Development and interspecific transferability of genic microsatellite markers in Spartina spp. with different genome size

Flow cytometry analysis showed variation of nuclear DNA content among different species of Spartina. Spartina alterniflora had the biggest genome (1763.9 Mbp) and S. cynosuroides had the smallest genome (756.35 Mbp), whereas the genomes of S. patens (969.36 Mbp) and S. spartinae (979.78 Mbp) were comparable. Mining simple sequence repeats (SSR) from 1227 expressed sequence tags (EST) generated from salt stressed S. alterniflora showed an abundance of di- and tri-nucleotide repeats. Of 100 ESSR (EST-derived SSR) loci with five or more repeats, 81 loci were successfully amplified in eight S. alterniflora genotypes and 15 (22.2%) ESSR markers were polymorphic. Eleven of the 15 polymorphic ESSRs showed amplification across six different species of Spartina while 100% cross transferability was observed with at least one species of Spartina. The average number of alleles per marker was 3.9 and 5.8 within S. alterniflora and among Spartina species, respectively. The ESSR markers discriminated different members within and between species of Spartina genus.     

The positive and negative effects of exotic Spartina alterniflora in China

Spartina alterniflora is a perennial salt marsh grass native to the Atlantic and Gulf Coasts of North America. Recognized for its effects of diminishing strong tide even storms and accelerating sediment deposition, S. alterniflora was introduced into China in 1979. Now the artificial vegetation of Spartina has expanded to around 50 000 h m² along the east coast of China due to its strong capability of propagating by seeds and rhizome fragments. Although it was listed among 16 harmful exotic species in China 3 years ago, we need to evaluate its positive and negative effects in the coastal region of China objectively. This paper reviews some major positive effects of S. alterniflora in China, e.g. being a dominant primary producer, buffering against tides, accelerating accretion and reclamation, absorbing nutrients and digesting pollutants, as well as some major negative effects, e.g. occupying the niche of local species, altering the mudflat habitat, changing and even diminishing biodiversity, and damaging the aquiculture in the tidal land. In addition, its biomaterial uses and biological substitution as a means of ecological regulation is also discussed.     

The macrobenthos in Spartina alterniflora salt marshes of the Wanggang tidal-flat,Jiangsu coast,China

On the Jiangsu coast, eastern China, Spartina alterniflora, which was introduced artificially into the region, is becoming a dominant plant species in the inter-tidal salt marshes. In order to evaluate the environmental and ecological impact of the colonization of S. alterniflora, we carried out investigations into the benthic macrofauna of the Spartina marshes of the Wanggang area, central Jiangsu coast, in 2006 and 2007. Based on analysis of the data sets obtained, 12 species of macrobenthos have been identified for the Wanggang salt marsh, including S. alterniflora, Cerithidea cingulata, Littorna scabra, Bithynia fuchsiana, Macrophthalmus japonicus, Uca arcuata, Nereis sp., Boleophthalmus petinirostris, Cyclina sinensis, Bullacta exarata, Angustassiminea castanea and Glaucomya chinensis. The results indicate that some of the native species have adapted to the new ecological environment associated with the cordgrass S. alterniflora. The biomass of macrobenthos varies significantly over different parts of the salt marsh. Further, there is a seasonal change in bio-density, with the density in summer (July and August) > autumn (November) > early summer (May). At the landward edge and over the central part of the S. alterniflora marsh, the bio-diversity is higher than the other areas of the marsh.     

A study of the population dynamics of Spartina alterniflora at Jiuduansha shoals,Shanghai, China

This study investigated the population expansion pattern of an exotic species of Spartina alterniflora for a period of 7 years, after it had been newly introduced to the neonatal shoals of Jiuduansha (GPS), in the Yangtze Estuary, Shanghai. Remote sensing, in conjunction with geographical information systems (GIS) and global positioning systems (GPS) was used to map saltmarsh vegetation on the Jiuduansha shoals and the classifications were then checked using in situ field surveys of selected areas. The results showed that the S. alterniflora population had expanded from 55 hm² when first introduced in 1997, to 1014 hm² in 2004. The population expansion pattern of S. alterniflora on the Jiuduansha shoals was compatible with the common feature of invasions, i.e. the initial colonization, a lag time and the onset of rapid population growth and range expansion. In the first year of plantation (1997), about 35 hm² of S. alterniflora was successfully colonized on the Jiuduansha shoals. The period between 1998 and 2000 was characterized by a lag time, and the area of S. alterniflora increased only to 101.6 hm². The year 2000 marked an onset of rapid population growth and range expansion and the annual expanding rate reached 25–116%, which exceeded any of the indigenous species and indicated the strong competitive capability, rapid range expansion and wide ecological niche of S. alterniflora.The advent of remote sensing, in conjunction with geographical information systems and global positioning systems, provides a potential tool for mapping vegetation, and for monitoring population dynamics and range expansion of invasive species on a large scale. The implications for population and community dynamics, biodiversity conservation and wetland management in terms of the analysis of the sequence of events associated with the initial colonization, a lag time, rate of geographic spread and features of geographic spread of the exotic S. alterniflora and the native P. australis on the Jiuduansha shoals are discussed.     

