, and most Cyanothece. Orientia tsutsugamushi showed significant pseudogene enrichment in the 20 kbp closest to IS elements, while the cyanobacterium A. variabilis and the bacteria B. pertussis, C. amoebophilus, M. mycoides, S. flexneri and the Wolbachia symbionts showed the same trend but with lower significance (Figure 10).
The average enrichment of pseudogenes ranged from 20% to 200% within the first 5 kbp distance from IS elements and dropped to a fourth of this at 200 kbp distance. At 500 kbp distance from IS elements, most of the investigated organisms showed no statistically significant pseudogene enrichment Additional file 5).
When a bacterium is sheltered by a “host” organism, the host typically provide functions originally handled by the microorganism, making some genes in the symbiont superfluous. Such redundant genes may be colonized by mobile DNA elements and interrupted. The damage to the microorganism fitness is then minimal as it lives in a relaxed habitat of a eukaryotic host, plant or animal. The presence of superfluous genes may thus lead to an increase in the number of IS elements in the genome, as there may be no negative consequence and as these genes offer sites for safe insertion of IS elements. However, a large number of active IS elements in the symbiont means a greater risk for critical genes being negatively affected or even destroyed by transposition events, hampering the behaviour of the microorganisms and leading to slower growth of the symbiont. This may, up to a point, be beneficial to the host, as it may benefit from a fixed small bacterial population rather than a freely expanding one.
Decreases in IS abundance is facilitated in two ways, via i) inactivation of insertion elements by natural mutations and by pseudogenization, sometimes brought about by other IS elements, and via ii) deletions of large regions of the genome through recombination events. Bacteria seem to have a bias towards genome reduction , and the presence of many repeated elements may itself help to reduce genome sizes by providing repeated sequences able to participate in homologous recombinations.
Other investigators have focused on genetic exchange as a major factor for IS abundance, and argue that facultative symbionts should have a high IS abundance because of genetic inflow from their symbiotic partners, while obligate symbionts should have a low frequency of ISs due to their isolation. This trend was proven in an investigation of 384 bacterial genomes in . However, the organisms investigated here do not show the same trend, instead obligate symbionts harboured more IS elements than facultative symbionts. This difference may be due to a smaller and more biased set of genomes analysed here, but it could also be a result of the relaxed selection pressure that are imposed on early obligate endosymbionts before their genomes become smaller and more vulnerable to change. Since NoAz is an obligate inhabitant of a semi-open cavity shared with other microorganisms , the IS content is likely influenced both by a relaxed selection pressure and genetic exchange.
The genome of the symbiont of Azolla suggests that it may be in the middle of an evolutionary scenario of IS-mediated reductive evolution. This is concluded from the fact that it holds a high portion of IS elements and pseudogenes, while for instance its nitrogen-fixing function (and all nif genes) are still preserved . As many of the ISs in the NoAz genome are present in high copy numbers (10-80 copies), and the majority of IS elements found are full length, NoAz may have an active contingent of IS elements that continue to shape its genome. An active IS population is however not limited to NoAz: several other of the investigated bacteria, both symbiotic and free-living, show a considerable level of IS elements, and also tend to have a high proportion of full-length copies. In free-living organisms, functions lost due to IS insertions cannot be substituted by a symbiotic host, and hence, other mechanisms of surviving contingents of active ISs in the genome must be in operation. One mechanism may be to hold extended ‘safe’ genomic portions unaffected by IS element insertions e.g. non-coding regions, or to allow some degree of IS insertions, e.g. in duplicated genes of larger genomes. Many IS-rich cyanobacteria do show a large number of paralogous genes , and most of the other IS rich relatives analysed here have genome sizes above average even for Clade I cyanobacteria (Figure 7). Large and flexible genomes may also be prone to take up ‘compensatory’ genomic material from the environment via horizontal gene transfer which may outweigh the loss of productivity caused by lethal IS insertions. Compared to NoAz and non-cyanobacterial symbionts, the free-living cyanobacteria investigated here show a considerably lower number of pseudogenes, with the exception of the filamentous cyanobacterium T. erythraeum. Although differences in pseudogene annotation cannot be ruled out, such data suggest a higher sensitivity to pseudogenization in free-living organisms and that individuals with a high load of pseudogenes simply do not survive.
