Rate Of DNA Loss Research Articles

Genome downsizing after polyploidy: mechanisms, rates and selection pressures.

An analysis of over 10000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70Mb/million years, 4-482bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO2 uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales.

Entecavir combining Chinese herbal medicine for HBeAg-positive chronic hepatitis B patients: a randomized, controlled trial.

Traditional Chinese medicine (TCM) is widely accepted and prescribed in China alongside Nucleoside analogs (NAs). In this double-blind, placebo-controlled, randomized, multi-center trial, we evaluated whether entecavir (ETV) plus TCM formulas Tiao-Gan-Yi-Pi granule (TGYP) and Tiao-Gan-Jian-Pi-Jie-Du granule (TGJPJD) increase the rate of hepatitis B e antigen (HBeAg) loss in Chinese patients. 596 eligible participants were randomly assigned, in a 1:1 ratio, to two study groupsin this 108-week trial: The experiment group was assigned ETV plus the TCM formula. The control group was assigned ETV plus a TCM placebo. We compared the rate of HBeAg loss by the end of week 108 between the two arms as the primary outcome. Secondary outcomes included hepatitis B surface antigen (HBsAg) level, proportion of undetectable HBV-DNA, and liver enzymes (ALT, AST, GGT) at week 108. The combination therapy achieved superior HBeAg loss at 108weeks, without additional adverse events. The rate of HBeAg loss at week 108 was 37.54% (95% CI 31.9-43.2%) in the experiment group and 27.21% (95% CI 22.0-32.4%) in the control group. There was a statistically significant difference between the two arms of 10.33% (95% CI 8.4-12.3%, p = 0.008). The DNA loss rate, serum HBsAg level, and liver enzymes were similar between the groups by the end of 108th week. Combining the Chinese herbal formula with ETV therapy demonstrated superior HBeAg clearance compared with ETV monotherapy. This finding indicates that this combined therapy could produce an improved therapeutic effect and safety profile. ChiCTR-TRC-12002784 (Chinese Clinical Trial Registry).

A DNA-modified hydrogel for simultaneous purification, concentration and detection of targeted cfDNA in human serum.

Cell-free DNA (cfDNA) in blood, which stems from the fetus of pregnant women and tumor in cancer patients, has gained attention in molecular diagnosis. However, cfDNA is less stable, and its amount in the serum is extremely low; these are critical barriers for the utilization of this resource. In this study, a DNA-modified polyacrylamide hydrogel (DNA-Gel) was prepared, and a specialized device was designed to simultaneously catch, purify, concentrate, and detect targeted cfDNA by electrophoresis. We demonstrated that 20–1000 bp ssDNA and dsDNA could be caught and released by the DNA-Gel-based device with high specificity and sensitivity. Upon increasing the number of cycles and electrophoresis time, higher DNA purity and density were achieved, and the separation of serum proteins, untargeted cfDNA, and other charged molecules was promoted. As low as 10 pg μL−1 of DNA could be detected using the DNA-Gel after four cycles of concentration. We also detected 1 fg μL−1 of DNA in the serum with 16 cycles of concentration, followed by 25 PCR cycles. We also designed a device to obtain DNA from the DNA-Gel. We found that the DNA loss rate was around 50%, and A260/A280 was close to 1.7. Thus, we have designed a cost-effective and highly economical device to purify DNA at low concentrations with high specificity and selectivity.

Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.

Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., <30 bp) deletions than do other vertebrate genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.

Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders.

Among animals, genome sizes range from 20 Mb to 130 Gb, with 380-fold variation across vertebrates. Most of the largest vertebrate genomes are found in salamanders, an amphibian clade of 660 species. Thus, salamanders are an important system for studying causes and consequences of genomic gigantism. Previously, we showed that plethodontid salamander genomes accumulate higher levels of long terminal repeat (LTR) retrotransposons than do other vertebrates, although the evolutionary origins of such sequences remained unexplored. We also showed that some salamanders in the family Plethodontidae have relatively slow rates of DNA loss through small insertions and deletions. Here, we present new data from Cryptobranchus alleganiensis, the hellbender. Cryptobranchus and Plethodontidae span the basal phylogenetic split within salamanders; thus, analyses incorporating these taxa can shed light on the genome of the ancestral crown salamander lineage, which underwent expansion. We show that high levels of LTR retrotransposons likely characterize all crown salamanders, suggesting that disproportionate expansion of this transposable element (TE) class contributed to genomic expansion. Phylogenetic and age distribution analyses of salamander LTR retrotransposons indicate that salamanders’ high TE levels reflect persistence and diversification of ancestral TEs rather than horizontal transfer events. Finally, we show that relatively slow DNA loss rates through small indels likely characterize all crown salamanders, suggesting that a decreased DNA loss rate contributed to genomic expansion at the clade’s base. Our identification of shared genomic features across phylogenetically distant salamanders is a first step toward identifying the evolutionary processes underlying accumulation and persistence of high levels of repetitive sequence in salamander genomes.