Estimation of nuclear genome size of the genus Mycetophylax Emery, 1913: Evidence of no whole-genome duplication in Neoattini

Genome size estimates and their evolution can be useful for studying the phylogenetic relationships and taxonomy of a particular group. In the present study, the genome sizes of the three species that comprise the Mycetophylax genus were estimated by flow cytometry (FCM). There was little variation in genome size among them. The mean haploid genome size value of male and female individuals of Mycetophylax morschi was 312.96 Mbp (0.32 pg) and that of Mycetophylax conformis and Mycetophylax simplex females were 312.96 Mbp (0.32 pg) and 381.42 Mbp (0.39 pg), respectively. At first glance, this variation could be related with the heterochromatin content. Our results, together with other previous reports, have contributed to our knowledge about Attini genome size and will be useful to improve the understanding of the evolution of this tribe. It will help select potential model species in Attini for future genomic and sequencing projects.     

Sulfur storage changed by exotic Spartina alterniflora in coastal saltmarshes of China

For the purpose of ecological engineering, Spartina alterniflora was introduced to China in 1979 and now covers about 112,000 ha of China's coastal lands. It was hypothesized that S. alterniflora could actively change the habitat environment, thus facilitating its competition over native species. In Yancheng Nature Reserve, sulfur storage of sediments and plant tissues was compared among marshes dominated by the exotic S. alterniflora and adjacent native Suaeda salsa and Phragmites australis and bare mudflat. Results showed that the S. alterniflora marsh contained the highest content of water-soluble, adsorbed, carbonate-occluded and total sulfur in the sediment. The sulfur levels were higher in the center than at the edges of the S. alterniflora marsh. Native marshes showed no significant difference in sediment sulfur levels. With greater biomass and higher tissue sulfur concentrations, plant sulfur storage of S. alterniflora vegetation was also larger than those of the native vegetations. Because higher concentrations of sulfur increase the competitive advantage of S. alterniflora over native halophytes, the results of the research showing that S. alterniflora increased marsh sulfur storage may shed light on the mechanism of expansion of monospecific vegetation in coastal China.     

Temporal–spatial variation and source analysis of carbon and nitrogen in a tidal wetland of Luoyuan Bay

Carbon and nitrogen are important elements in biogeochemical studies of tidal wetlands. Three wetland zones in Luoyuan Bay in the Fujian province were chosen for this study; the Spartina alterniflora flat zone with Spartina alterniflora growing, the silt zone with no Spartina alterniflora growing and the Spartina alterniflora-silt flat zone – a transition zone between the two. The spatial and seasonal variations of total organic carbon (TOC), total nitrogen (TN), stable isotopes of organic material (δ¹³C, δ¹⁵N), C/N ratio, average particle size and sediment composition in surface and vertical sediments of different ecological zones were analyzed. Carbon and nitrogen accumulation and particle size effects in the different ecological zones were discussed and the indicators of δ¹³C and C/N ratios were also compared. TOC, TN, δ¹³C contents, C/N ratios, and average particle size varied within the ranges of 0.611–1.133%, 0.053–0.090%, ?22.60 to ?18.92‰, 12.3–15.7, and 6.4–8.7 μm, respectively. Sediments were mainly silt-sized. Besides δ¹⁵N values, the other parameters, such as TOC, TN, δ¹³C contents, C/N ratios, and average particle size showed an obvious zonal distribution in surface sediments. The distribution of TOC and TN contents reflected the distribution of Spartina alterniflora within the bay. The profile and seasonal variations of these parameters in different ecological zones indicated that variations in the Spartina alterniflora flat and transition zones were complex because of the effect of Spartina alterniflora. Vertical and seasonal variations were sampled in the silt flat area. The profile and seasonal variations of TOC, TN and δ¹³C were similar in the transition zone and the Spartina alterniflora flat zone. Seasonal concentrations of TOC, TN and δ¹³C decreased from autumn > spring > winter > summer. The seasonal variation of carbon and nitrogen in the sediments may be influenced by temperature, particle size, plankton and benthos. The particle size effect was significant in the surface sediments and profile sediments of the transition zone. However, other factors had a greater effect on the distributions of TOC and TN in the Spartina alterniflora flat and silt flat zones. C/N ratios in sediments of the Spartina alterniflora flat, transition zone and silt flat were close to or > 12, indicating that the organic material source was dominated by terrestrial inputs. However, δ¹³C values decreased from the Spartina alterniflora flat zone > transition zone > silt flat zone indicating that the organic material source was predominantly from marine inputs. Thus the indications from C/N ratios and δ¹³C were different. There was no clear relationship between C/N ratios and δ¹³C values and a better relationship between δ¹³C values and TOC concentrations suggested that δ¹³C values provided a better indication of the organic source. Limited amounts of organic material came from Spartina alterniflora. This study has provided basic data for researching biogeochemical processes of biogenic elements in tidal wetlands and vegetation restoration, and has also provided a reference for assessing and protecting the environment and ecological systems in wetlands.     