The tendency for pseudogenes to appear in proximity to IS elements highlights the dynamic nature of “cut-and-paste” mobile genetic elements. Genomes with high levels of intact IS elements represent snapshots of IS positions at this moment in time, and these IS elements may have transposed in recent evolutionary time. We propose here that the pseudogenes observed close to IS elements in NoAz, as well as in the other organisms, may be genomic scars from recently transposed IS elements, currently located some distance away. This behaviour of ‘local hopping’ and pseudogenization would favour reductive evolution of the genome, as regions containing superfluous genes will accumulate IS elements. This in turn will i) increase the chance of inactivation of genes in the same genomic region and ii) increase the number of repeated sequences in the region, thus increasing deletion instances of this area. Proximity between IS elements and pseudogenes also implies a higher risk for pseudogenes than for functional genes to be included in a deleted region.
Since it is not known how much of the NoAz genome that is still superfluous to the contemporary NoAz-Azolla symbiosis, it is hard to determine whether the IS concentration in the genome of NoAz is still increasing, or whether it has reached a stable IS population fit for this particular plant symbiosis at this stage. Along with the deletion of pseudogenes and superfluous regions, the number of safe spaces for IS insertion will decrease, which in turn will increase the risk for hosting active IS elements and favouring their inactivation and ultimate deletion. Our estimates predict that the genome of NoAz will decrease a conservative estimate of at least 1 Mbp, once all IS elements and pseudogenes have been removed, leaving a genome size of approximately 4.5 Mbps.
Our results show that the 24 verified or putative species of IS elements in the symbiotic cyanobacterium NoAz cover 14.3% of its genome, which is comparable to the IS density in the obligately symbiotic pathogens O. tsutsugamushi (previously Rickettsia tsutsugamushi) and Mycoplasma mycoides, but notably also to the IS frequency in the free-living cyanobacteria M. aeruginosa and C. watsonii.
The prevalence of pseudogenes is linked to the prevalence of IS elements, and we suggest that the IS-proximal pseudogenes may be the result of “local hopping” of the IS elements. We propose that this process facilitates the reductive evolution discovered recently  not only in NoAz/Azolla but also in other well-studied symbiotic bacteria such as Wolbachia and O. tsutsugamushi.
Finding and identifying repeats
To identify ISs in the investigated prokaryotic organisms, a database of potential ISs was assembled from two sources: Firstly, the program RepeatScout  was used to identify all repeated nucleotide sequences with >500 nt length in the investigated organisms. Repeats associated to non-mobile repeated genes, e.g. rRNA, photosynthesis genes and other regular genes present in multiple copies in the genome, were removed.
Secondly, all IS annotated nucleotide sequences, in total 3377 in July 2012, were downloaded from the ISfinder site , a web repository of known ISs. The repeats found by RepeatScout were named with an abbreviation of the name of the originating organism, the letter ‘R’ and a number, e.g. ‘Npun_R_21’ is a repeat from the organism N. punctiforme, the twenty-first found by RepeatScout. The ISs from ISfinder retained their original names, all starting with ‘IS’. ISfinder and RepeatScout sequences were collected into a single Fasta file. Redundancies, generated when ISfinder sequences were also detected by RepeatScout, were removed, with the ISfinder name taking precedence.
Each of the collected nucleotide sequences was used as query in a Blastn search against each of the genomes, one at a time. All areas of the genome that received hits with a Blastn expect value < 1e-6 were collected. Often several queries scored hits on the same region of a genome, together making up a “footprint” in the genome.
In the next step, each footprint was analysed to determine what repeats it consisted of. This was performed by using the footprints as queries against the database of repeats. The repeat sequence that received the highest score with the footprint as query was chosen as the most likely IS to occupy the footprint. In some cases, the best scoring repeat didn’t cover the entire footprint. The search was then repeated with the remaining footprint as query. The process was repeated until all parts of the footprints had been identified.
Next, the identity of the repeated sequences was analysed by using the repeats as queries in a Blastx search against NCBI’s nr database. Repeats that showed Blastx similarity to transposases with an expect value of E < 1e-5 were considered putative ISs. Further, repeats with no or unknown Blastx hits were considered putatively mobile DNA if they had more than five copies in a single genome. In some cases the classification of a sequence was ambiguous: sequences were then assigned to the general class of Mobile Genetic Element (MGE) based on a compound judgement of their number of copies and nature of similar sequences as determined by Blastn and Blastx.
The above process yielded a genbank file for each of the investigated genomes, where the verified and putative ISs are described with position, species and quality of identification.
