Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective

BACKGROUND

The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences.

RESULTS

Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries.

CONCLUSIONS

The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus

Despite increasing sequencing efforts, numerous fish families still lack a reference genome, which complicates genetic research. One such understudied family is the sand lances (Ammodytidae, literally: 'sand burrower'), a globally distributed clade of over 30 fish species that tend to avoid tidal currents by burrowing into the sand. Here, we present the first annotated chromosome-level genome assembly of the great sand eel (Hyperoplus lanceolatus). The genome assembly was generated using Oxford Nanopore Technologies long sequencing reads and Illumina short reads for polishing. The final assembly has a total length of 808.5 Mbp, of which 97.1% were anchored into 24 chromosome-scale scaffolds using proximity-ligation scaffolding. It is highly contiguous with a scaffold and contig N50 of 33.7 Mbp and 31.3 Mbp, respectively, and has a BUSCO completeness score of 96.9%. The presented genome assembly is a valuable resource for future studies of sand lances, as this family is of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes.

When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials

The autonomous transposable element LINE-1 is a highly abundant element that makes up between 15% and 20% of therian mammal genomes. Since their origin before the divergence of marsupials and placental mammals, LINE-1 elements have contributed actively to the genome landscape. A previous in silico screen of the Tasmanian devil genome revealed a lack of functional coding LINE-1 sequences. In this study we present the results of an in vitro analysis from a partial LINE-1 reverse transcriptase coding sequence in five marsupial species. Our experimental screen supports the in silico findings of the genome-wide degradation of LINE-1 sequences in the Tasmanian devil, and identifies a high frequency of degraded LINE-1 sequences in other Australian marsupials. The comparison between the experimentally obtained LINE-1 sequences and reference genome assemblies suggests that conclusions from in silico analyses of retrotransposition activity can be influenced by incomplete genome assemblies from short reads.

A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)

Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage.

Crystallization during volume reduction of solutions with a composition corresponding to that in the collecting duct: the influence of hydroxyapatite seed crystals and urinary macromolecules

To examine the effect of hydroxyapatite (HAP) seed crystals and urinary macromolecules on the crystallization under conditions similar to those in the collecting duct, we evaporated 100 ml samples of salt solutions with an ion composition assumed to correspond to that in the collecting duct without and with HAP seed crystals. The crystallization in seeded solutions was assessed both with and without dialysed urine (dU). After evaporation the number and volume of crystals were recorded in a Coulter Multisizer and the crystal morphology examined with scanning electron microscopy (SEM) and X-ray crystallography. Addition of HAP crystals was apparently followed by an approximately 15-20% increase in heterogeneous nucleation of calcium oxalate (CaOx). In these experiments SEM and X-ray crystallography showed a high percentage of CaOx in the precipitate. In samples reduced to 40-69 ml, addition of dU to the collecting duct solution containing HAP seed resulted in a greater mean (SD) number of crystals; 3895 (1841) in samples with dU and 1785 (583) in samples without. This was mainly explained by an increased mean (SD) number of small crystals. The mean crystal volume was 17.8 (1.1) and 34.3 (9.1) in samples reduced to 40 69 ml with and without dU, respectively. This might reflect the inhibitory effect of dU on the growth and/or aggregation of the CaOx-CaP precipitate or a promoted nucleation resulting in a large number of small crystals. It is concluded that calcium phosphate formed above the collecting duct might induce heterogeneous nucleation of CaOx at lower levels of the renal collecting system, and that urinary macromolecules are powerful modifiers of these processes.

