Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis

Mitochondria are archetypal eukaryotic organelles that were acquired by endosymbiosis of an ancient species of alpha‐proteobacteria by the last eukaryotic common ancestor. The genetic information contained within the mitochondrial genome has been an important source of information for resolving relationships among eukaryotic taxa. In this study, we utilized mitochondrial and chloroplast genomes to explore relationships among prasinophytes. Prasinophytes are represented by diverse early‐diverging green algae whose physical structures and genomes have the potential to elucidate the traits of the last common ancestor of the Viridiplantae (or Chloroplastida). We constructed de novo mitochondrial genomes for two prasinophyte algal species, Pyramimonas parkeae and Cymbomonas tetramitiformis, representing the prasinophyte clade. Comparisons of genome structure and gene order between these species and to those of other prasinophytes revealed that the mitochondrial genomes of P. parkeae and C. tetramitiformis are more similar to each other than to other prasinophytes, consistent with other molecular inferences of the close relationship between these two species. Phylogenetic analyses using the inferred amino acid sequences of mitochondrial and chloroplast protein‐coding genes resolved a clade consisting of P. parkeae and C. tetramitiformis; and this group (representing the prasinophyte clade I) branched with the clade II, consistent with previous studies based on the use of nuclear gene markers.     

Genome organisation of the marine Roseobacter clade member Marinovum algicola

The Roseobacter clade, belonging to the family Rhodobacteraceae of the class Alphaproteobacteria, is one of the major bacterial groups in marine environments. A remarkable wealth of diverse large plasmids has been detected in members of this lineage. Here, we analysed the genome structure and extrachromosomal DNA content of four strains of the roseobacter species Marinovum algicola by pulsed-field gel electrophoresis. They were originally isolated from toxic dinoflagellates and possess multireplicon genomes with sizes between 5.20 and 5.35 Mb. In addition to the single circular chromosomes (3.60–3.74 Mb), whose organisation seem to be conserved, 9 to 12 extrachromosomal replicons have been detected for each strain. This number is unprecedented for roseobacters and proposes a sophisticated regulation of replication and partitioning to ensure stable maintenance. The plasmid lengths range from 7 to 477 kb and our analyses document a circular conformation for all but one of them, which might represent a linear plasmid-like prophage. In striking contrast to other roseobacters, up to one-third of the genomic information (1.75 Mb) is plasmid borne in Marinovum algicola. The plasmid patterns of some strains are conspicuously different, indicating that recombination and conjugative gene transfer are dominant mechanisms for microevolution within the Roseobacter clade.     

The ancestor of the <Emphasis Type="Italic">Paulinella</Emphasis> chromatophore obtained a carboxysomal operon by horizontal gene transfer from a <Emphasis Type="Italic">Nitrococcus</Emphasis>-like γ-proteobacterium

Background  

Paulinella chromatophora is a freshwater filose amoeba with photosynthetic endosymbionts (chromatophores) of cyanobacterial origin that are closely related to free-living Prochlorococcus and Synechococcus species (PS-clade). Members of the PS-clade of cyanobacteria contain a proteobacterial form 1A RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) that was acquired by horizontal gene transfer (HGT) of a carboxysomal operon. In rDNA-phylogenies, the Paulinella chromatophore diverged basal to the PS-clade, raising the question whether the HGT occurred before or after the split of the chromatophore ancestor.     

Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes

Prasinophytes form a paraphyletic assemblage of early diverging green algae, which have the potential to reveal the traits of the last common ancestor of the main two green lineages: (i) chlorophyte algae and (ii) streptophyte algae. Understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary processes that may have occurred in both green lineages. In this study, we sequenced the chloroplast genome of Pyramimonas parkeae NIES254 and compared it with that of P. parkeae CCMP726, the only other fully sequenced P. parkeae chloroplast genome. The results revealed that P. parkeae chloroplast genomes are surprisingly variable. The chloroplast genome of NIES254 was larger than that of CCMP726 by 3,204 bp, the NIES254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and the IR was 1,086 bp shorter than that of CCMP726. Similarity values of the two strains were almost zero in four large hot spot regions. Finally, the strains differed in copy number for three protein‐coding genes: ycf20, psaC, and ndhE. Phylogenetic analyses using 16S and 18S rDNA and rbcL sequences resolved a clade consisting of these two P. parkeae strains and a clade consisting of these plus other Pyramimonas isolates. These results are consistent with past studies indicating that prasinophyte chloroplast genomes display a higher level of variation than is commonly found among land plants. Consequently, prasinophyte chloroplast genomes may be less useful for inferring the early history of Viridiplantae than has been the case for land plant diversification.     

Food attraction and population growth of fungivorous nematodes with different fungi

Food attraction of the fungivorous nematodes Aphelenchus avenae and Aphelenchoides spp. to seven fungal species (Pyrenochaeta lycopersici, Botrytis cinerea, Rhizoctonia solani strains AG 3 and AG 2‐1, Verticillium dahliae, Pochonia bulbillosa, Mortierella hyalina and Trichoderma harzianum) was determined on agar plates by counting the number of test nematodes present on the mycelium of each fungus 24 h after inoculation. Population growth of A. avenae and Aphelenchoides spp. on five of the seven fungi included in the attraction test (P. lycopersici, R. solani strain AG 3, V. dahliae, P. bulbillosa and T. harzianum) was also determined on agar plates by counting nematode numbers every week during a 6‐week period. A. avenae and Aphelenchoides spp. were attracted to all the fungi tested. A. avenae was preferentially attracted to V. dahliae (P < 0.0001), and Aphelenchoides spp. did not show any preference except for low attraction to R. solani. A. avenae and Aphelenchoides spp. reproduced on all fungal species tested. After 6 weeks of incubation, the highest number of nematodes was found on P. lycopersici and P. bulbillosa, while the lowest number occurred on R. solani for A. avenae and on T. harzianum for Aphelenchoides spp. The suitability of a fungus as a host was not clearly related to the attraction to that fungus.     

nGASP – the nematode genome annotation assessment project

Background  

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase.     

Speciation in <Emphasis Type="Italic">Chlamydia</Emphasis>: Genomewide Phylogenetic Analyses Identified a Reliable Set of Acquired Genes

Horizontal gene transfer (HGT), a process through which genomes acquire sequences from distantly related organisms, is believed to be a major source of genetic diversity in bacteria. A central question concerning the impact of HGT on bacterial genome evolution is the proportion of horizontally transferred sequences within genomes. This issue, however, remains unresolved because the various methods developed to detect potential HGT events identify different sets of genes. The present-day consensus is that phylogenetic analysis of individual genes is still the most objective and accurate approach for determining the occurrence and directionality of HGT. Here we present a genome-scale phylogenetic analysis of protein-encoding genes from five closely related Chlamydia, identifying a reliable set of sequences that have arisen via HGT since the divergence of the Chlamydia lineage. According to our knowledge, this is the first systematic phylogenetic inference-based attempt to establish a reliable set of acquired genes in a bacterial genome. Although Chlamydia are obligate intracellular parasites of higher eukaryotes, and thus suspected to be isolated from HGT more than the free-living species, our results show that their diversification has involved the introduction of foreign sequences into their genome. Furthermore, we also identified a complete set of genes that have undergone deletion, duplication, or rearrangement during this evolutionary period leading to the radiation of Chlamydia species. Our analysis may provide a deeper insight into how these medically important pathogens emerged and evolved from a common ancestor.     

The evolutionary position of nematodes

Background  

The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes.     

