Genome sizes for all genera of Cycadales

Nuclear DNA content (2C) is reported for all genera of the Cycadales, using flow cytometry with propidium iodide. Nuclear DNA content ranges from 24 to 64 pg in cycads. This implies that the largest genome contains roughly 40 × 10(9) more base pairs than the smallest genome. The narrow range in nuclear DNA content within a genus is remarkable for such an old group. Furthermore, 42 of the 58 plants measured, covering five genera, have 18 chromosomes. They vary from 36.1 to 64.7 pg, covering the whole range of genome sizes (excluding the genome of Cycas). Hence, their does not seem to be a correlation between genome size and the number of chromosomes.     

Compositional Properties of Green-Plant Plastid Genomes

We studied variation of GC contents among plastid (Pt) genomes of green plants. In the green plants, the GC contents of the whole Pt genomes range from 42.14 to 28.81%. These values are similar to those observed in the mitochondrial (Mt) genomes of the green plants, however, the GC contents in the Pt genomes are not related to those in the Mt genomes or the nuclear (Nc) genomes. In addition, some compositional properties of the three types of genomes are different. Thus, it is suggested that the GC contents of the Pt genomes are maintained independently of the other genomes within a cell. We found that the compositional bias toward AT is strong at the third codon position and in intergenic spacer (IGS) regions in the Pt genomes, and the GC contents (GC3 and GCIGS) at these sites are generally similar within each genome. Additionally, the GC3 and GCIGS are strongly related to the whole-genome GC content. Therefore, the interspecific variation of the GC contents in the Pt genomes is suggested to be mainly caused by the variation of the GC3 and GCIGS, both of which are considered to be under weak selective constraints. Using a maximum likelihood approach, we estimated equilibrium GC3 (eqGC₃) of 12 genes in the land-plant Pt genomes. We found an increase in eqGC₃ after the divergence of liverworts. These results suggest that genome-wide factors such as GC mutational bias are important for the biased base composition in the Pt genomes.Reviewing Editor: Dr. Brian Morton     

Genome size and DNA base composition of geophytes: the mirror of phenology and ecology?

Background and Aims

Genome size is known to affect various plant traits such as stomatal size, seed mass, and flower or shoot phenology. However, these associations are not well understood for species with very large genomes, which are laregly represented by geophytic plants. No detailed associations are known between DNA base composition and genome size or species ecology.

Methods

Genome sizes and GC contents were measured in 219 geophytes together with tentative morpho-anatomical and ecological traits.

Key Results

Increased genome size was associated with earliness of flowering and tendency to grow in humid conditions, and there was a positive correlation between an increase in stomatal size in species with extremely large genomes. Seed mass of geophytes was closely related to their ecology, but not to genomic parameters. Genomic DNA GC content showed a unimodal relationship with genome size but no relationship with species ecology.

Conclusions

Evolution of genome size in geophytes is closely related to their ecology and phenology and is also associated with remarkable changes in DNA base composition. Although geophytism together with producing larger cells appears to be an advantageous strategy for fast development of an organism in seasonal habitats, the drought sensitivity of large stomata may restrict the occurrence of geophytes with very large genomes to regions not subject to water stress.     

Utilization of intergeneric somatic hybrids as an index discriminating taxa in the genus Citrus and its related species

Embryogenic protoplasts of Shogun mandarin (Citrus reticulata Blanco) were electrically fused with mesophyll protoplasts from Citropsis gabunensis Swing. & M. Kell, and two green embryoids were regenerated after 3 months of culture. Two months after transfer to the regeneration medium, numerous plantlets were obtained from the embryoids. These plants grew vigorously, had well-developed root systems, and exhibited leaf characteristics intermediate to those of the parents. The absolute nuclear genome size of the regenerated plant SH2 (1.75 pg/4C) was the sum of those of the Shogun mandarin (0.75 pg/2C) and C. gabunensis (0.97 pg/2C). The chromosome counts of the young leaves revealed that they were tetraploids (2n=4x=36). Random amplified polymorphic DNA (RAPD) analysis of the two lines (SH1 and SH2) verified their hybridity. Cytoplasmic genome analysis using universal primers reveal that their chloroplast (cp) DNA banding pattern is identical to that of C. gabunensis, while the banding pattern of the mitochondrial (mt) DNA is identical to that of the Shogun mandarin. These somatic hybrids are important materials for investigating the phylogenetic relationships between these two genera in the subfamily Aurantioideae.     

Unlocking Holocentric Chromosomes: New Perspectives from Comparative and Functional Genomics?