Effect of NaCl on growth and Cd accumulation of halophyte Spartina alterniflora under CdCl2 stress

A study quantifying the effect of NaCl on growth and Cd accumulation of Spartina alterniflora subjected to Cd stress was conducted. Seedlings were cultivated in the presence of 1 or 3 mM Cd alone, or combined with NaCl (50 or 100 mM). The results showed that NaCl magnified the phytotoxicity of moderate Cd stress (1 mM Cd) on plants due to reduced levels of plant biomass, plant height, and chlorophyll a + b, while no synergistic effects were recorded under severe Cd stress (3 mM Cd). Proline and Ca^2 + accumulated along with additional NaCl under moderate Cd stress, instead of reduced or unchanged levels under severe Cd stress owing to different adoption strategies caused by NaCl under different Cd stresses. NaCl reduced the oxidative stress in Cd-treated plants through increasing levels of antioxidative enzymes (catalase (CAT) and peroxidase (POD)) under moderate Cd stress. With NaCl addition, Cd^2 + contents in S. alterniflora increased and reduced under moderate and severe Cd stress, respectively. However, total Cd^2 + amounts increased with increasing NaCl concentration due to biological dilution. NaCl improved the increase of Cd^2 + translocation factor (TF) under moderate Cd stress, indicating that NaCl might improve Cd^2 + uptake and translocation from roots to shoots, and enhance the phytoextraction of S. alterniflora on Cd; while phytostabilization of Cd under severe Cd stress may be possible due to the reduced TF. Thus, NaCl alleviated phytotoxicity caused by Cd stress through improved management of osmotic solutes and oxidative status, and affected Cd accumulations in S. alterniflora differently under moderate and severe Cd stresses.     

Cytological and electrophoretic karyotyping of the chestnut blight fungus Cryphonectria parasitica

The karyotypes of nine strains including three transformants of the chestnut blight fungus Cryphonectria parasitica were analyzed by pulsed-field gel electrophoresis (PFGE) and cytology using a fluorescence microscope. Cytology of the mitotic metaphase showed n = 9 for both standard strain EP155 and field strain GH2 infected by Cryphonectria hypovirus 3. Chromosomes were morphologically characterized by size, heterochromatic segment, and constriction. PFGE resolved 5 or 6 chromosomal DNA bands ranging from 3.3 Mbp to 9.7 Mbp, but accurate determination of the chromosome number was hampered by clumping of some bands. Banding profiles in PFGE were similar among the strains except for GH2, in which a chromosome translocation was detected by Southern blot analysis. By integrating the data from cytology and PFGE, the genome size of C. parasitica was estimated to be ca. 50 Mbp. This is the first report of a cytological karyotype in the order Diaporthales.     