Effects of microbivore species composition and basal resource enrichment on trophic-level biomasses in an experimental microbial-based soil food web

Previous theoretical and empirical evidence suggests that species composition within trophic levels may profoundly affect the response of trophic-level biomasses to enhanced basal resources. To test whether species composition of microbivorous nematodes has such an effect in microbial-based soil food webs, I created three microcosm food webs, consisting of bacteria, fungi, bacterial-feeding nematodes (Acrobeloides tricornus, Caenorhabditis elegans), fungal-feeding nematodes (Aphelenchus avenae, Aphelenchoides sp.) and a predatory nematode (Prionchulus punctatus). The food webs differed in species composition at the second trophic level: food web A included A. tricornus and Aph. avenae, food web B included C. elegans and Aphelenchoides sp., and food web AB included all four species. I increased basal resources by adding glucose to half of the replicates of each food web, and sampled microcosms destructively four times during a 22-week experiment to estimate the biomass of organisms at each trophic level. Microbivore species composition significantly affected bacterivore and fungivore biomass but not bacterial, fungal or predator biomass. Greatest bacterivore and fungivore biomass was found in food web A, intermediate biomass in food web AB, and smallest biomass in food web B. Basal resource addition increased the biomass of microbes and microbivores but did not affect predator biomass. Importantly, microbivore species composition did not significantly modify the effect of additional resources on trophic-level biomasses. The presence of a competitor reduced the biomass of A. tricornus and Aph. avenae, in that the biomass of these species was less in food web AB than in food web A, whereas the biomass of C. elegans and Aphelenchoides sp. was not affected by their potential competitors. The biomass of Aph. avenae increased with additional resources in the absence of the competitor only, while the biomass of A. tricornus and Aphelenchoides sp. increased also in the presence of their competitors. The results imply that microbivore species composition may determine the second-level biomass in simple microbe-nematode food webs, but may not significantly affect biomass at other levels or modify the response of trophic-level biomasses to enhanced basal resources. The study also shows that even if the role of predation in a food web is diminished, the positive response of organisms to increased resource availability may still be hindered by competition. Received: 22 June 1998 / Accepted: 28 August 1998     

Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification,characterization and distribution (Diptera: Culicidae)

Simple sequence repeats (SSRs) exist in both eukaryotic and prokaryotic genomes and are the most popular genetic markers, but the SSRs of mosquito genomes are still not well understood. In this study, we identified and analyzed the SSRs in 23 mosquito species using Drosophila melanogaster as reference at the whole-genome level. The results show that SSR numbers (33 076-560 175/genome) and genome sizes (574.57-1342.21 Mb) are significantly positively correlated (R~= 0.8992, P < 0.01), but the correlation in individual species varies in these mosquito species. In six types of SSR, mono- to trinucleotide SSRs are dominant with cumulative percentages of 95.14%-99.00% and densities of 195.65/Mb-787.51/Mb, whereas tetra- to hexanucleotide SSRs are rare with 1.12%-4.22% and 3.76/Mb-40.23/Mb. The (A/T)n,(AC/GT)n and (AGC/GCT)n are the most frequent motifs in mononucleotide, dinucleotide and trinucleotide SSRs, respectively, and the motif frequencies of tetra- to hexanucleotide SSRs appear to be species-specific. The 10-20 bp length of SSRs are dominant with the number of 11() 561 ± 93 482 and the frequency of 87.25%± 5.73% on average, and the number and frequency decline with the increase oflength. Most SSRs(83.34%± 7.72%) are located in intergenic regions, followed by intron regions (11.59%± 5.59%), exon regions (3.74%± 1.95%), and untranslated regions (1.32%± 1.39%). The mono-, di- and trinucleotide SSRs are the main SSRs in both gene regions (98.55%± 0.85%) and exon regions (99.27%± 0.52%). An average of 42.52% of total genes contains SSRs, and the preference for SSR occurrenee in different gene subcategories are species-specific. The study provides useful insights into the SSR diversity, characteristics and distribution in 23 mosquito species of genomes.     