The effect of pH changes on the crystallization of calcium salts in solutions with an ion composition corresponding to that in the distal tubule

The effect of pH changes on the crystallization in solutions with an ion composition assumed to correspond to that of urine in the distal part of the distal tubule was examined by recording the number and volume of crystals with a Coulter Multisizer and by studying the crystal morphology with scanning electron microscopy at different degrees of volume reduction. The experiments were carried out with 100 ml samples at different starting pH values without and with 20% of dialysed urine (dU). The number of crystals increased in response to the volume reduction. In solutions without dU, 100 or more crystals with a diameter in the range 2.4-45 microm were observed already at a volume reduction of 40% when the initial pH was 7.28. For solutions with a pH of 5.80 and 6.45 the corresponding values were 60% and 80%, respectively. In the presence of dU, an appearance of crystals was recorded at volume reductions of less than 20%. In solutions with an initial pH of 5.80 and 6.45, the crystal number was greater with dU than without; such a difference was not recorded at pH 7.28. In samples containing dU, the mean crystal volume (MCV) varied very little when the sample volume was reduced. The same was found in solutions without dU when the initial pH was 5.80 and 7.28, whereas the MCV was greater in the samples with pH 6.45. Scanning electron microscopy of solutions reduced to 30-40% of the original volume showed that calcium phosphate had formed in solutions with a starting pH of 7.28 and 6.45. In solutions with pH 5.80 calcium oxalate crystals were observed with calcium phosphate.

Crystallization during volume reduction of solutions with an ion-composition corresponding to that in the distal tubuli

The effect of macromolecules on the crystallization in solutions with an ion-composition and a pH corresponding to that of urine in the distal part of the distal tubuli was examined by recording the number and volume of crystals in a Coulter Multisizer and by studying the crystal morphology with scanning electron microscopy at different degrees of evaporation. The experiments were carried out with 100 ml samples of salt solutions with and without different concentrations of dialysed urine (dU) from normal subjects. Addition of dU resulted in a greater number of crystals and a reduction in the mean crystal volume (MCV). Under the experimental conditions, the maximal effect of the macromolecules appeared to be accomplished in solutions with an initial dU concentration of 10%. The precipitate was strongly suggestive of calcium phosphate (CaP) as shown by scanning electron microscopy and Raman spectroscopy. This conclusion was further supported by the ion-activity products of calcium oxalate (CaOx) and different CaP salts in those samples in which crystal formation was recorded. The obtained results give support to the view that macromolecules might exert a promotive effect on the nucleation of CaP. The macromolecules also appear to counteract the development of large CaP crystals, but whether this is due to an inhibition of crystal growth, an inhibition of crystal aggregation or both could not be concluded from these experiments. The way in which CaP crystals initially form in the nephron might be of importance for the subsequent crystallization of CaOx and the formation of CaOx containing stones.

The influence of hydroxyapatite seed on the crystallization induced by volume reduction of solutions with an ion composition corresponding to that in the distal tubule at different pH levels

OBJECTIVE

To simulate the crystallization process that might occur in the nephron segment from the distal part of the distal tubule (DTd) to the end of the collecting duct (CD), we evaporated salt solutions with an ion composition assumed to correspond to that in the DTd.

MATERIAL AND METHODS

100-mL samples of DTd solutions with and without dialysed urine (dU) and with hydroxyapatite (HAP) seed crystals were evaporated to a final volume of 10-20 mL at different starting pH levels. After evaporation, the number and volume of crystals were recorded in a Coulter Multisizer and the crystal morphology examined by scanning electron microscopy and x-ray crystallography.

RESULTS AND CONCLUSIONS

Volume reduction of solutions with a pH of 6.5 resulted in a crystallization of calcium phosphate (CaP) and calcium oxalate (CaOx). An increased fraction of CaOx in the precipitate was observed when the pH was decreased. In solutions with an initial pH of 5.5, 6.0 and 6.5, the number and volume of crystals were smaller in samples analysed after 60 min than in those analysed immediately after the evaporation. This might reflect dissolution of crystals, as expected, most pronounced in the most acid solutions, but apparently counteracted by dU. The results obtained in these experiments suggest that CaP formed high in the nephron might induce heterogeneous nucleation of CaOx when subjected to the lower pH levels and increased supersaturation with CaOx encountered in the CD. With an alkaline pH in the CD, a pronounced crystallization of CaP can be anticipated.

Is citrate an inhibitor of calcium oxalate crystal growth in high concentrations of urine?