Peginterferon-α2a combined with response-guided short-term lamivudine improves response rate in hepatitis B e antigen-positive hepatitis B patients

The hepatitis B e antigen (HBeAg) seroconversion rate in HBeAg-positive chronic hepatitis B patients treated with peginterferon-α2a (peg-IFN α2a) is still low (about 30%). The aim of this study was to find a new combination therapy of peg-IFN α2a with lamivudine to improve the efficacy in HBeAg-positive chronic hepatitis B patients. All patients started with peg-IFN α2a treatment at a dose of 135 μg/week. If the concentration of hepatitis B virus (HBV) DNA was greater than 1.0×10 copies/ml and if the patient was positive for HBeAg at 12 weeks of treatment, lamivudine was included into the treatment for 12 weeks. Thereafter, the patients continued on peg-IFN α2a alone for the full 52-week treatment course. Thirty-two patients were recruited, and eight of them achieved HBV DNA concentrations of less than 1.0×10 copies/ml or HBeAg loss at 12 weeks of treatment when lamivudine was not administered (group A). The other 24 patients received additional lamivudine, started from 12 weeks of treatment for 12 weeks (group B). At the end of treatment (EOT), in the peg-IFN α2a monotherapy group (group A), eight patients (100%) had HBV DNA loss, six patients (75%) achieved HBeAg seroconversion, and eight patients (100%) achieved alanine aminotransferase (ALT) normalization. This level of response was sustained for 24 weeks after treatment in all patients with an early response. In the peg-IFN α2a combined short-term lamivudine group (group B), 12 patients (50%) had HBV DNA loss, nine patients (38%) achieved HBeAg seroconversion, one patient (4%) achieved hepatitis B surface antigen loss, and 15 patients (63%) achieved ALT normalization at EOT. One patient had an HBV DNA rebound and an HBeAg reversion 24 weeks after treatment. The total HBV DNA loss rate, HBeAg seroconversion rate, hepatitis B surface antigen loss rate, and ALT normalization rate in all patients were 59, 47, 3, and 69%, respectively, at EOT and were 56, 44, 3, and 69% 24 weeks after treatment, respectively. This study indicates that the response-guided approach resulted in an overall HBeAg seroconversion rate of 47% at EOT and 44% 24 weeks after treatment. This promising strategy to increase response rates with peg-IFN α2a warrants further investigation.

Efficacy of sequential use of telbivudine in hepatitis B e antigen‐positive chronic hepatitis B patients with partial responses to pegylated interferon: a pilot study

The aim of this study was to investigate the efficacy of sequential use of telbivudine in hepatitis B e antigen (HBeAg)-positive chronic hepatitis B patients with partial responses to pegylated interferon. Patients with partial responses to 48 weeks of pegylated interferon treatment were divided into two groups. In group A, patients stopped pegylated interferon directly without sequential treatment. In group B, patients received sequential treatment with telbivudine 600 mg/day. HBeAg, HBeAb, hepatitis B virus (HBV) DNA, alanine aminotransferase (ALT) and creatine kinase levels were determined at baseline and at weeks 12, 24, 36 and 48. Responses and safety were assessed after 48 weeks of telbivudine treatment. Thirty-six patients were recruited. Eighteen of these patients stopped pegylated interferon without sequential treatment (group A). After 48 weeks of follow-up, five patients (28%) had undergone HBeAg seroconversion, nine patients (50%) had undetectable levels of HBV DNA, and 11 patients (61%) achieved normal alanine aminotransferase (ALT) levels. The other 18 patients received sequential telbivudine treatment (group B). After 48 weeks of treatment, 11 patients (61%) had undergone HBeAg seroconversion, and all patients had undetectable levels of HBV DNA and normal ALT levels. All patients tolerated sequential telbivudine treatment, and only slightly elevated creatine kinase levels were observed. Switching to telbivudine therapy was efficient and safe in HBeAg-positive chronic hepatitis B patients with partial responses to 48 weeks of pegylated interferon. Sequential treatment with telbivudine resulted in an HBeAg seroconversion rate of 61% and an HBV DNA loss rate of 100% after 48 weeks. This promising strategy warrants further investigation.

