Decrease In Genome Size Research Articles

Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

Ligusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

Antagonistic effects of whole-genome duplications and dysploidy on genome sizes in the pantropical monocot family Marantaceae: Consequences in the light of a new molecular phylogeny

Changes in chromosome number and structure, as well as alterations in genome size, are important cytological characters that often reflect speciation events. Due to a wide variety of previously reported chromosome numbers the species-rich arrowroot family (Marantaceae) is an ideal system to investigate the role of chromosomal changes in species diversification, especially of dysploidy and polyploidy. The mechanisms and direction of changes during evolution as well as ancestral states of chromosomal characters are largely unknown. This study provides a detailed survey of chromosomal and genome size variation in 43 Marantaceae accessions (37 species, 16 genera) from the whole distribution range. Phylogenetic tree mapping suggests that x = 13 is the ancestral basic chromosome number. Descending dysploidy to x = 9, 10, 11, and 12 occurred ten times in parallel within each of the five main clades. In contrast, ascending dysploidy to x = 14, occurred only once. Ploidy level variation was confined to basic numbers x = 9, 11, and 13 and was observed in four out of the five clades. The occurrence of triploids and pentaploids points towards heteroploid diploid-tetraploid and tetraploid-hexaploid hybridizations. Trends in genome evolution as exposed by regression analyses revealed a massive genome size increase after dysploidy - and a genome size decrease after polyploidy. A schematic illustration of possible origins and the modes of chromosomal changes in a biogeographical context is presented. Exemplified by the family Marantaceae, it is shown how variable chromosomal evolution can be and how it contributes to species richness and speciation in the plant kingdom.

Is the evolution of carnivory connected with genome size reduction?

As repeatedly shown, the remarkable variation in the genome size of angiosperms can be shaped by extrinsic selective pressures, including nutrient availability. Carnivory has evolved independently in 10 angiosperm clades, but all carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory and genome reduction could be responses to the same environmental pressure. Indeed, the smallest genomes among flowering plants are found in the carnivorous family Lentibulariaceae, where a unique mutation in cytochrome c oxidase (COX) is suspected to promote genome miniaturization. Despite these hypotheses, a phylogenetically informed test of genome size and nutrient availability across carnivorous clades has so far been missing. Using linear mixed models, we compared genome sizes of 127 carnivorous plants from 7 diverse angiosperm clades with 1072 of their noncarnivorous relatives. We also tested whether genome size in Lentibulariaceae reflects the presence of the COX mutation. The genome sizes of carnivorous plants do not differ significantly from those of their noncarnivorous relatives. Based on available data, no significant association between the COX mutation and genome miniaturization could be confirmed, not even when considering polyploidy. Carnivory alone does not seem to significantly affect genome size decrease. Plausibly, it might actually counterbalance the effect of nutrient limitation on genome size evolution. The role of the COX mutation in genome miniaturization needs to be evaluated by analysis of a broader data set because current knowledge of its presence across Lentibulariaceae covers less than 10% of the species diversity in this family.

The First Plastid Genome of the Holoparasitic Genus Prosopanche (Hydnoraceae).

Plastomes of parasitic and mycoheterotrophic plants show different degrees of reduction depending on the plants’ level of heterotrophy and host dependence in comparison to photoautotrophic sister species, and the amount of time since heterotrophic dependence was established. In all but the most recent heterotrophic lineages, this reduction involves substantial decrease in genome size and gene content and sometimes alterations of genome structure. Here, we present the first plastid genome of the holoparasitic genus Prosopanche, which shows clear signs of functionality. The plastome of Prosopanche americana has a length of 28,191 bp and contains only 24 unique genes, i.e., 14 ribosomal protein genes, four ribosomal RNA genes, five genes coding for tRNAs and three genes with other or unknown function (accD, ycf1, ycf2). The inverted repeat has been lost. Despite the split of Prosopanche and Hydnora about 54 MYA ago, the level of genome reduction is strikingly congruent between the two holoparasites although highly dissimilar nucleotide sequences are observed. Our results lead to two possible evolutionary scenarios that will be tested in the future with a larger sampling: 1) a Hydnoraceae plastome, similar to those of Hydnora and Prosopanche today, existed already in the most recent common ancestor and has not changed much with respect to gene content and structure, or 2) the genome similarities we observe today are the result of two independent evolutionary trajectories leading to almost the same endpoint. The first hypothesis would be most parsimonious whereas the second would point to taxon dependent essential gene sets for plants released from photosynthetic constraints.