Growth of tissue culture–regenerated salt marsh monocots in a simulated marsh field plot: Implication for wetland creation and restoration

Phenotypically and genetically variable salt marsh plants are needed for wetland creation and restoration efforts. Selected tissue culture regenerants of five salt marsh monocots, Spartina patens, Spartina alterniflora, Juncus gerardi, Juncus roemerianus, and Scirpus robustus, were planted in a simulated marsh field plot that was flood-irrigated with 10 ppt salt water to compare their phenotypic variation for potential use in wetland projects. Plant growth was evaluated after one growing season. Phenotypic variation among regenerants was found in S. alterniflora, S. patens and J. gerardi, indicating the occurrence of somaclonal variation. In S. alterniflora, significant differences occurred among regenerants in stem density. In J. gerardi, significant differences occurred in height and clone circumference. In S. patens, two of the nine regenerants exhibited higher biomass and stem density than some of the other regenerants. By using the random amplified polymorphic DNA (RAPD) technique, genome DNA variation in S. patens regenerants was detected. Genetic variation not only occurred among phenotypically different regenerants, but also among those phenotypically similar for the characteristics measured. Tissue culture–regenerated plants often have desirable genetic characteristics and adaptability as a result of somaclonal variation and may enable a species to perform its ecological functions in created or restored wetlands where ideal environments cannot be achieved. Thus, some previously unrestorable sites may be restorable or marginal marshes made more productive.     

Variability of soil carbon sequestration capability and microbial activity of different types of salt marsh soils at Chongming Dongtan

Variations in the soil carbon sequestration capability of different types of salt marsh soils at Chongming Dongtan and its influencing factors were studied by analyzing the soil organic carbon (SOC) content, organic matter input and microbial activities. The results indicated that the total SOC content at Area A (southeast of Dongtan, sandy soil with Phragmites communis) was only 46.11% of that of Area B (northeast of Dongtan, clay soil with mixed P. communis and Spartina alterniflora) (P = 0.000 < 0.05), but their organic matter input per year was almost identical. These findings implied that Area B had a lower output of SOC. The microbial biomass at Area A was 3.83 times greater than that at Area B (P = 0.049 < 0.05); the soil catalase and invertase activities at Area A, which were related to carbon metabolism, were 60.31% (P = 0.006 < 0.05) and 34.33% (P = 0.021 < 0.05) higher than at Area B, respectively; and the soil respiration at Area A was also higher than at Area B. These findings implied that the microbial activities at Area A were greater than those at Area B, and therefore the carbon metabolism was rapid, resulting in increased SOC output at Area A. Increased water content and salinity in the clay soil at Area B may inhibit the microbial activities, thereby reducing the decomposition of the organic matter and enhancing carbon sequestration. In addition, some artificial measures for controlling spread of S. alterniflora at Area B (mowing/digging and tillage (M + D); mowing/digging and tillage/waterlogging (M + D + W)) were found to generally improve the microbial activity of soil, thereby increasing SOC output. However, when the two different physical controlling modes were compared, the SOC and microbial activities of the soil subjected to the M + D + W treatment were relatively high and low, respectively, due to waterlogging restraining the microbial metabolism. These findings indicated that the difference in microbial activities was the important factor leading to variability in the SOC sequestration capability between Areas A and B. Additionally, with the exception of soil texture and vegetation types, environmental conditions and artificial turbulence also influenced microbial activities of soil, and hence SOC output and organic carbon sequestration capability.     

Complete mitochondrial genome of Coelomactra antiquata (Mollusca: Bivalvia): The first representative from the family Mactridae with novel gene order and unusual tandem repeats

The complete mitochondrial genome plays an important role in the accurate inference of phylogenetic relationships among metazoans. Mactridae, also known as trough shells or duck clams, is an important family of marine bivalve clams in the order Veneroida. Here we present the complete mitochondrial genome sequence of the Xishishe Coelomactra antiquata (Mollusca: Bivalvia), which is the first representative from the family Mactridae. The mitochondrial genome of C. antiquata is of 17,384 bp in length, and encodes 35 genes, including 12 protein-coding, 21 transfer RNA, and 2 ribosomal RNA genes. Compared with the typical gene content of animal mitochondrial genomes, atp8 and tRNAS₂ are missing. Gene order of the mitochondrial genome of C. antiquata is unique compared with others from Veneroida. In the mitochondrial genome of the C. antiquata, a total of 2189 bp of non-coding nucleotides are scattered among 26 non-coding regions. The largest non-coding region contains one section of tandem repeats (99 bp × 11), which is the second largest tandem repeats found in the mitochondrial genomes from Veneroida. The phylogenetic trees based on mitochondrial genomes support the monophyly of Veneridae and Lucinidae, and the relationship at the family level: ((Veneridae + Mactridae) + (Cardiidae + Solecurtidae)) + Lucinidae. The phylogenetic result is consistent with the morphological classification. Meanwhile, bootstrap values are very high (BP = 94–100), suggesting that the evolutionary relationship based on mitochondrial genomes is very reliable.     