The presence of chromosomes with diffuse centromeres (holocentric chromosomes) has been reported in several taxa since more than fifty years, but a full understanding of their origin is still lacking. Comparative and functional genomics are nowadays furnishing new data to better understand holocentric chromosome evolution thus opening new perspectives to analyse karyotype rearrangements in species with holocentric chromosomes in particular evidencing unusual common features, such as the uniform GC content and gene distribution along chromosomes.     

Biological Implications of Isochore Boundaries in the Human Genome

Abstract

The human genome is composed of large sequence segments with fairly homogeneous GC content, namely isochores, which have been linked to many important functions; biological implications of most isochore boundaries, however, remain elusive, partly due to the difficulty in determining these boundaries at high resolution. Using the segmentation algorithm based on the quadratic divergence, we re-determined all 79 boundaries of previously identified human isochores at single-nucleotide resolution, and then compared the boundary coordinates with other genome features. We found that 55.7% of isochore boundaries coincide with termini of repeat elements; 45.6% of isochore boundaries coincide with termini of highly conserved sequences based on alignment of 17 vertebrate genomes, i.e., the highly conserved genome sequence switches to a less or non-conserved one at the isochore boundary; some isochore boundaries coincide with abrupt change of CpG island distribution (note that one boundary can associate with more than one genome feature). In addition, sequences around isochore boundaries are highly conserved. It seems reasonable to deduce that the boundaries of all the isochores studied here would be replication timing sites in the human genome. These results suggest possible key roles of the isochore boundaries and may further our understanding of the human genome organization.     

Genome size and GC content evolution of Festuca: ancestral expansion and subsequent reduction

Background and Aims: Plant evolution is well known to be frequently associated withremarkable changes in genome size and composition; however,the knowledge of long-term evolutionary dynamics of these processesstill remains very limited. Here a study is made of the finedynamics of quantitative genome evolution in Festuca (fescue),the largest genus in Poaceae (grasses). Methods: Using flow cytometry (PI, DAPI), measurements were made of DNAcontent (2C-value), monoploid genome size (Cx-value), averagechromosome size (C/n-value) and cytosine + guanine (GC) contentof 101 Festuca taxa and 14 of their close relatives. The resultswere compared with the existing phylogeny based on ITS and trnL-Fsequences. Key Results: The divergence of the fescue lineage from related Poeae waspredated by about a 2-fold monoploid genome and chromosome sizeenlargement, and apparent GC content enrichment. The backwardreduction of these parameters, running parallel in both mainevolutionary lineages of fine-leaved and broad-leaved fescues,appears to diverge among the existing species groups. The mostdramatic reductions are associated with the most recently andrapidly evolving groups which, in combination with recent intraspecificgenome size variability, indicate that the reduction processis probably ongoing and evolutionarily young. This dynamicsmay be a consequence of GC-rich retrotransposon proliferationand removal. Polyploids derived from parents with a large genomesize and high GC content (mostly allopolyploids) had smallerCx- and C/n-values and only slightly deviated from parentalGC content, whereas polyploids derived from parents with smallgenome and low GC content (mostly autopolyploids) generallyhad a markedly increased GC content and slightly higher Cx-and C/n-values. Conclusions: The present study indicates the high potential of general quantitativecharacters of the genome for understanding the long-term processesof genome evolution, testing evolutionary hypotheses and theirusefulness for large-scale genomic projects. Taken together,the results suggest that there is an evolutionary advantagefor small genomes in Festuca.     

Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes

The genomes of ray-finned fishes (Actinopterygii) are well known for their evolutionary dynamism as reflected by drastic alterations in DNA content often via regional and whole-genome duplications, differential patterns of gene silencing or loss, shifts in the insertion-to-deletion ratios of genomic segments, and major re-patternings of chromosomes via non-homologous recombination. In sharp contrast, chromosome numbers in somatic karyotypes have been highly conserved over vast evolutionary timescales – a histogram of available counts is strongly leptokurtic with more than 50% of surveyed species displaying either 48 or 50 chromosomes. Here we employ comparative phylogenetic analyses to examine the evolutionary history of alterations in fish chromosome numbers. The most parsimonious ancestral state for major actinopterygiian clades is 48 chromosomes. When interpreted in a phylogenetic context, chromosome numbers evidence many recent instances of polyploidization in various lineages but there is no clear indication of a singular polyploidization event that has been hypothesized to have immediately preceded the teleost radiation. After factoring out evident polyploidizations, a correlation between chromosome numbers and genome sizes across the Actinopterygii is marginally statistically significant (p = 0.012) but exceedingly weak (R ² = 0.0096). Overall, our phylogenetic analysis indicates a mosaic evolutionary pattern in which the forces that govern labile features of fish genomes must operate largely independently of those that operate to conserve chromosome numbers.     

