Chloroplast DNA Intraspecific Phylogeography of Prairie Cordgrass (Spartina pectinata Bosc ex Link)

Chloroplast DNA (cpDNA) sequences are appropriate for studying intraspecific phylogeography. Comparing cpDNA phylogeny with different cytotypes provides insights into the origin and establishment of polyploid species. We have previously defined the geographic distribution of cytotypes in prairie cordgrass throughout the different regions of the United States. In this study, chloroplast haplotype variation is explored in 54 populations of prairie cordgrass, using nine noncoding chloroplast regions. These chloroplast analyses were combined with the cytotype surveys of prairie cordgrass to infer the phylogeography and to elucidate the origin of the different cytotypes. In this study, we identified three haplotypes, Prairie Cordgrass Group 1 (PCG1), Prairie Cordgrass Group 2 (PCG2), and Prairie Cordgrass Group 3 (PCG3). In general, related haplotypes were strongly associated with geographic distribution. Useful insertions–deletions (indels) were also found among prairie cordgrass populations. The PCG1 haplotypes collected inthe East North Central to the New England regions of the US, were polyploid (tetraploid, hexaploid, and octoploids), while the PCG2 haplotypes, found in southern South Dakota, Iowa, and Missouri, were primarily octoploids, but also included a small number of tetraploids. The PCG3 haplotypes were octoploids and were collected in North Dakota, South Dakota, and Minnesota.     

Seed Reduction in Prairie Cordgrass, Spartina pectinata Link., by the Floret-Feeding Caterpillar Aethes spartinana (Barnes and McDunnough)

Insect damage to prairie cordgrass, Spartina pectinata Link., is conspicuously high in Illinois, where attempts to collect native seed show the majority of spikelets damaged with small holes. Dissection of spikes during summer reveals minute caterpillars boring though glumes and feeding on florets inside. In 2009?C2010, panicles of prairie cordgrass from across its native range were used to estimate the percentage of insect-related damage and losses to seed production. Collections of caterpillars from panicles and stems were used to identify one floret-feeding species, estimate its distribution in the central USA, and assess its feeding patterns within spikes. Insect feeding damaged 38% of spikelets across eight states, though injury differed significantly between states. Regression of developed prairie cordgrass seeds onto insect damage suggests a 1:1 loss ratio (i.e., 50% damaged spikelets reduces seed production by 50%). Collections of caterpillars from six midwestern states suggest that larvae of a tortricid moth, Aethes spartinana (Barnes and McDunnough), are responsible for most insect damage to cordgrass spikelets. Larvae of A. spartinana generally feed on a series of consecutive spikelets, with high infestations (>50% insect damage) showing damage concentrated in the middle of spikes. Because larvae are concealed by moving into adjacent spikelets and later tunneling into cordgrass stems, they may be difficult to control using insecticides. While direct effects of the caterpillar on biomass yields for prairie cordgrass are not known, for states like Illinois (where damage to spikelets often exceeds 70%), breeding and seed production efforts may be severely limited without efforts to manage A. spartinana.     

Transcriptome Analysis of the Heritable Salt Tolerance of Prairie Cordgrass (<Emphasis Type="Italic">Spartina pectinata Link</Emphasis>)

The salt-tolerant capability of the candidate bioenergy crop prairie cordgrass greatly surpasses that of previously characterized prairie grass species and most other plants. To understand the mechanism of inherited salt tolerance, we compared phenotypic and genetic qualities in half-sib families of prairie cordgrass after salt treatment. Each family was treated with a 400 mM NaCl solution or a water control and then measured for various health phenotypes. Phenotypes associated with salt tolerance were shown to be moderately heritable between parent and offspring. RNA-seq analysis revealed differential regulation in unique pathways including metabolism, signaling, photosynthesis, and the circadian rhythm. The studies herein suggest that alternative regulation of the photosynthetic pathway could confer increased salt resistance in halophytes and can be monitored phenotypically or genetically in breeding programs. The improvement of salt-tolerant traits in prairie cordgrass would increase its potential to be grown as a bioenergy crop on lands that are not suitable for the growth of food crops.     