Analysis of genetic variation in selected stocks of hatchery flounder,Paralichthys olivaceus,using AFLP markers

Amplified fragment length polymorphism (AFLP) analysis was performed in order to evaluate genetic characteristics of one common population and two selective hatchery populations of flounder Paralichthys olivaceus. A group of 60 genotypes belonging to three populations was screened using 10 different AFLP primer combinations. A total of 491 loci were produced in the three studied populations. The loci of 65.78%, 61.47% and 60.92% were polymorphic over all the genotypes tested in common, susceptible and resistant populations, respectively. The number of polymorphic loci detected by single primer combination ranged from 21 to 43. The average heterozygosity of common, susceptible and resistant populations was 0.1656, 0.1609 and 0.1586, respectively, which showed no significant difference. Compared with the common population, the two selective hatchery populations, susceptible and resistant, showed significant genetic differences including a smaller (P < 0.05) number of total loci, a smaller (P < 0.05) number of total polymorphic loci and a smaller (P < 0.05) percentage of low frequency (0–0.2) polymorphic loci. AFLP banding pattern was transformed into binary data and matrices were processed with POPGENE and TFPGA software. Similarity relationships were described graphically by a dendrogram, which clustered the three populations. The AFLP fingerprinting technique was confirmed to be a reproducible and sensitive tool for the study of population genetics of flounder. The present study confirmed that it was important to detect the genetic variability of the selective hatchery populations for the conservation of natural flounder resources.     

An expanded genetic linkage map of an intervarietal Agaricus bisporus var. bisporus × A. bisporus var. burnettii hybrid based on AFLP,SSR and CAPS markers sheds light on the recombination behaviour of the species

A genetic linkage map for the edible basidiomycete Agaricus bisporus was constructed from 118 haploid homokaryons derived from an intervarietal A. bisporus var. bisporus × A. bisporus var. burnettii hybrid. Two hundred and thirty-one AFLP, 21 SSR, 68 CAPS markers together with the MAT, BSN, PPC1 loci and one allozyme locus (ADH) were evenly spread over 13 linkage groups corresponding to the chromosomes of A. bisporus. The map covers 1156 cM, with an average marker spacing of 3.9 cM and encompasses nearly the whole genome. The average number of crossovers per chromosome per individual is 0.86. Normal recombination over the entire genome occurs in the heterothallic variety, burnettii, contrary to the homothallic variety, bisporus, which showed adaptive genome-wide suppressed recombination. This first comprehensive genetic linkage map for A. bisporus provides foundations for quantitative trait analyses and breeding programme monitoring, as well as genome organisation studies.     

Characterization of genetic variance within and among five populations of Sperata seenghala (Skyes, 1839) revealed by random amplified polymorphic DNA markers

The genetic diversity among five populations (Bhadbada reservoir, Mohinisagar reservoir, Bansagar reservoir, Bargi reservoir and Gandhisagar reservoir) was revealed using random amplified polymorphic DNA markers. 10 random primers screened, 5 primers revealed various banding patterns and yielded 71 total loci as an average of which 39.60 (55.77%) were polymorphic between the population and 86.84% within the population of Sperata seenghala. Population wise the highest genetic polymorphism was obtained in Bhadbada reservoir as 67.61% whereas the lowest was in Gandhisagar reservoir as 49.30%. However, Analysis of Molecular Variance indicated low genetic diversity (H_pop = 0.0921 ± 0.1249; I = 0.1584 ± 0.1942) in Bansagar reservoir. Relative genetic differentiation (G_ST = 0.3993) and restricted gene flow (N_m = 0.7523) as an average indicated low gene diversity among the fish populations. The un-weighted pair group method with averages (UPGMA) dendrogram showed 05 major clusters, each cluster representing a population. Fish population of Mohinisagar reservoir showed high genetic distance (0.3981) with respective Bargi reservoir population and highest genetic identity (0.8846) reflected between Bansagar and Gandhisagar reservoir. Highest genetic distance between Mohinisagar and Bargi reservoir fish populations shows no significant correlation between genetic and geographical distance of the genotypes collected from different lentic and geographical isolated water bodies. This investigation indicated that lowest genetic diversity existed in different geographic populations of S. seenghala. All the five populations were found to be low in genetic variation, which is useful information for future conservation measures of S. seenghala confined in natural water bodies of Madhya Pradesh.     