Evidencing genome downsizing as a result of multiple robertsonian translocations in the subfamily allioideae (Amararyllidaceae)

Large genomes and a history of chromosome rearrangements have made the subfamily Allioideae an interesting model to understand chromosome evolution. The majority of its genera show high karyotype diversity mainly due to polyploidy and Robertsonian translocations (RT) events. The three lineages of Allioideae present different levels of RT, evidenced by metacentric-rich karyotypes observed in Allieae and Tulbaghieae, and a variable proportion between metacentric/acrocentrics in Gilliesieae. Extreme condition of centric fissions occurs in the genera Ipheion, Zoellnerallium and Miersia, whose results in karyotypes formed almost exclusively by acrocentric chromosomes. In this work we investigate how RT drives genome size and chromosome number variation in species of Allioideae. For this, we estimated the genome size by flow cytometry and compiled chromosome number data for 37 species of Allioideae. We employed comparative phylogenetic methods in a Bayesian tree based on ITS1-5.8S-ITS2 sequences. Genome size ranged from 1C = 9.03 picograms (pg) in Ipheon uniflorum to 1C = 54.97 pg in Leucocoryne ixioides. Our analyses revealed that metacentric-rich karyotype is the plesiomorphic state in the subfamily Allioideae and RT as a driving force in genome size variation. This is demonstrated in the relationships Leucocoryne (2n = 14M+4A) /Zoellnerallium (2n = 8M+16A) and Tristagma (2n = 6M+2A)/Ipheion (2n = 14A) with a strong reduction of DNA content (49.5% and 61.47%, respectively) associated to multiple fissions. These changes in Zoellnerallium and Ipheon genomes occurred independently around 12 myr. This relationship was not observed in the Chilean species Speea humilis (2n = 8M+2SM+2A)/ Miersia chilensis (2n = 2SM+18A) with recent differentiation (5 mya), suggesting that multiple centric fusions may require additional evolutionary time to decrease genome size. Our phylogenetic independent contrast analysis of genome size and chromosome number revealed that these traits have a negative correlation (r²=0.18 and p=0.01). This corroborates a tendency of decrease in genome size after events that increase chromosome number such as fissions. Possibly, changes in chromosome linkage may increase meiotic recombination frequency, which might lead to higher probability of unequal crossing over. This mechanism could associate the loss of repetitive sequences to centric fission, explaining downsizing in Allioideae acrocentric-rich genomes.

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins.

To reveal impacts of sexual mode on genome content, we compared chromosome-scale assemblies of the outcrossing nematode Caenorhabditis nigoni to its self-fertile sibling species, C. briggsaeC. nigoni's genome resembles that of outcrossing relatives but encodes 31% more protein-coding genes than C. briggsaeC. nigoni genes lacking C. briggsae orthologs were disproportionately small and male-biased in expression. These include the male secreted short (mss) gene family, which encodes sperm surface glycoproteins conserved only in outcrossing species. Sperm from mss-null males of outcrossing C. remanei failed to compete with wild-type sperm, despite normal fertility in noncompetitive mating. Restoring mss to C. briggsae males was sufficient to enhance sperm competitiveness. Thus, sex has a pervasive influence on genome content that can be used to identify sperm competition factors.

Evolutionary characterization of Ty3/gypsy-like LTR retrotransposons in the parasitic cestode Echinococcus granulosus.

Cyclophyllidean cestodes including Echinococcus granulosus have a smaller genome and show characteristics such as loss of the gut, a segmented body plan, and accelerated growth rate in hosts compared with other tissue-invading helminths. In an effort to address the molecular mechanism relevant to genome shrinkage, the evolutionary status of long-terminal-repeat (LTR) retrotransposons, which are known as the most potent genomic modulators, was investigated in the E. granulosus draft genome. A majority of the E. granulosus LTR retrotransposons were classified into a novel characteristic clade, named Saci-2, of the Ty3/gypsy family, while the remaining elements belonged to the CsRn1 clade of identical family. Their nucleotide sequences were heavily corrupted by frequent base substitutions and segmental losses. The ceased mobile activity of the major retrotransposons and the following intrinsic DNA loss in their inactive progenies might have contributed to decrease in genome size. Apart from the degenerate copies, a gag gene originating from a CsRn1-like element exhibited substantial evidences suggesting its domestication including a preserved coding profile and transcriptional activity, the presence of syntenic orthologues in cestodes, and selective pressure acting on the gene. To my knowledge, the endogenized gag gene is reported for the first time in invertebrates, though its biological function remains elusive.

A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History.

The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.