A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae,Lepidoptera)

Antheraea pernyi is a semi‐domesticated lepidopteran insect species valuable to the silk industry, human health, and ecological tourism. Owing to its economic influence and developmental properties, it serves as an ideal model for investigating divergence of the Bombycoidea super family. However, studies on the karyotype evolution and functional genomics of A. pernyi are limited by scarce genomic resource. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first high‐quality A. pernyi genome from a single male individual. The genome is 720.67 Mb long with 49 chromosomes and a 13.77‐Mb scaffold N50. Approximately 441.75 Mb, accounting for 60.74% of the genome, was identified as repeats. The genome comprises 21,431 protein‐coding genes, 85.22% of which were functionally annotated. Comparative genomics analysis suggested that A. pernyi diverged from its common ancestor with A. yamamai ~30.3 million years ago, and that chromosome fission contributed to the increased chromosome number. The genome assembled in this work will not only facilitate future research on A. pernyi and related species but also help to progress comparative genomics analyses in Lepidoptera.     

F supergroup <Emphasis Type="Italic">Wolbachia</Emphasis> in bush crickets: what do patterns of sequence variation reveal about this supergroup and horizontal transfer between nematodes and arthropods?

Wolbachia pipientis, an intracellular, α-proteobacterium, is commonly found in arthropods and filarial nematodes. Most infected insects are known to harbor strains of Wolbachia from supergroups A or B, whereas supergroups C and D occur only in filarial nematodes. Here, we present molecular evidence from two genes (ftsZ and 16S rDNA) that 2 Orthopterans (the bush cricket species Orocharis saltator and Hapithus agitator; Gryllidae: Eneopterinae) are infected with Wolbachia from the F supergroup. Additionally, a series of PCR tests revealed that these bush cricket specimens did not harbor nematodes, thus indicating that our positive results were not a by-product of nematodes being present in these cricket samples. Patterns of molecular variation suggest that (1) strains of F supergroup Wolbachia exhibit less genetic variation than the nematode-specific C and D supergroups but more than the A and B supergroups found in arthropods and (2) that there is no evidence of recombination within F supergroup strains. The above data support previous findings that F supergroup Wolbachia is not only harbored in both nematodes and arthropods, but that horizontal transfer has likely occurred recently between these diverse taxonomic groups (although the exact details of such horizontal transmissions remain unclear). Moreover, the limited genetic variation and lack of recombination in the F supergroup suggest that this clade of Wolbachia has radiated relatively rapidly with either (1) little time for recombination to occur or (2) selection against recombination as occurs in the mutualistic C and D strains of Wolbachia – both of which remain to be explored further.     

Evidence of recent interkingdom horizontal gene transfer between bacteria and <Emphasis Type="Italic">Candida parapsilosis</Emphasis>

Background  

To date very few incidences of interdomain gene transfer into fungi have been identified. Here, we used the emerging genome sequences of Candida albicans WO-1, Candida tropicalis, Candida parapsilosis, Clavispora lusitaniae, Pichia guilliermondii, and Lodderomyces elongisporus to identify recent interdomain HGT events. We refer to these as CTG species because they translate the CTG codon as serine rather than leucine, and share a recent common ancestor.     

The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall., is an ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type. We generated a final consensus genome sequence of 366 Mb comprising eight chromosomes. The N50 scaffold was ~44 Mb with the longest chromosome being 66.5 Mb. The chloroplast and mitochondrial genomes were 158,217 bp and 383,281 bp long, which is in accordance with previously published plastid sequences. This is the first report of the genome of ground cherry (P. fruticosa) sequenced by long read technology only. The datasets obtained from this study provide a foundation for future breeding, molecular and evolutionary analysis in Prunus studies.     