Chloroplast DNA variation within prairie cordgrass (Spartina pectinata Link) populations in the U.S.

Chloroplast DNA (cpDNA) is most often maternally inherited and highly conserved leading to previous observation of little to no sequence variation. Comparing cpDNA haplotypes have provided valuable insight into the establishment and migration of polyploid populations. However, to use chloroplast haplotypes to their full potential intrapopulational variation needs to be addressed. In this study, cpDNA haplotype variation was surveyed within 16 natural populations of prairie cordgrass (Spartina pectinata Link) located east of the 100th west meridian and north of the 35th north parallel in the U.S.A. using two non-coding, polymorphic chloroplast regions. Two main clades were defined with subclades as follows: haplotype 1 and haplotype 2A and 2B. It was discovered that seven populations showed intrapopulational chloroplast genome variation. Of the total amount of variation, 95.5% occurred within the octoploid populations and 4.5% occurred within the tetraploid populations. Both variant haplotypes, 2A and 2B, were found in a larger sampling of one of the natural populations, but no variation was found in a mixed ploidy population. The intrapopulational cpDNA variation we found in this study cannot directly be related to mechanisms of introduction of the non-native populations into native populations. Therefore, this cpDNA variation could be novel natural variation that has been fixed as the octoploid populations were established and moved northwest. This analysis provides insight into determining the usefulness of indels and single nucleotide polymorphisms for population identification and may provide information in regards to the origin of chloroplast variation and its subsequent fixation and establishment in natural prairie cordgrass populations.     

Substantial Genome Size Variation in Taraxacum stenocephalum (Asteraceae, Lactuceae)

There are only a few exceptions to the rule that polyploidy in Taraxacum is associated with agamospermy. One of them is the sexual, tetraploid species Taraxacum stenocephalum. Incidentally, remarkable variation in karyology was found in this species. The present study aims to confirm this variation by an extensive screen of nuclear DNA content. Individuals from two large populations in the Lesser and Greater Caucasus, Georgia were analyzed using flow cytometry to ascertain intraspecific nuclear DNA content variation. Across the whole data set comprising all 159 individuals, a 1.223-fold difference was detected based on propidium iodide (PI) analyses. To verify this finding, we compared flow-cytometric data obtained using DAPI (4′,6-diamidino-2-phenylindole) and PI staining using a representative subset of individuals. This comparison revealed a 1.194-fold difference in DNA content for DAPI and a 1.219-fold difference for PI. Mean nuclear genome size in absolute terms (2C value ± s.d.) was estimated at 4.38?±?0.21 pg, ranging from 4.01 pg to 4.89 pg, despite the invariable chromosome counts of 2n?=?32. A regression analysis comparing the datasets for DAPI and PI staining found a strong correlation between data obtained by the DAPI and PI dyes (R?=?0.976; P?=?0.0001). Simultaneous high-resolution flow-cytometric analyses also proved the accuracy of our findings. We discuss possible sources of these large differences in DNA content within Taraxacum stenocephalum. Further research is needed to identify the source of this remarkable variation.     

Genome Size Variation in Some Tropical Hardwoods

4-C DNA values of 36 tropical hardwood species belonging to 13 families show a range from 2.08 to 20.07 pg, a 9.64-fold difference. DNA per chromosome values show a 10-fold difference. The minimum range of variation (1.2-fold) is shown by Annonaceae and Sapindaceae while the maximum range (6.23-fold) is shown by Euphorbiaceae, and Fabaceae and Rutaceae show 1.7 and 1.9-fold differences, respectively. On an average, Euphorbiaceae and Rutaceae have been found to possess the largest and the smallest genome sizes respectively.     