Strong correlation between cross‐amplification success and genetic distance across all members of ‘True Salamanders’ (Amphibia: Salamandridae) revealed by Salamandra salamandra‐specific microsatellite loci

The unpredictable and low cross-amplification success of microsatellite loci tested for congeneric amphibian species has mainly been explained by the size and complexity of amphibian genomes, but also by taxonomy that is inconsistent with phylogenetic relationships among taxa. Here, we tested whether the cross-amplification success of nine new and 11 published microsatellite loci cloned for an amphibian source species, the fire salamander (Salamandra salamandra), correlated with the genetic distance across all members of True Salamanders (genera Chioglossa, Lyciasalamandra, Mertensiella and Salamandra that form a monophyletic clade within the family of Salamandridae) serving as target species. Cross-amplification success varied strongly among the species and showed a highly significant negative relationship with genetic distance and amplification success. Even though lineages of S.salamandra and Lyciasalamndra have separated more than 30 Ma, a within genus amplification success rate of 65% was achieved for species of Lyciasalamandra thus demonstrating that an efficient cross-species amplification of microsatellite loci in amphibians is feasible even across large evolutionary distances. A decrease in genome size, on the other hand, paralleled also a decrease in amplified loci and therefore contradicted previous results and expectations that amplification success should increase with a decrease in genome size. However, in line with other studies, our comprehensive dataset clearly shows that cross-amplification success of microsatellite loci is well explained by phylogenetic divergence between species. As taxonomic classifications on the species and genus level do not necessarily mirror phylogenetic divergence between species, the pure belonging of species to the same taxonomic units (i.e. species or genus) might be less useful to predict cross-amplification success of microsatellite loci between such species.

Estimation of the nuclear DNA content in some representative of genus Dioscorea

Nuclear DNA content of 54 accessions of 6 Dioscorea species collected from West African countries were determined using flow cytometry. Observed ploidy levels are diploid (2x), triploid (3x), tetraploid (4x), hexaploid (6x) and octoploid (8x). DNA index varied from 0.36 to 1.54 depending on the cultivar and considered specie. Estimated nuclear DNA sizes ranged from 0.702 ± 0.004 pg for G1 nuclei of diploid Dioscorea dumetorum to 2.573 ± 0.020 pg for G1 nuclei of octoploid Dioscorea cayenensis. Our result showed that there is a decrease in genome size with higher ploidy level. The study contributes a step towards a genome understanding of this group of plants. Key words: Dioscorea, DNA content, flow cytometry, genome, ploidy level.

Evolution of genome size across some cultivated Allium species

Allium L. (Alliaceae), a genus of major economic importance, exhibits a great diversity in various morphological characters and particularly in life form, with bulbs and rhizomes. Allium species show variation in several cytogenetic characters such as basic chromosome number, ploidy level, and genome size. The purpose of the present investigation was to study the evolution of nuclear DNA amount, GC content, and life form. A phylogenetic approach was used on a sample of 30 Allium species, including major vegetable crops and their wild allies, belonging to the 3 major subgenera Allium, Amerallium, and Rhizirideum and 14 sections. A phylogeny was constructed using internal transcribed spacer (ITS) sequences of 43 accessions representing 30 species, and the nuclear DNA amount and the GC content of 24 Allium species were investigated by flow cytometry. For the first time, the nuclear DNA content of Allium cyaneum and Allium vavilovii was measured, and the GC content of 16 species was measured. We addressed the following questions: (i) Is the variation in nuclear DNA amount and GC content linked to the evolutionary history of these edible Allium species and their wild relatives? (ii) How did life form (rhizome or bulb) evolve in edible Allium? Our results revealed significant interspecific variation in the nuclear DNA amount as well as in the GC content. No correlation was found between the GC content and the nuclear DNA amount. The reconstruction of nuclear DNA amount on the phylogeny showed a tendency towards a decrease in genome size within the genus. The reconstruction of life form history showed that rhizomes evolved in the subgenus Rhizirideum from an ancestral bulbous life form and were subsequently lost at least twice independently in this subgenus.