INTER‐ AND INTRASPECIFIC RELATIONSHIPS BETWEEN NUCLEAR DNA CONTENT AND CELL SIZE IN SELECTED MEMBERS OF THE CENTRIC DIATOM GENUS THALASSIOSIRA (BACILLARIOPHYCEAE)1

The enormous species diversity of diatoms correlates with the remarkable range of cell sizes in this group. Nuclear DNA content relates fundamentally to cell volume in other eukaryotic cells. The relationship of cell volume to G1 DNA content was determined among selected members of the genus Thalassiosira, one of the most species‐rich and well‐studied centric diatom genera. Both minimum and maximum species‐specific cell volume correlated positively with G1 DNA content. Phylogeny based on 5.8 S and ITS rDNA sequences indicated that multiple changes in G1 DNA content and cell volume occurred in Thalassiosira evolution, leading to a 1,000‐fold range in both parameters in the group. Within the Thalassiosira weissflogii (Grunow) G. A. Fryxell et Grunow species complex, G1 DNA content varied 3‐fold: differences related to geographic origin and time since isolation; doubling and tripling of G1 DNA content occurred since isolation in certain T. weissflogii isolates; and subcultures of T. weissflogii CCMP 1336 diverged in DNA content by 50% within 7 years of separation. Actin, β‐tubulin, and Spo11/TopVIA genes were selected for quantitative PCR estimation of haploid genome size in subclones of selected T. weissflogii isolates because they occur only once in the T. pseudonana Hasle et Heimdal genome. Comparison of haploid genome size estimates with G1 DNA content suggested that the most recent T. weissflogii isolate was diploid, whereas other T. weissflogii isolates appeared to be polyploid and/or aneuploid. Aberrant meiotic and mitotic cell divisions were observed, which might relate to polyploidization. The structural flexibility of diatom genomes has important implications for their evolutionary diversification and stability during laboratory maintenance.     

MORPHOLOGY,PLOIDY, PIGMENT COMPOSITION,AND GENOME SIZE OF CULTURED STRAINS OF PHAEOCYSTIS (PRYMNESIOPHYCEAE)1

We examined cell morphology, ploidy level, cell size, pigment composition, and genome size in 16 cultured strains of Phaeocystis Lagerheim. Two strains originated from the Antarctic, 3 from the tropical Western Atlantic, and 11 from temperate regions (Eastern Atlantic, English Channel, North Sea, and Mediterranean Sea). Thirteen strains made colonies morphologically similar to P. glo-bosa Scherffel, whereas three never formed colonies under any circumstances. Five-rayed star-like structures with filaments were observed in 11 strains. In several strains, two ploidy levels were observed, one (haploid) linked to flagellates and one (diploid) linked to colonies. Cell size did not appear to be a very good criterion for distinguishing strains since size distributions overlapped. Pigment analysis by reversed-phase-high-performance liquid chroma-tography allowed the strains to be grouped into three clusters that differed from each other mainly by the relative proportions of three carotenoids: fucoxanthin, 19′-hex-anoyloxyfucoxanthin, and diadinoxanthin. All strains contained low levels of 19′-butanoyloxyfucoxanthin. Differences in genome size measured by flow cytometry delimited at least five groups. On the basis of both pigment composition and genome size, six clusters were defined, one corresponding to an Antarctic species (possibly P. antarc-tica), one to P. globosa, and the rest probably to several yet-undescribed species or subspecies. Two main conclusions emerge from this study. First, the taxonomy of the genus Phaeocystis needs to be clarified through a combination of morphological, biochemical, and molecular studies. Second, sexuality is a prevalent phenomenon in Phaeocystis, but controls of the sexual cycle are most likely strain-dependent.     

Correlations between egg size and egg energetic content within and among biotypes of the genus Poeciliopsis

That a positive correlation exists between egg size and egg energetic content is an assumption of empirical and theoretical studies of life-history evolution. Although assumed, this relationship lacks substantiative support, particularly at the intraspecific level. To this end, we evaluated the validity of this assumption within and among clonal and bisexual females of the desert fish Poeciliopsis . As anticipated, we found generally high correlations between the two variables at all levels studied. Thus, egg volume remains a reliable and often precise indicator of maternal investment in this species.     

稀有鮈鲫与其他模式实验鱼类基因组大小的比较

稀有(鱼句)鲫 (Gobiocypris rarusYe et Fu)是我国特有的小型实验鱼类,具有性成熟期短、繁殖季节长、产卵频率高等特点[1],已在生态毒理和鱼病学等研究中得到应用,显示了它作为实验鱼类的良好潜力。