Limited Genome Size Variation in Sesleria albicans

The extent and significance of intraspecific genome size variationin plants continues to be a matter of discussion: in some speciesconsiderable variation has been described, while no variationhas been detected in other taxa. In the present study, intraspecificgenome size variation was analysed in a perennial grass Sesleriaalbicans Kit. ex Schult. (Poaceae). Flow cytometry was usedfor the analysis of nuclear DNA content in ten geographicallyisolated populations ofS. albicans . Despite long-term isolationand lack of gene-flow between the populations, only negligibleinter-population differences were found. Although the differencesbetween the populations were statistically significant, themaximum inter-population difference reached only 1.6% of themean 2C value (9.78 ± 0.04 pg). The variation was notcorrelated with geographical location or with altitude of thepopulations analysed. The present study clearly demonstratesthat S. albicans belongs to the plant taxa with a highly stablegenome size. Copyright 2000 Annals of Botany Company Sesleria albicans, genome size, nuclear DNA content, intraspecific variation, flow cytometry, Europe     

动物线粒体基因组变异研究进展

动物mtDNA大多是共价闭合的环状双链分子,一般由2个非编码区和37个编码基因组成,不同动物线粒体基因组大小变异明显.孑遗疟虫(Plasmodium reichenowi)的线粒体基因组最小,仅为5966bp;领鞭毛虫(Monosiga brevicollis)的最大,达76568bp.动物线粒体基因组大小变异的原因主要有:控制区串联重复元件的变异;基因重复;基因重叠与基因间隔区大小的差异;基因缺失和增加.     

Polycross Seed of Genetically Diverse Smooth Cordgrass (Spartina alterniflora) for Erosion Control and Habitat Restoration

Although seed‐based planting is common in crop systems, it is relatively a new concept in coastal erosion control and habitat restoration. This paper discusses the potential use of seed‐based revegetation to accommodate large‐scale erosion control using a highly diverse population of smooth cordgrass (Spartina alterniflora) from controlled polycross to attain desirable genetic diversity suitable for habitat restoration. Seed‐based restoration provides a more versatile alternative approach to the current clonal revegetation technique in many regions, including the Gulf Coast of the United States. The objectives of this study were to (1) describe seed production and cultural aspects of the polycross population and (2) discuss the potential use of polycross seeds for direct seeding applications and other innovative restoration approaches using seed‐derived planting materials. The polycross population was produced using 15 genetically diverse and high‐seed producing smooth cordgrass lines selected from native populations. The average seed set of the polycross population was 58.5 ± 6.3% with an average germination rate of 82.2 ± 9%. As comparison, Vermilion, the only available smooth cordgrass cultivar, has a seed set of 20.6 ± 5% and a germination rate of 35 ± 8%. The average yield of S. alterniflora seed from the polycross population was 277.5 kg/ha, which is equivalent to approximately 26 million viable seeds. Seed can be stored in 100% humidity at a temperature of 2 ± 1°C for 6–9 months.     

Neopolyploidy in Spartina pectinata Link: 1. Morphological analysis of tetraploid and hexaploid plants in a mixed natural population

Prairie cordgrass has been reported as a multi-polyploidy species having three cytotypes: tetra- (2n?=?4x?=?40), hexa- (2n?=?6x?=?60), and octoploid (2n?=?8x?=?80). A mixed-ploidy population comprising tetraploids and hexaploids was recently found at a single location in Illinois. However, adaptation and morphological differences between tetra- and hexaploids occurring in natural conditions as well as the contact zones of these cytotypes have yet to be determined. In this study, the cytotypes of 147 individuals of prairie cordgrass collected across the contact zone (4x?+?6x) were determined by flow cytometry using somatic G1 nuclei, and the results were confirmed by chromosome counts. Nineteen morphological characteristics were compared between the cytotypes. Tetra- and hexaploid plants have 2C genome sizes of 1.57 and 2.36?pg with chromosome counts of 40 and 60, respectively. This increase in polyploidy resulted in a greater variability of morphological expression in Illinois prairie cordgrass. Substantial differences in the flowering time, stomatal size, and plant morphological characteristics were observed between tetra- and hexaploids. The results indicate that the increasing of ploidy level in prairie cordgrass resulted in increased plant size in ploidy mixtures. The recent event of ploidy mixtures in prairie cordgrass natural populations offers unique opportunities for studying the formation and establishment of neopolyploidy.     