Evolution of Genome Size in Brassicaceae

Brassicaceae, with nearly 340 genera and more than 3350 species, anchors the low range of angiosperm genome sizes. The relatively narrow range of DNA content (0.16 pg < 1C < 1.95 pg) was maintained in spite of extensive chromosomal change. The aim of this study was to erect a cytological and molecular phylogenetic framework for a selected subset of the Brassicacae, and use this as a template to examine genome size evolution in Brassicaceae. DNA contents were determined by flow cytometry and chromosomes were counted for 34 species of the family Brassicaceae and for ten Arabidopsis thaliana ecotypes. The amplified and sequenced ITS region for 23 taxa (plus six other taxa with known ITS sequences) were aligned and used to infer evolutionary relationship by parsimony analysis. DNA content in the species studied ranged over 8-fold (1C = 0.16-1.31 pg), and 4.4-fold (1C = 0.16-0.71 pg) excluding allotetraploid Brassica species. The 1C DNA contents of ten Arabidopsis thaliana ecotypes showed little variation, ranging from 0.16 pg to 0.17 pg. The tree roots at an ancestral genome size of approximately 1x = 0.2 pg. Arabidopsis thaliana (1C = 0.16 pg; approximately 157 Mbp) has the smallest genome size in Brassicaceae studied here and apparently represents an evolutionary decrease in genome size. Two other branches that represent probable evolutionary decreases in genome size terminate in Lepidium virginicum and Brassica rapa. Branches in the phylogenetic tree that represent probable evolutionary increases in genome size terminate in Arabidopsis halleri, A. lyrata, Arabis hirsuta, Capsella rubella, Caulanthus heterophyllus, Crucihimalaya, Lepidium sativum, Sisymbrium and Thlaspi arvense. Branches within one clade containing Brassica were identified that represent two ancient ploidy events (2x to 4x and 4x to 6x) that were predicted from published comparative mapping studies.

Genome reduction in a hemiclonal frog Rana esculenta from radioactively contaminated areas.

A decrease in genome size was found in the hemiclonal hybridogenetic frog Rana esculenta (R. ridibunda x R. lessonae) from areas of radioactive contamination that resulted from the Chernobyl fallout. This genome reduction was of up to 4% and correlated with the background level of gamma-radiation (linear regression corresponded on average to -0.4% per doubling of radiation level). No change in genome size was observed in the coexisting parental species R. lessonae. There was no correlation between genome size and body mass in R. esculenta froglets, which have metamorphosed in the year of the study. The hemiclonal forms may become a suitable object for study on biological significance of individual DNA sequences (and of genome size as a whole) because mutant animals with deletions in a specified genome can arise after a low radiation dose. The proneness to genetic damage makes such forms also a prospective bioindicator of radioactive (and possibly other mutagenic) pollution with the effects of genetic damage conveniently and rapidly monitored by DNA flow cytometry.

Flow-cytometric analyses of intraspecific genome size variations in Bacillus atticus (Insecta, Phasmatodea)

The stick insect Bacillus atticus comprises several populations with different chromosome numbers that are distributed over a large range of the Mediterranean basin. Here we have analyzed the DNA content of nine diploid and three triploid populations by flow-cytometry. The mean genome size of the diploids showed a significant decrease from east to west, ranging from 5.29 ± 0.12 pg for the population from Crete (east) to 4.28 ± 0.10 pg for the population from Sardinia (far west). This longitudinal trend of a decrease in genome size from east to west was also found for the triploid populations (from 6.80 pg for the population in Turkey to 6.08 ± 0.01 pg for the population on the Isle of Rhodes). Differences in DNA content between populations belonging to the same species have been described in animals, but the evolutionary implications of these differences are as yet unclear. What emerges from the present study is a correlation between genome-size variations and geographic distribution. The adaptive nature of genome-size variations in response to environmental changes is discussed, and the class of DNA involved hypothesized.Key words: C value, flow cytometry, genome size trends, intraspecific DNA variation, DNA classes.

A molecular clock based on the expansion of gene families.

There is evidence to suggest that eukaryotic genomes are subject to frequent insertions and deletions of non-coding DNA. This may lead to a gradual increase or decrease in genome size, or to a dynamic equilibrium in which the overall size remains constant. We argue, however, that there is a bias favouring an accumulation of non-coding DNA in the proximity of genes. Such bias causes a progressive change in genome structure regardless of whether the overall genome size increases, decreases or remains constant. We show that this change may serve as a 'molecular clock', supplementing that provided by nucleotide substitution rates.

Evolution of genome size in darkling beetles (Tenebrionidae, Coleoptera)

Thirty-seven species of tenebrionid beetles from mainland Spain and the Balearic Islands and Canary Islands have been surveyed for nuclear DNA content of Feulgen-stained spermatids. The range of 1C genome sizes among 44 species checked to date is relatively moderate at nearly fivefold, from 0.18 to 0.86 pg, with an average value of 0.36 pg, but it contrasts with the small range of chromosome numbers in these beetles. Highly significant correlations (p &lt; 0.001) between genome size and either spermatid area or whole metaphase I chromosomal area were found in these species. Moreover, their nuclear DNA content also correlated significantly (p &lt; 0.05) with diploid chromosome number. A striking difference between the average DNA content of Tentyriinae and Tenebrionidae was also detected, that of the Tentyriinae being clearly smaller. A possible trend towards decrease in genome size could possibly explain most of evolutionary divergence in Tenebrionidae except for Blaps and some Opatrini, which have probably undergone substantial increases of nuclear DNA content.Key words: genome size, Tenebrionidae, evolution.