The effect of citrate on calcium oxalate (CaOx) crystal growth was studied in a system in which series of samples containing [45Ca]calcium chloride were brought to different levels of supersaturation with various concentrations of oxalate. The crystallization was assessed by measuring the amount of isotope remaining in solution 30 min after the addition of CaOx seed crystals to samples containing citrate in concentrations corresponding to those in final urine. The experiments were carried out both in pure salt solutions and in solutions with dialysed urine. Increased concentrations of citrate resulted in a reduced crystallization of CaOx in both the presence and absence of dialysed urine, but with the lowest rate of crystallization in the samples containing urine. The increased concentration of 45Ca remaining in solution reflected a reduced crystallization, which could possibly be explained both by a reduced supersaturation and by an increased inhibition of CaOx crystal growth. The direct effects of citrate on CaOx crystal growth were assessed by calculating the ion-activity product of CaOx (APCaOx) at corresponding degrees of crystallization. The APCaOx recorded at a 30% reduction of the amount of isotope in solution increased with increasing concentrations of citrate between 1.0 and 1.5 mmol/l samples both with and without dialysed urine. These findings indicate that citrate has a weak direct inhibitory effect on CaOx crystal growth, which adds to the reduced growth rate brought about by urinary macromolecules and a decreased supersaturation.

Crystallization properties in urine from calcium oxalate stone formers

PURPOSE

We determine whether stone formers and normal subjects can be distinguished in terms of supersaturation with calcium oxalate, and inhibition of calcium oxalate growth and aggregation.

MATERIALS AND METHODS

An estimate of the ion activity product of calcium oxalate was obtained from the analysis of calcium, oxalate, citrate and magnesium in 16-hour urine samples obtained between 6 a.m. and 10 p.m. The inhibition of calcium oxalate crystal growth and aggregation was assessed in 8-hour urine specimens obtained between 10 p.m. and 6 a.m.

RESULTS

The ion activity product of calcium oxalate was higher and inhibition of crystal aggregation was lower in stone formers than in normal subjects. Inhibition of crystal growth was lower only in male stone formers. Quotient 1 (10(2) x ion activity product of calcium oxalate/inhibition of crystal growth), quotient 2 (10(2) x ion activity product of calcium oxalate/inhibition of crystal aggregation) and quotient 3 (10(4) x ion activity product of calcium oxalate/[inhibition of crystal growth x inhibition of crystal aggregation]) were significantly higher in stone formers.

CONCLUSIONS

The biochemical risk situation in calcium oxalate stone formers can be summarized by quotient 2 or 3.

The effects of citrate and urine on calcium oxalate crystal aggregation

The rate of crystal sedimentation in a suspension of calcium oxalate monohydrate (COM) crystals was determined spectrophotometrically in the presence and absence of dialysed urine and citrate. A reduced rate of crystal sedimentation after stirring was recorded in suspensions containing citrate in concentrations between 0.33 and 1.67 mmol/l. The sedimentation rate was reduced in the presence of a 0.3-3.3% concentration of dialysed urine, with increased inhibition of crystal sedimentation when the concentration of urine was increased. A comparison of the inhibition of COM crystal sedimentation in whole urine and in dialysed urine from normal subjects and stone-formers disclosed significantly higher values (P < 0.05) in the dialysed urine. The results support previous observations that physiological concentrations of citrate might efficiently inhibit the aggregation of COM crystals. Furthermore even low concentrations of both whole urine and dialysed urine are apparently very efficient inhibitors of COM crystal aggregation.

Effects of citrate on the different phases of calcium oxalate crystallization

Urinary citrate appears to be an important factor in the crystallization process of calcium oxalate and calcium phosphate. The urinary excretion of citrate was found to be significantly lower in patients with calcium oxalate stone disease as compared with normal subjects, and about 30 per cent of the calcium stone formers can be considered as hypocitraturic. The lowest excretion of citrate was recorded in urine collected during the night. Citrate has significant effects on supersaturation with respect to both calcium oxalate and calcium phosphate, it also inhibits the growth of these crystals. In addition, citrate appears to be capable of inhibiting the aggregation of crystals composed of calcium oxalate, brushite, and hydroxyapatite. The heterogenous growth of calcium oxalate on calcium phosphate is also counteracted by citrate. As a consequence of the crucial role of citrate in these processes, stone prevention with alkaline citrate has become an attractive form of treatment in patients with recurrent stone formation. Single evening dose administration of sodium potassium citrate resulted in an of sodium potassium citrate resulted in an increased excretion of citrate, reduced levels of the calcium/citrate ratio as well as supersaturation with respect to calcium oxalate and a decreased rate of stone formation. However, conflicting results of stone preventive treatment with alkaline citrate have been reported by different groups, and long-term follow-up of patients treated in a randomized way is necessary to definitely assess the efficacy of alkaline citrate.