Genome Size in Sphagnum (Peat Moss)

Abstract: Genome size was determined in thirty Austrian species of Sphagnum, using Feulgen absorbance photometry conducted on a video-based image analysis system (CIRES), and for comparison on a scanning cytophotometer (Leitz MPV II) with strongly correlated results. Pisum sativum (1C = 4.42pg DNA) was used for internal standardization. Between species, two levels of ploidy, haploid and diploid, could be unambiguously identified (although this identification remains, strictly speaking, hypothetical, as long as exact parallel chromosome counts are not available). Twenty-six haploid species yielded values from 0.392 pg to 0.506 pg DNA (1C), and four diploid species (including two varieties of S. palustre) from 0.814 pg to 0.952 pg. The average ratio between levels was 1:2.049. Variation between species within sections was lower than between sections. In some cases significant differences between accessions of one species were found. The genome size of Sphagnum palustre presented here strongly deviates from one estimate of this species in the literature.     

Intrapopulation Genome Size Variation in D. melanogaster Reflects Life History Variation and Plasticity

We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions.     

Effects of Life Histories on Genome Size Variation in Squamata

Genome size changes significantly among taxonomic levels, and this variation is often related to the patterns shaped by the phylogeny, life histories and ecological factors. However, there are mixed evidences on the main factors affecting molecular evolution in animals.In this study, we used phylogenetic comparative analysis to investigate the evolutionary rate of genome size and the relationships between genome size and life histories(i.e.,hatchling mass, clutch size, clutches per year, age at sexual maturity, lifespan and body mass) among 199 squamata species. Our results showed that the evolutionary rate of genome size in Lacertilia was significantly faster than Serpentes. Moreover, we also found that larger species showed larger hatchling mass, more clutches per year and clutch size and longer lifespan. However, genome size was negatively associated with clutch size and clutches per year, but not associated with body mass we looked at.The findings suggest that larger species do not possess the evolution of large genomes in squamata.     

Ecological genetic interactions between a clonal host plant (Spartina pectinata) and associated rust fungi Puccinia seymouriana and Puccinia sparganioides

The spatial scale of genetic diversity among patches of a host plant could affect the likelihood of pathogen adaptation to the host. If host patches are genetically distinct, pathogen adaptation to local host genotypes may occur. To study this issue, we focused on the ecological and genetic interactions between two rust fungi, Puccinia seymouriana and P. sparganioides, and the clonal prairie grass, Spartina pectinata. In a field transplant experiment, disease levels differed among plants from different patches, suggesting variation in resistance. Over a 4.5-km scale, disease levels were not higher on plants transplanted back into their source patch as opposed to other locations, providing no evidence for local adaptation in the pathogen. However, on the spatial scales examined (ranging from 0.2 km to 120 km), there was no relationship between the physical distance separating host patches and their similarity in isozyme banding patterns, implying that plants from more distant patches are not necessarily more genetically distinct than plants from nearby patches. Plants derived from the most distant location had, on average, the lowest mean number of pustules at the end of the summer, suggesting the need for reciprocal transplant studies to be performed on a larger spatial scale.     