Two new species of <Emphasis Type="Italic">Aphelenchoides</Emphasis> (Nematoda: Aphelenchida: Aphelenchoidea: Aphelenchidae) from Manipur,India

Analysis of the soil samples collected from around rhizospheric region of mulberry plants grown in Yurembam Rose Garden, Yurembam, Imphal West, Manipur yielded several soil and plant parasitic nematodes. Among them four species of Aphelenchoides were recorded. Upon detailed study, two species of Aphelenchoides were found to be new to science. Aphelenchoides dhanachandi sp. n. is characterized by ventrally curved body, clearly set off cephalic region and tail ending into a sharp pointed terminus, and stylet slender, 13.6–15.3 (14 ± 0.7) μm long with indistinct basal swellings and tamarind seed-shaped median bulb. Aphelenchoides neoechinocaudatus sp. n. is characterized by straight body with four incisures in the lateral field, flatten cephalic region, slender stylet with indistinct basal swellings, 11.9 μm long, elongated pear-shaped median bulb and short tail with pointed mucro. The two species are illustrated here.     

An Aphelenchoides sp. nematode Parasitic of Polianthes tuberosa in the Mekong Delta

Polianthes tuberosa is a commercially valuable flower crop in the Mekong Delta of Vietnam that is propagated by the harvesting and planting of bulbs. The cultivation of P. tuberosa is complicated by an endemic nematode infection that damages a high proportion of the plants. Based on morphological criteria and ribosomal RNA gene sequencing, we have determined that the infection is caused by an Aphelenchoides sp. nematode and is most likely Aphelenchoides besseyi. By scoring various parts of harvested plants with flowers for the presence of viable nematodes over a period of six months, we determined that the nematode is an ectoparasite that can survive the intercrop periods, especially in the bulbs that are used to plant new crops. A comparison of farming practices in the Mekong Delta failed to identify useful control methods, but rather indicated that fields that have cultivated P. tuberosa for the longest periods suffer the worst damage from the nematode infection. Finally, we demonstrated that the nematode is capable of infecting 30 rice cultivars but does not cause the white tip disease usually associated with A. besseyi infection.     

Erratum to: Phylogeny and biogeography of the genus Stevia (Asteraceae: Eupatorieae): an example of diversification in the Asteraceae in the new world

The genus Stevia comprises approximately 200 species, which are distributed in North and South America, and are representative of the species diversity of the Asteraceae in the New World. We reconstructed the phylogenetic relationships using sequences of ITS and cpDNA and estimated the divergence times of the major clade of this genus. Our results suggested that Stevia originated in Mexico 7.0–7.3 million years ago (Mya). Two large clades, one with shrub species and another with herb species, were separated at about 6.6 Mya. The phylogenetic reconstruction suggested that an ancestor of Stevia was a small shrub in temperate pine–oak forests and the evolutionary change from a shrub state to a herb state occurred only once. A Brazilian clade was nested in a Mexican herb clade, and its origin was estimated to be 5.2 Mya, suggesting that the migration from North America to South America occurred after the formation of the Isthmus of Panama. The species diversity in Mexico appears to reflect the habitat diversity within the temperate pine–oak forest zone. The presence of many conspecific diploid–polyploid clades in the phylogenetic tree reflects the high frequency of polyploidization among the perennial Stevia species.

     

Unexpected phylogenetic relationships within the world's largest limbless skink species (Acontias plumbeus) highlight the need for a review of the taxonomic status of Acontias poecilus

Acontias plumbeus has traditionally been considered a monotypic, invariable species, a fact that highly contrasts with documented examples of high phylogenetic complexity and phenotypic diversity in other members of the Acontinae. We employed mitochondrial and nuclear DNA markers to investigate genetic structuring among A. plumbeus populations and the relationship between A. plumbeus and the closely related A. poecilus. Molecular genetic analyses revealed three clades with non‐overlapping distributions: an Eastern clade, a widely distributed Northern clade, and a Southern clade that includes topotypical A. poecilus. Morphometric analyses of preserved specimens showed that Southern clade populations are comprised of individuals with absolute and proportionally smaller body sizes than their Northern and Eastern relatives. Phylogenetic affinities within A. plumbeus indicate a complex biogeographic scenario within South Africa and suggest that A. poecilus should be considered a junior synonym of A. plumbeus instead of a truly valid species.