Accommodating the load

Very large genomes, that is, those above 20 Gb, are rare but widely distributed throughout the eukaryotes. They are found within the diatoms, dinoflagellates, metazoans and green plants, but so far have not been found in the excavates. There is a known positive correlation between genome size and the proportion of the genome composed of transposable elements (TEs). Very large genomes may therefore be expected to be almost entirely composed of TEs. Of the large genomes examined, in the angiosperms, gymnosperms and the dinoflagellates only a small portion of the genome was identified as TEs, most of these genomes were unidentified and may be novel or diverse TEs. In the salamanders and lungfish, 25 to 47% of the genome were identifiable retrotransposons, that is, TEs that copy themselves before insertion. However, the predominant class of TEs found in the lungfish was not the same as that found in the salamanders. The little data we have at the moment suggests therefore that the diversity and abundance of TEs is variable between taxa with large genomes, similar to patterns found in taxa with smaller genomes. Based on results from the human genome, we suggest that the ‘missing’ portion of the lungfish and salamander genomes are old, highly divergent, and therefore inactive copies of TEs. The data available indicate that, unlike plants with large genomes, neither the lungfish nor the salamanders show an increased risk of extinction. Based on a slow rate of DNA loss in salamanders it has been suggested that the large salamander genome is the result of run-away genome expansion involving genome size increases via TE proliferation associated with reduced recombination rate. We know of no studies on DNA loss or recombination rates in lungfish genomes, however a similar scenario could describe the process of genome expansion in the lungfish. A series of waves of TE transposition and sequence decay would describe the pattern of TE content seen in both the lungfish and the salamanders. The lungfish and salamanders, therefore, may accommodate their large load of TEs because these TEs have accumulated gradually over a long period of time and have been subject to inactivation and decay.

170 ASSESSMENT OF FRESH AND FROZEN - THAWED BOTTLENOSE DOLPHIN (TURSIOPS TRUNCATUS) SPERM DNA FRAGMENTATION USING THE SPERM CHROMATIN DISPERSION TEST

There has been significant development over the last 20 years to improve genetic management of the captive bottlenose dolphin (Tursiops truncatus) by means of genome resource banking and assisted reproduction. Although standard semen parameters have been analysed in some detail, very little is known about sperm DNA fragmentation (SDF) in this species. The aim of this study was to develop a sperm chromatin dispersion test (SCDt) for the bottlenose dolphin to establish the baseline level of SDF immediately after ejaculation and cryopreservation and to determine the dynamic loss of sperm DNA quality after ex vivo handing and incubation in conditions that mimic the female reproductive tract. Semen from 8 bottlenose dolphins was collected by manual stimulation. Initial validation of the SCDt was conducted by means of in situ nick translation and neutral comet assay using a proven fertile male. To investigate the dynamic loss of sperm chromatin (rate of sDF loss), thawed sperm samples were incubated at 37.9°C for up to 48 h, and aliquots of spermatozoa were assessed after 1, 4, 8, 24, and 48 h. Dolphin sperm nuclei with fragmented DNA exhibited large halos of dispersed DNA fragments, whereas those with nonfragmented DNA displayed small halos of nondispersed DNA. A high correlation (r2 = 0.82; P ≤ 0.01) was found between the respective assessments of the SCDt and the neutral comet assay. All nucleoids resulting in a large halo of dispersed chromatin were intensely positive to in situ nick translation. The level of sDF fragmentation observed immediately after ejaculation in fresh and frozen samples was relatively low (1–5%). After comparing different ejaculates of the same individual, differences were found. Chromatin stability was high during the first 48 h of ejaculation or post-thawing and incubation. Evaluation of the sDF dynamics of fresh and frozen–thawed spermatozoa revealed no significant increase in the baseline level of sDF or in the relative increase of DNA damage after 48 h of incubation. Our data suggest that cryopreservation does not induce a dramatic increase in sperm chromatin damage. Interestingly, sperm samples derived from aged animals resulted in an increased rate of DNA loss, which was observed after 60 min post-incubation.