Corynebacterium sanguinis sp. nov., a clinical and environmental associated corynebacterium

Clinical and environmental-associated strains (n = 17), genotypically related to Corynebacterium spp., yet distinct from any species of the genus Corynebacterium with validly published names, have been isolated during the last 20 years and tentatively identified as Corynebacterium sanguinis, although the combination, “Corynebacterium sanguinis” was never validly published. The comprehensive genotypic and phenotypic characterisations and genomic analyses in this study support the proposal for recognizing the species within the genus Corynebacterium, for which the name, Corynebacterium sanguinis sp. nov., is reaffirmed and proposed. Strains of Corynebacterium sanguinis are Gram-positive, non-motile, non-spore-forming, short, pleomorphic and coryneform bacilli, growing aerobically, with CO₂. They contain mycolic acids, major respiratory menaquinones, MK-8 (II-H₂) and MK-9 (II-H₂), and polar lipids, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphoglycolipid, glycolipids and a novel lipid that remains to be characterized and identified. Strains of Corynebacterium sanguinis are genotypically most similar to Corynebacterium lipophiliflavum, with 16S rRNA gene sequence similarities of 98.3% and rpoB sequence similarities of 94.9–95.2%. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were able to clearly differentiate Corynebacterium sanguinis from the most closely related species. The genome size of Corynebacterium sanguinis is 2.28–2.37 Mbp with 65.1–65.5 mol% G + C content. A total of 2202–2318 ORFs were predicted, comprising 2141–2251 protein-encoding genes. The type strain is CCUG 58655^T (=CCM 8873^T = NCTC 14287^T).     

Electrophoresis karyotype and chromosome-length polymorphism of Histoplasma capsulatum clinical isolates from Latin America

Intact chromosomes of 19 clinical isolates of Histoplasma capsulatum recently obtained in Argentina, Mexico and Guatemala and the laboratory reference strain G186B from Panama were analyzed using pulsed-field gel electrophoresis. Chromosomal banding patterns of the human isolates revealed 5–7 bands, ranging from 1.3 to 10 Mbp in size. Strain G186B showed five bands of approximately 1.1, 2.8, 3.3, 5.4 and 9.7 Mbp. Thirteen different electrokaryotypes were identified, indicating that the genome of H. capsulatum varies widely in nature, as observed previously in laboratory strains. No definite association was found between electrokaryotype and geographical or clinical source.     

Pantoea endophytica sp. nov., novel endophytic bacteria isolated from maize planting in different geographic regions of northern China

Four endophytic bacterial strains were isolated from root, stem and leaf of maize planted in different regions of northern China. The four strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. Furthermore, the average nucleotide identity (ANI) values among them were higher than 95%, suggesting they all belong to one species. Based on 16S rRNA gene phylogeny, the four strains were clustered together with Pantoea rodasii LMG 26273^T and Pantoea rwandensis LMG 26275^T, but on a separate branch. Multilocus sequence analysis (MLSA) indicated that the four strains form a novel Pantoea species. Authenticity of the novel species was confirmed by ANI comparisons between strain 596^T and its closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. The genome size of 596^T was 5.1Mbp, comprising 4896 predicted genes with DNA G + C content of 57.8 mol%. The respiratory quinone was ubiquinone-8 (Q-8) and the polar lipid profile consisted of phosphatidylethanolamin, diphosphatidylglycerol, phosphatidylglycerol, unidentified aminophospholipid and unidentified phospholipid. The major fatty acids of strain 596^T were C_16:0, summed feature 2 (C_12:0 aldehyde), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, the four isolates are considered to represent a novel species of the genus Pantoea, for which the name Pantoea endophytica sp. nov., is proposed, with 596^T (= DSM 100,785^T = CGMCC 1.15280^T) as type strain.     

Characterization of microsatellite loci in Spartina species (Poaceae)

The cordgrasses in the genus Spartina have become model organisms for studying biological invasions from both ecological and genetic perspectives. Here we characterize 11 disomic loci in Spartina alterniflora that show promise for population studies and for studying hybridization events between S. alterniflora and S. foliosa. Comparisons among invasive and native S. alterniflora populations showed that levels of allelic variation are lower in invasive populations. In addition, nearly all loci that amplified in S. foliosa populations and in a swarm of S. alterniflora×foliosa hybrids were polymorphic. We also found that several loci amplified successfully in other Spartina species.     

Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: An ultra-large metazoan mitochondrial genome

The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8–10 length variants. The motifs of the HTR arrays are about 353–362 bp and the number of repeats ranges from 1 to 11.