Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER

Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales

Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing a significant role in the cultivation of horticultural, ornamental, and medicinal plant varieties. Whole-genome duplication (WGD) and its subsequent post-polyploid diploidization (PPD) process represent the most drastic type of karyotype evolution, injecting significant potential for promoting the diversity of this lineage. However, polyploidization histories, as well as genome and subgenome fractionation following WGD events in Lamiales species, are still not well investigated. In this study, we constructed a chromosome-level genome assembly of Lindenbergia philippensis (Orobanchaceae) and conducted comparative genomic analyses with 14 other Lamiales species. L. philippensis is positioned closest to the parasitic lineage within Orobanchaceae and has a conserved karyotype. Through a combination of Ks analysis and syntenic depth analysis, we reconstructed and validated polyploidization histories of Lamiales species. Our results indicated that Primulina huaijiensis underwent three rounds of diploidization events following the γ-WGT event, rather than two rounds as reported. Besides, we reconfirmed that most Lamiales species shared a common diploidization event (L-WGD). Subsequently, we constructed the Lamiales Ancestral Karyotype (LAK), comprising 11 proto-chromosomes, and elucidated its evolutionary trajectory, highlighting the highly flexible reshuffling of the Lamiales paleogenome. We identified biased fractionation of subgenomes following the L-WGD event across eight species, and highlighted the positive impacts of non-WGD genes on gene family expansion. This study provides novel genomic resources and insights into polyploidy and karyotype remodeling of Lamiales species, essential for advancing our understanding of species diversification and genome evolution.

Chromosome-level genome assembly provides insights into the genetic diversity, evolution, and flower development of Prunus conradinae

Prunus conradinae, a valuable flowering cherry belonging to the Rosaceae family subgenus Cerasus and endemic to China, has high economic and ornamental value. However, a high-quality P. conradinae genome is unavailable, which hinders our understanding of its genetic relationships and phylogenesis, and ultimately, the possibility of mining of key genes for important traits. Herein, we have successfully assembled a chromosome-scale P. conradinae genome, identifying 31,134 protein-coding genes, with 98.22% of them functionally annotated. Furthermore, we determined that repetitive sequences constitute 46.23% of the genome. Structural variation detection revealed some syntenic regions, inversions, translocations, and duplications, highlighting the genetic diversity and complexity of Cerasus. Phylogenetic analysis demonstrated that P. conradinae is most closely related to P. campanulata, from which it diverged ~ 19.1 million years ago (Mya). P. avium diverged earlier than P. cerasus and P. conradinae. Similar to the other Prunus species, P. conradinae underwent a common whole-genome duplication event at ~ 138.60 Mya. Furthermore, 79 MADS-box members were identified in P. conradinae, accompanied by the expansion of the SHORT VEGETATIVE PHASE subfamily. Our findings shed light on the complex genetic relationships, and genome evolution of P. conradinae and will facilitate research on the molecular breeding and functions of key genes related to important horticultural and economic characteristics of subgenus Cerasus.

Chromosome-scale genome assembly of medicinal plant Tinospora sagittata (Oliv.) Gagnep. from the Menispermaceae family

Tinospora sagittata (Oliv.) Gagnep. is an important medicinal tetraploid plant in the Menispermaceae family. Its tuber, Radix Tinosporae, used in traditional Chinese medicine, is rich in diterpenoids and benzylisoquinoline alkaloids (BIAs). To enhance our understanding of medicinal compounds' biosynthesis and Menispermaceae's evolution, we herein report assembling a high-quality chromosome-scale genome with both PacBio HiFi and Illumina sequencing technologies. PacBio Sequel II generated 2.5 million circular consensus sequencing (CCS) reads, and a hybrid assembly strategy with Illumina sequencing resulted in 4483 contigs. The assembled genome size was 2.33 Gb, consisting of 4070 scaffolds (N50 = 42.06 Mb), of which 92.05% were assigned to 26 pseudochromosomes. T. sagittata's chromosomal-scale genome assembly, the first species in Menispermaceae, aids Menispermaceae evolution and T. sagittata's secondary metabolites biosynthesis understanding.