Slow DNA Loss in the Gigantic Genomes of Salamanders

Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., ∼1–30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes—the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we estimated genome-wide DNA loss rates in non-LTR retrotransposon sequences from five other vertebrate genomes: Anolis carolinensis, Danio rerio, Gallus gallus, Homo sapiens, and Xenopus tropicalis. Our results show that salamanders have significantly lower rates of DNA loss than do other vertebrates. More specifically, salamanders experience lower numbers of deletions relative to insertions, and both deletions and insertions are skewed toward smaller sizes. On the basis of these patterns, we conclude that slow DNA loss contributes to genomic gigantism in salamanders. We also identify candidate molecular mechanisms underlying these differences and suggest that natural variation in indel dynamics provides a unique opportunity to study the basis of genome stability.

Accumulation and Rapid Decay of Non-LTR Retrotransposons in the Genome of the Three-Spine Stickleback

The diversity and abundance of non–long terminal repeat (LTR) retrotransposons (nLTR-RT) differ drastically among vertebrate genomes. At one extreme, the genome of placental mammals is littered with hundreds of thousands of copies resulting from the activity of a single clade of nLTR-RT, the L1 clade. In contrast, fish genomes contain a much more diverse repertoire of nLTR-RT, represented by numerous active clades and families. Yet, the number of nLTR-RT copies in teleostean fish is two orders of magnitude smaller than in mammals. The vast majority of insertions appear to be very recent, suggesting that nLTR-RT do not accumulate in fish genomes. This pattern had previously been explained by a high rate of turnover, in which the insertion of new elements is offset by the selective loss of deleterious inserts. The turnover model was proposed because of the similarity between fish and Drosophila genomes with regard to their nLTR-RT profile. However, it is unclear if this model applies to fish. In fact, a previous study performed on the puffer fish suggested that transposable element insertions behave as neutral alleles. Here we examined the dynamics of amplification of nLTR-RT in the three-spine stickleback (Gasterosteus aculeatus). In this species, the vast majority of nLTR-RT insertions are relatively young, as suggested by their low level of divergence. Contrary to expectations, a majority of these insertions are fixed in lake and oceanic populations; thus, nLTR-RT do indeed accumulate in the genome of their fish host. This is not to say that nLTR-RTs are fully neutral, as the lack of fixed long elements in this genome suggests a deleterious effect related to their length. This analysis does not support the turnover model and strongly suggests that a much higher rate of DNA loss in fish than in mammals is responsible for the relatively small number of nLTR-RT copies and for the scarcity of ancient elements in fish genomes. We further demonstrate that nLTR-RT decay in fish occurs mostly through large deletions and not by the accumulation of small deletions.

The transposable element profile of the Anolis genome

The recent sequencing of the lizard genome provides a unique opportunity to examine the evolution of vertebrate genomes in a phylogenetic context. The lizard genome contains an extraordinary diversity of active transposable elements that far exceeds the diversity reported in extant mammals and birds. Retrotransposons and DNA transposons are represented by multiple active families, contributing to the very diverse repetitive landscape of the lizard. Surprisingly, ancient transposon copies are relatively rare suggesting that the transposon copy number is tightly controlled in lizard. This bias in favor of young copies results from the joint effect of purifying selection acting on novel insertions and a high rate of DNA loss. Recent analyses have revealed that the repetitive landscape of reptiles differ drastically from other extant amniotes by their diversity but also by the dynamics of amplification of their transposons. Thus, from the point of view of mobile elements, reptile genomes show more similarity to fish and amphibians than to other amniotes.

Rapid and quantitative assessment of KSHV LANA-mediated DNA replication

Kaposi's sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) mediates DNA replication of terminal repeat (TR) DNA to enable viral episome persistence in latently infected cells. Southern blotting is routinely used to detect LANA-replicated DNA. We developed and validated a real-time PCR assay for TR-associated DNA and compared it with Southern blot analysis. Both PCR and Southern blot detected LANA-replicated DNA, but the PCR assay was more rapid and did not require radioisotope. PCR detection at 24 and 72 hours post-transfection demonstrated rapid loss of transfected TR DNA. LANA, and to a lesser extent a moderately deficient LANA mutant, reduced the rate of DNA loss through addition of replicated TR DNA and reduction in the loss of non-replicated DNA, the latter of which is consistent with LANA's nuclear segregation function. Therefore, this work develops a rapid, sensitive, and quantitative PCR (qPCR) assay to detect KSHV LANA-replicated DNA and demonstrates that LANA reduces TR DNA loss after transfection through replication and nuclear partitioning of TR DNA.