Genome Size Determination in Peronosporales (Oomycota) by Feulgen Image Analysis

Genome size was determined, by nuclear Feulgen staining and image analysis, in 46 accessions of 31 species of Peronosporales (Oomycota), including important plant pathogens such asBremia lactucae, Plasmopara viticola, Pseudoperonospora cubensis,andPseudoperonospora humuli.The 1C DNA contents ranged from 0.046 (45.6 Mb) to 0.163 pg (159.9 Mb). This is 0.041- to 0.144-fold that ofGlycine max(soybean, 1C = 1.134 pg), which was used as an internal standard for genome size determination. The linearity of Feulgen absorbance photometry method over this range was demonstrated by calibration ofAspergillusspecies (1C = 31–38 Mb) againstGlycine,which revealed differences of less than 6% compared to the published CHEF data. The low coefficients of variation (usually between 5 and 10%), repeatability of the results, and compatibility with CHEF data prove the resolution power of Feulgen image analysis. The applicability and limitations of Feulgen photometry are discussed in relation to other methods of genome size determination (CHEF gel electrophoresis, reassociation kinetics, genomic reconstruction) that have been previously applied to Oomycota.     

毛竹基因组大小测定

毛竹（Phyllostachys edulis）属禾本科（Poaceae）竹亚科（Bambusoideae）刚竹属（Phyllostachys）,是我国分布和栽培面积最大的经济竹种,有着广泛的开发前景。本实验以水稻（Oryza sativa）为内标,用流式细胞仪对水稻和竹子样品的PI发射荧光强度进行测定,通过比较水稻与毛竹样品峰值的倍数关系,计算出毛竹的基因组大小。对24组样品进行重复测试,测得毛竹基因组大小为2075.025±13.08Mb,即2C DNA含量为4.24pg（以1pg DNA=0.978×10^9bp计算）。毛竹基因组大小测定为毛竹基因组文库的建立及其基因组学研究奠定了重要基础。     

毛竹基因组大小测定

毛竹(Phyllostachys edulis)属禾本科(Poaceae)竹亚科(Bambusoideae)刚竹属(Phyllostachys), 是我国分布和栽培面积最大的经济竹种, 有着广泛的开发前景。本实验以水稻(Oryza sativa)为内标, 用流式细胞仪对水稻和竹子样品的PI发射荧光强度进行测定, 通过比较水稻与毛竹样品峰值的倍数关系, 计算出毛竹的基因组大小。对24组样品进行重复测试, 测得毛竹基因组大小为 2 075.025±13.08 Mb, 即2 C DNA含量为4.24 pg(以1 pg DNA = 0.978×109 bp计算)。毛竹基因组大小测定为毛竹基因组文库的建立及其基因组学研究奠定了重要基础。     

Variation in Age and Size in Fennoscandian Three-Spined Sticklebacks (Gasterosteus aculeatus)

Average age and maximum life span of breeding adult three-spined sticklebacks (Gasterosteus aculeatus) were determined in eight Fennoscandian localities with the aid of skeletochronology. The average age varied from 1.8 to 3.6 years, and maximum life span from three to six years depending on the locality. On average, fish from marine populations were significantly older than those from freshwater populations, but variation within habitat types was large. We also found significant differences in mean body size among different habitat types and populations, but only the population differences remained significant after accounting for variation due to age effects. These results show that generation length and longevity in three-spined sticklebacks can vary significantly from one locality to another, and that population differences in mean body size cannot be explained as a simple consequence of differences in population age structure. We also describe a nanistic population from northern Finland exhibiting long life span and small body size.     

Population Variation in Patch and Party Size in Muriquis (Brachyteles arachnoides)

We examined the relationship between food patch size and feeding party size with comparative data from two populations of muriquis (Brachyteles arachnoides) in the 37,797-ha forest at the Parque Estadual de Carlos Botelho (PECB), São Paulo, and the 800-ha forest at the Estação Biológica de Caratinga (EBC), Minas Gerais. Precipitation was more abundant and less seasonal at PECB than EBC, and the density of large trees (>25.0 cm) was higher at PECB (206 ha ^–1 ) than at EBC (132 ha ^–1 ). At both sites, the size of feeding parties is positively related to the size of food patches. As predicted, food patches at PECB are significantly larger than those at EBC for both fruit and leaf sources. Contrary to expectations, feeding parties were larger at EBC than PECB. The higher population density of muriquis and sympatric primates at EBC may make large associations more advantageous to these muriquis than to muriquis living at lower population densities in PECB.