Investigation of local hopping
Test for non-randomness: The probability that at least x IS elements will end up in a certain segment of the genome was computed with the binomial probability density function, which is used to find the probability of at least x successes out of n trials, given the probability p for success. In this case, a “success” occurred if an IS element were within a certain distance from another IS element. The probability p of this occurring is equal to distance divided by replicon size, if the placement of IS elements on the replicon is random. For n IS elements to end up within a certain distance from another IS element, we must get n-1 successes, since there is a 100% chance of one IS element being somewhere on the replicon, but a lower chance that more elements will be located within a certain distance from it. Likewise, the number of trials n is equal to (total number of IS elements-1). In this computation, only IS elements with lengths >70% of the full sequence were counted.
Test if uncorrected p-distance correlates with genomic distance:
If IS elements jump locally rather than randomly across the genome, closely located IS elements would reasonably have closely related nucleotide sequences, while IS elements separated by larger distances in the genome would have undergone several transposition events and would have deviated from each other due to mutations accumulated over time.
To test this, all IS elements with lengths >90% of the full sequence were aligned using the built-in Geneious 5.6.6  algorithm for multiple alignments (default parameters). This produced a matrix where the percentage of bases which are identical between two IS elements (the uncorrected p-distance) were given for every pair of IS elements. The uncorrected p-distances for each pair were plotted against the distance between the two IS elements and a linear model was fitted (lm function implemented in R ). The p-value generated by this test indicates the probability that the slope of the linear regression is really zero, i.e. that genomic distance has no impact on the uncorrected p-distance between a pair of IS elements. Although the fit was done using a linear curve, it is more likely that the patterns follows a more complex, but still negative, model.
To exemplify the genomic co-location of similar IS elements, a circular tree was drawn on top of a circle representing the NoAz genome. This tree was constructed by first aligning the NoAz_R_21 elements present in the NoAz genome (same procedure as above). Next the Geneious 5.6.6 Tree Builder was used to construct a neighbour-joining tree (Tamura-Nei distance model, IS element at position 800870 used as out group).
Pseudogenes in proximity to insertion sequences
A python program was constructed to count the number of pseudogenes within 5,10, 50, 100, 200 and 500 kbp of all annotated genes and IS elements in all contigs of the investigated organisms, using the genbank files produced above together with the original genbank files from NBCIs organism database (NCBI bacterial genome database). For each organism, the count of pseudogenes in the vicinity of non-IS genes was compared to the count of pseudogenes in the vicinity of IS elements, and subjected to the Wilcoxon rank sum test (standard parameters, double-sided) using R . Since the question at hand was whether IS elements affected the integrity of genes native to the organism, the pseudogene count and statistical test were also carried out with IS-like pseudogenes excluded from the count, leaving only “native” genes. Furthermore a count was performed on a dataset where pseudogenes within 1000 bp of the gene or IS element were omitted, since pseudogenes this close to an IS may possibly be unidentified fragments belonging to the IS element nearby. These graphs were almost identical to the first.
Mobile Genetic Element
‘Nostoc azollae’ 0708
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R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2014.
The financial support by the Swedish Energy Agency and the Swedish Research Council Formas is gratefully acknowledged.
The authors declare that they have no competing interests.
TVS wrote and operated the software used in the identification, analysis and statistical treatments of the repeated elements. He collected data about genomes and ISs, and wrote the main part of the paper. JL participated in the Blastx identification of repeat types. JN participated in the design of the project. BB conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.
Detailed information of repeats found, by genome. Organism: Name of bacterium. Abbreviation: Abbreviation of bacterium name. GC content: GC content of bacterium genome. Taxonomy ID: NCBI taxonomy ID of organism. Genome size: Size of organism genome, in Mbps. Number of contigs: Number of contigs obtained in in the sequencing of the genome. Genome closed: Have all contigs been found and assigned a position in the genome?. Number of IS hits: Number of found positions with IS elements. Number of phage hits: Number of found positions with phage remains. Number of MGE hits: Number of found positions with putatively mobile DNA. Number of DNA interacting hits: Number of found positions with DNA interacting repeats. Number of unknown but repeated hits: Number of found positions with repeated but unidentified sequences. Number of genes: Number of genes annotated for organism. Number of pseudogenes: Number of pseudogenes annotated for organism. Percentage of pseudogenes: Number of pseudogenes/number of genes. Genome occupied by ISs: Total length of all IS elements, in bp. Fraction of genome occupied by ISs: Total length of IS/Total size of genome. Genome occupied by phages: Total length of all phage remains, in bp. Fraction of genome occupied by phages: Total length of phage remains/Total size of genome. Genome occupied by DNA interacting repeats: Total length of DNA interacting repeats, in bp. Genome occupied by putative MGEs: Total length of putatively mobile repeats, in bp. Genome occupied by unidentified repeats: Total length of highly repeated unidentified sequences, in bp. Size of genome without repeats: Size of genome when all repeats are removed. Size distribution of found sequences: The size distribution of the repeats found in the organism, expressed as a percentage of the original length of the repeats (as decided by RepeatScout or ISfinder).