The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis.

DNA transposons have considerably affected the size and structure of eukaryotic genomes and have been an important source of evolutionary novelties. In vertebrates, DNA transposons are discontinuously distributed due to the frequent extinction and recolonization of these genomes by active elements. We performed a detailed analysis of the DNA transposons in the genome of the lizard Anolis carolinensis, the first non-avian reptile to have its genome sequenced. Elements belonging to six of the previously recognized superfamilies of elements (hAT, Tc1/Mariner, Helitron, PIF/Harbinger, Polinton/Maverick, and Chapaev) were identified. However, only four (hAT, Tc1/Mariner, Helitron, and Chapaev) of these superfamilies have successfully amplified in the anole genome, producing 67 distinct families. The majority (57/67) are nonautonomous and demonstrate an extraordinary diversity of structure, resulting from frequent interelement recombination and incorporation of extraneous DNA sequences. The age distribution of transposon families differs among superfamilies and reveals different dynamics of amplification. Chapaev is the only superfamily to be extinct and is represented only by old copies. The hAT, Tc1/Mariner, and Helitron superfamilies show different pattern of amplification, yet they are predominantly represented by young families, whereas divergent families are exceedingly rare. Although it is likely that some elements, in particular long ones, are subjected to purifying selection and do not reach fixation, the majority of families are neutral and accumulate in the anole genome in large numbers. We propose that the scarcity of old copies in the anole genome results from the rapid decay of elements, caused by a high rate of DNA loss.

A pilot study of peginterferon alfa-2a combined with short-term lamivudine therapy in HBeAg-positive chronic hepatitis B patients

To investigate the efficacy of by combining a 12-week course of lamivudine in those HBeAg-positive hepatitis B patients receiving peginterferon alfa-2a (peg-IFN alpha-2a) therapy. A total of 58 patients initiated a 52-week course of peginterferon alfa-2a were enrolled and divided into 3 groups. The patients with HBV DNA undetectable or HBeAg negative at week 12 were divided into group A, in this group treatment continued to week 52 with peg-IFN alpha-2a alone; The rest patients were divided into group B1 and B2, in group B1, lamivudine was combined at a course of 12 weeks, while in group B2 treatment continued to week 52 with peg-IFN alpha-2a alone. Clinical responses were assessed at week 52. 8 out of 58 patients achieved undetectable HBV DNA or HBeAg loss at week 12 and divide into group A. In this group the HBV DNA loss rate, HBeAg seroconversion rate, HBsAg loss rate and ALT normalization rate were 100% (8/8), 75% (6/8), 0% (0/8) and 100% (8/8) respectively at the end of treatment. In this group the HBV DNA loss rate, HBeAg seroconversion rate, HBsAg loss rate and ALT normalization rate were 100% (8/8), 75% (6/8), 0% (0/8) and 100%(8/8) respectively at the end of treatment. The rest 50 patients without early response to peg-IFN alpha-2a at week 12 were divided into group B1 (24 patients enrolled) and B2 (26 patients). At the end of treatment, the HBV DNA loss rate, HBeAg seroconversion rate, HBsAg loss rate and ALT normalization rate in Group B1 were 50% (12/24), 38% (9/24), 4% (1/24) and 63% (15/24) respectively, and 31% (8/26), 27% (7/26), 0% (0/26) and 35% (9/26) respectively in group B2. Those patients with early responses to peg-IFN alpha-2a therapy can achieve high clinical responses at the end of 52-week treatment. The combining therapy of lamivudine for a course of 12-weeks can improve the clinical responses for the patients without early responses to peg-IFN alpha-2a.

Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants.