Effects of urinary macromolecules on the crystallization of calcium oxalate

The macromolecular fraction of urine with a molecular weight above 3,000 was isolated by dialysis. In the dialysed urine the rate of calcium oxalate (CaOx) crystallization was reduced both in the presence and absence of CaOx seed crystals. There was a clear relationship between crystallization and the relative concentration of the dialysed urine, with the highest crystallization propensity at the lowest concentration of macromolecules. Dilution of dialysed urine also affected crystal size distribution, with a predominance of small (2.8-4.5 microns) crystals in 100% dialysed urine and of large (5.6-14.0 microns) crystals in 5% dialysed urine. This is consistent with a macromolecular inhibition of both crystal growth and aggregation. Analysis of the crystal size distribution 120 min after supersaturation of whole urine to a level at which approximately 100 crystals in the size interval 3.5-5 microns were detected in a Coulter counter surprisingly disclosed a higher mean crystal volume in urine samples from normal subjects than from stone formers. This gives support to the assumptions that macromolecules might be of importance during the initial phase of CaOx crystallization and that urine from stone formers and normal subjects might be different in this respect.

Inhibition of calcium oxalate crystallization in urine

Chromatographic separation of urine showed inhibition of calcium oxalate (CaOx)-crystallization among substances with both large and small molecular weights. Ultrafiltration showed that approximately 80 per cent of the inhibiting activity, as determined in 2 per cent urine, originated from substances with a molecular weight above 1,000. Dialysed urine was diluted to 7.5 mmol of creatinine per 1 and supersaturated with respect to CaOx. The rate of crystallization in these samples was slower in normal subjects than in stone formers (p less than 0.05). The inhibiting activity in diluted urine from the two groups did not differ and neither did the concentration of alcian blue precipitable polyanions. From measurements in diluted urine it was apparent that inhibition was demonstrable with a urine concentration as low as 0.3 per cent.

[14C]Oxalate absorption by normal persons, calcium oxalate stone formers, and patients with surgically disturbed intestinal function

Intestinal absorption of oxalate can be judged from the urinary excretion of orally administered [14C]oxalate. Fifteen normal subjects, 21 patients with "idiopathic" calcium oxalate stone disease and a high oxalate excretion, four patients operated with ileocecal resection, and seven patients operated with jejunoileal bypass were so investigated. We saw no significant difference in the amount of isotope excreted by normal subjects and idiopathic stone formers; 13.6% (SD 5.9%) and 14.4% (SD 6.5%), respectively, of the administered dose was accounted for in the urine. The patients with resection or bypass showed a quite different pattern of isotope excretion, and 18.3% (SD 7.0%) and 36.8% (SD 14.0%), respectively, of the isotope was accounted for in the urine.

[14C]Oxalate absorption by normal persons, calcium oxalate stone formers, and patients with surgically disturbed intestinal function

Intestinal absorption of oxalate can be judged from the urinary excretion of orally administered [14C]oxalate. Fifteen normal subjects, 21 patients with "idiopathic" calcium oxalate stone disease and a high oxalate excretion, four patients operated with ileocecal resection, and seven patients operated with jejunoileal bypass were so investigated. We saw no significant difference in the amount of isotope excreted by normal subjects and idiopathic stone formers; 13.6% (SD 5.9%) and 14.4% (SD 6.5%), respectively, of the administered dose was accounted for in the urine. The patients with resection or bypass showed a quite different pattern of isotope excretion, and 18.3% (SD 7.0%) and 36.8% (SD 14.0%), respectively, of the isotope was accounted for in the urine.