Table of found repeated sequences. Repeat name: Name of the repeat. Classification: indicator of the kind of repeated sequence, described at bottom of file Length: The length of the repeat as found by RepeatScout, or listed in ISfinder. Family: What IS family the repeat belongs to according to the ISfinder family classification. “-” indicate the repeat is too dissimilar to any known family to be classified into one. “LOW” indicates an expect value above 10e-3 for the blast search used to determine family. ISfinder blastx result: The best result when sequence was used as query in a blastx search against the aa sequences at the ISfinder site. ISfinder score fraction: Score from the above search, divided with the length of the query sequence. NCBI blastx result: The best result when sequence was used as query in a blastx search against the nr sequences at NCBI. NCBI blastx score fraction: Score from the above search, divided with the length of the query sequence. Size distribution of found sequences (% of total length): The size distribution of the repeats found in all organisms, expressed as a percentage of the original length of the repeat (as decided by RepeatScout or ISfinder). Sequence: The original sequence of the repeats, as decided by RepeatScout or ISfinder.
Detailed table of repeats found. Classification data: reason for assigning the repeat a certain classification. Length: Length of the repeat. Total number of hits: Total number of this repeat, in all lengths, in all organisms. Size distribution of found sequences (% of total length): Size distribution of the repeats found in all organisms. Found in species: All species of bacteria where at least one copy of the repeat was observed. ISfinder blastx hit: Best score blastx hit against a database of ISfinder amino acid sequences. Local blastn hit on repeats and ISfinder sequences: Best score blastn hit against a database of ISfinder nucleotide sequences and RepeatScout generated repeats. ISfinder blastn hit: Best score blastn hit against a database of ISfinder nucleotide sequences only. NCBI nr blastx best score hit: Best score blastx hit against NCBI’s nr database. Best score NCBI nr blastx known protein: Best score blastx hit against NCBI’s nr database that is not “unknown” or “hypothetical”. Best NCBI blastx “transposase” hit: Best score blastx hit against NCBI’s nr database that indicates sequence is transposase. Best NCBI blastx phage hit: Best score blastx hit against NCBI’s nr database that indicates sequence is of phage origin. Best NCBI blastx phage hit: Best score blastx hit against NCBI’s nr database that indicates sequence is DNA interacting. Best NCBI blastx putative MGE hit: Best score blastx hit against NCBI’s nr database indicating mobility or self-replication. Known non-MGE hit with NCBI blastx: Best score blastx hit against NCBI’s nr database that indicates that the sequence encodes a non-MGE protein. Best score NCBI blastn nt hit: Best score blastn hit against NCBI’s nt database. Sequence: Nucleotide sequence of the repeat.
Plots of uncorrected p-distance compared to genomic separation for some repeats in NoAz. Plots of decreasing uncorrected p-distance as sequences move further from each other on the chromosome. Each point in the graphs represents a pair of IS elements of the same type. Their location on the X-axis represents the number of nucleotides separating the pair, and the location of the Y-axis represents uncorrected p-distance, i.e. the fraction of nucleotides that are identical in the pair. The red line indicates most likely slope for the decrease of uncorrected p-distance with genomic distance. “Slope” indicates the lines equation, and “p” the likelihood that the slope of the line is actually zero. Since so many factors (varying “jump” distance, genomic rearrangements, mutations) influence IS placement and similarity, it is not surprising that the spread around the line is very large.
Graphs of decrease in pseudogene enrichment with increasing distance from IS elements for all investigated organisms. X-axis: Distance from gene or IS elements within which all pseudogenes are counted. Y axis: Pseudogene enrichment, i.e. (average number of pseudogenes within distance to IS elements)/(average number of pseudogenes within distance to regular genes). Green circles indicate that the difference in pseudogene enrichment is statistically significant (p < 0.05), red circles indicate that the difference is not significant.
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Vigil-Stenman, T., Larsson, J., Nylander, J.A.A. et al. Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis. BMC Genomics 16, 193 (2015). https://doi.org/10.1186/s12864-015-1386-7
- Genomic streamlining
- Insertion sequences
- Local hopping
- Nitrogen fixation