Transposable elements, particularly LTR-retrotransposons, comprise the primary vehicle for genome size expansion in plants, while DNA removal through illegitimate recombination and intrastrand homologous recombination serve as the most important counteracting forces to plant genomic obesity. Despite extensive research, the relative impact of these opposing forces and hence the directionality of genome size change remains unknown. In Gossypium (cotton), the 3-fold genome size variation among diploids is due largely to copy number variation of the gypsy-like retrotransposon Gorge3. Here we combine comparative sequence analysis with a modeling approach to study the directionality of genome size change in Gossypium. We demonstrate that the rate of DNA removal in the smaller genomes is sufficient to reverse genome expansion through Gorge3 proliferation. These data indicate that rates of DNA loss can be highly variable even within a single plant genus, and that the known mechanisms of DNA loss can indeed reverse the march toward genomic obesity.

Evolution of genome size: A phylogenetic test of the DNA loss hypothesis

It has been recently suggested that the C-value paradox, the lack of an obvious association between organismal complexity and genome size, can result simply from biases in insertion and deletion rates--the DNA loss hypothesis. This hypothesis has been heavily criticized, particularly because its evidence, a negative relationship between genome size and DNA loss rate, is based on a highly selective use of the available data. In this study it is show that even the even the most favorable interpretation of the data favoring the DNA loss hypothesis is largely an artifact of phylogenetic nonindependence, supporting the assertion made by other authors that the mechanisms underlying genome size evolution might be more complex than envisioned by the DNA loss hypothesis.

Bacterial genome size reduction by experimental evolution

Bacterial evolution toward endosymbiosis with eukaryotic cells is associated with extensive bacterial genome reduction and loss of metabolic and regulatory capabilities. Here we examined the rate and process of genome reduction in the bacterium Salmonella enterica by a serial passage experimental evolution procedure. The initial rate of DNA loss was estimated to be 0.05 bp per chromosome per generation for a WT bacterium and approximately 50-fold higher for a mutS mutant defective in methyl-directed DNA mismatch repair. The endpoints were identified for seven chromosomal deletions isolated during serial passage and in two separate genetic selections. Deletions ranged in size from 1 to 202 kb, and most of them were not associated with DNA repeats, indicating that they were formed via RecA-independent recombination events. These results suggest that extensive genome reduction can occur on a short evolutionary time scale and that RecA-dependent homologous recombination only plays a limited role in this process of jettisoning superfluous DNA.

Deletion polymorphism in wheat chromosome regions with contrasting recombination rates.

Polymorphism for deletions was investigated in 1027 lines of tetraploid and hexaploid wheat and 420 lines of wheat diploid ancestors. A total of 26 deletions originating during the evolution of polyploid wheat were discovered among 155 investigated loci. Wheat chromosomes were divided into a proximal, low-recombination interval containing 69 loci and a distal, high-recombination interval containing 86 loci. A total of 23 deletions involved loci in the distal, high-recombination interval and only 3 involved loci in the proximal, low-recombination interval. The rates of DNA loss differed by several orders of magnitude in the two intervals. The rate of diploidization of polyploid wheat by deletions was estimated and was shown to have proceeded faster in the distal, high-recombination interval than in the proximal, low-recombination interval.

Insertion-deletion biases and the evolution of genome size.

Numerous theories have been proposed to account for the pronounced differences in the quantity of non-coding DNA among eukaryotic genomes, but the current repertoire remains incomplete because the only explicit mechanisms it provides involve DNA gain. It has been proposed more recently that biases in spontaneous insertions and deletions (indels) can lead to genome shrinkage by mutational mechanisms alone. The present article provides the first detailed critical discussion of this approach, and covers three different ideas related to it: (1) the general notion of DNA loss by deletion bias, (2) the "DNA loss hypothesis" which supposes that variation in genome size can be attributed to differences in DNA loss rate, and (3) the "mutational equilibrium model" which attempts to describe the long-term evolution of genome size. The mutational equilibrium model is found to be problematic, and it is noted that DNA loss by small indels is too slow in real time to determine variation in genome size above a relatively low threshold. Some alternative explanations for the observed patterns are provided, and the critique also identifies some potential problems with the current dataset. These include a failure to cite a more detailed (and somewhat contradictory) mammalian dataset, a questionable use of arithmetic means with highly skewed data, and important discrepancies among the particular DNA sequences so far analyzed. Overall, evolutionary reductions in genome size are considered important, but the specific mechanism relating to small deletion bias is far too weak to be accepted as a primary determinant of genome size variation in general.