A chromosome-scale genome of Rhus chinensis Mill. provides new insights into plant-insect interaction and gallotannins biosynthesis

Rhus chinensis Mill., an economically valuable Anacardiaceae species, is parasitized by the galling aphid Schlechtendalia chinensis, resulting in the formation of the Chinese gallnut (CG). Here, we report a chromosomal-level genome assembly of R. chinensis, with a total size of 389.40 Mb and scaffold N50 of 23.02 Mb. Comparative genomic and transcriptome analysis revealed that the enhanced structure of CG and nutritional metabolism contribute to improving the adaptability of R. chinensis to S. chinensis by supporting CG and galling aphid growth. CG was observed to be abundant in hydrolysable tannins (HT), particularly gallotannin and its isomers. Tandem repeat clusters of dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) and serine carboxypeptidase-like (SCPL) and their homologs involved in HT production were determined as specific to HT-rich species. The functional differentiation of DQD/SDH tandem duplicate genes and the significant contraction in the phenylalanine ammonia-lyase (PAL) gene family contributed to the accumulation of gallic acid and HT while minimizing the production of shikimic acid, flavonoids, and condensed tannins in CG. Furthermore, we identified one UDP glucosyltransferase (UGT84A), three carboxylesterase (CXE), and six SCPL genes from conserved tandem repeat clusters that are involved in gallotannin biosynthesis and hydrolysis in CG. We then constructed a regulatory network of these genes based on co-expression and transcription factor motif analysis. Our findings provide a genomic resource for the exploration of the underlying mechanisms of plant-galling insect interaction and highlight the importance of the functional divergence of tandem duplicate genes in the accumulation of secondary metabolites.

Chromosome-level genome assembly of the predatory stink bug Arma custos

The stink bug Arma custos (Hemiptera: Pentatomidae) is a predatory enemy successfully used for biocontrol of lepidopteran and coleopteran pests in notorious invasive species. In this study, a high-quality chromosome-scale genome assembly of A. custos was achieved through a combination of Illumina sequencing, PacBio HiFi sequencing, and Hi-C scaffolding techniques. The final assembled genome was 969.02 Mb in size, with 935.94 Mb anchored to seven chromosomes, and a scaffold N50 length of 135.75 Mb. This genome comprised 52.78% repetitive elements. The detected complete BUSCO score was 99.34%, indicating its completeness. A total of 13,708 protein-coding genes were predicted in the genome, and 13219 of them were annotated. This genome provides an invaluable resource for further research on various aspects of predatory bugs, such as biology, genetics, and functional genomics.

Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L

Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled P. pusilliflora genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we de novo assembled a chromosome-scale P. pusilliflora genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that P. pusilliflora is closely related to Prunus serrulata and Prunus yedoensis, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that P. pusilliflora has 643 expanded and 1128 contracted gene families. Furthermore, we found that P. pusilliflora is more resistant to Colletotrichum viniferum, Phytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus avium. P. pusilliflora also has considerably more nucleotide-binding site-type resistance gene analogs than P. avium, which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in P. pusilliflora. Furthermore, 81 MADS-box genes were identified in P. pusilliflora, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality P. pusilliflora genome will be valuable for further research on cherries and molecular breeding.

Comparative genomics reveals the diversification of triterpenoid biosynthesis and origin of ocotillol-type triterpenes in Panax

Gene duplication is assumed to be the major force driving the evolution of metabolite biosynthesis in plants. Freed from functional burdens, duplicated genes can mutate toward novelties until fixed due to selective fitness. However, the extent to which this mechanism has driven the diversification of metabolite biosynthesis remains to be tested. Here we performed comparative genomics analysis and functional characterization to evaluate the impact of gene duplication on the evolution of triterpenoid biosynthesis using Panax species as models. We found that whole-genome duplications (WGDs) occurred independently in Araliaceae and Apiaceae lineages. Comparative genomics revealed the evolutionary trajectories of triterpenoid biosynthesis in plants, which was mainly promoted by WGDs and tandem duplication. Lanosterol synthase (LAS) was likely derived from a tandem duplicate of cycloartenol synthase that predated the emergence of Nymphaeales. Under episodic diversifying selection, the LAS gene duplicates produced by γ whole-genome triplication have given rise to triterpene biosynthesis in core eudicots through neofunctionalization. Moreover, functional characterization revealed that oxidosqualene cyclases (OSCs) responsible for synthesizing dammarane-type triterpenes in Panax species were also capable of producing ocotillol-type triterpenes. Genomic and biochemical evidence suggested that Panax genes encoding the above OSCs originated from the specialization of one OSC gene duplicate produced from a recent WGD shared by Araliaceae (Pg-β). Our results reveal the crucial role of gene duplication in diversification of triterpenoid biosynthesis in plants and provide insight into the origin of ocotillol-type triterpenes in Panax species.

Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa)

The most commercialized kiwifruit, Actinidia chinensis var. deliciosa (Acd), is an allohexaploid (2n = 6x = 174), making high-quality assemblage genome challenging. We previously discovered a rare naturally occurring diploid Acd plant. Here, chromosome-level de novo genome assembly for this diploid Acd was reported, reaching approximately 621.98 Mb in length with contig and scaffold N50 values of 10.08 and 21.09 Mb, respectively, 99.66% of the bases anchored to 29 pseudochromosomes, and 38,990 protein-coding genes and 42.29% repetitive elements annotated. The divergence time of A. chinensis cv. 'Red5' and 'Hongyang' (11.1-27.7 mya) was more recent compared with the divergence time of them and Acd (19.9-41.2 mya), with the divergence time of A. eriantha cv. 'White' being the earliest (22.9-45.7 mya) among that of the four Actinidia species. The 4DTv distance distribution highlighted three recent whole-genome duplication events in Acd. This is the first high-quality diploid Acd genome, which lays an important foundation for not only kiwifruit functional genomics studies but also further elucidating genome evolution of allohexaploid Acd.

The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment

BACKGROUND

Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated.

RESULT

We assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae.

CONCLUSION

Ridgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.

Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila

Cactophilic species of the Drosophila buzzatii cluster (repleta group) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species form a tractable system to study the transition from chemically simpler breeding sites (like prickly pears of the genus Opuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of the buzzatii cluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization. Functional enrichment analyses of TRGs within the buzzatii cluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic changes brought about key mechanisms underlying the adaptation of the buzzatii cluster species to arid regions in South America.

Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data

The Asian swamp eel (Monopterus albus) is an excellent model species for studying sex change and chromosome evolution. M. albus is also widely reared in East Asia and South-East Asia because of its great nutritional value. The low fecundity of this species (about 300 eggs per fish) greatly hinders fries production and breeding programs. Interestingly, about 3–5% of the eels could remain as females for 3 years and lay more than 3,000 eggs per fish, which are referred to as non-sex-reversal (NSR) females. Here, we presented a new chromosome-level genome assembly of such NSR females using Illumina, HiFi, and Hi-C sequencing technologies. The new assembly (Mal.V2_NSR) is 838.39 Mb in length, and the N50 of the contigs is 49.8 Mb. Compared with the previous assembly obtained using the continuous long-read sequencing technology (Mal.V1_CLR), we found a remarkable increase of continuity in the new assembly Mal.V2_NSR with a 20-times longer contig N50. Chromosomes 2 and 12 were assembled into a single contig, respectively. Meanwhile, two highly contiguous haplotype assemblies were also obtained, with contig N50 being 14.54 and 12.13 Mb, respectively. BUSCO and Merqury analyses indicate completeness and high accuracy of these three assemblies. A comparative genomic analysis revealed substantial structural variations (SVs) between Mal.V2_NSR and Mal.V1_CLR and two phased haplotype assemblies, as well as whole chromosome fusion events when compared with the zig-zag eel. Additionally, our newly obtained assembly provides a genomic view of sex-related genes and a complete landscape of the MHC genes. Therefore, these high-quality genome assemblies would provide great help for future breeding works of the swamp eel, and it is a valuable new reference for genetic and genomic studies of this species.

The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions

BACKGROUND

To illustrate the molecular mechanism of mycoheterotrophic interactions between orchids and fungi, we assembled chromosome-level reference genome of Gastrodia menghaiensis (Orchidaceae) and analyzed the genomes of two species of Gastrodia.

RESULTS

Our analyses indicated that the genomes of Gastrodia are globally diminished in comparison to autotrophic orchids, even compared to Cuscuta (a plant parasite). Genes involved in arbuscular mycorrhizae colonization were found in genomes of Gastrodia, and many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids. The highly expressed genes for fatty acid and ammonium root transporters suggest that fungi receive material from orchids, although most raw materials flow from the fungi. Many nuclear genes (e.g. biosynthesis of aromatic amino acid L-tryptophan) supporting plastid functions are expanded compared to photosynthetic orchids, an indication of the importance of plastids even in totally mycoheterotrophic species.

CONCLUSION

Gastrodia menghaiensis has the smallest proteome thus far among angiosperms. Many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids.

A High-Quality, Chromosome-Level Genome Provides Insights Into Determinate Flowering Time and Color of Cotton Rose (Hibiscus mutabilis)

Hibiscus mutabilis (cotton rose) is a deciduous shrub or small tree of the Malvaceae family. Here, we report a chromosome-scale assembly of the H. mutabilis genome based on a combination of single-molecule sequencing and Hi-C technology. We obtained an optimized assembly of 2.68 Gb with a scaffold N50 length of 54.7 Mb. An integrated strategy of homology-based, de novo, and transcriptome-based gene predictions identified 118,222 protein-coding genes. Repetitive DNA sequences made up 58.55% of the genome, and LTR retrotransposons were the most common repetitive sequence type, accounting for 53.15% of the genome. Through the use of Hi-C data, we constructed a chromosome-scale assembly in which Nanopore scaffolds were assembled into 46 pseudomolecule sequences. We identified important genes involved in anthocyanin biosynthesis and documented copy number variation in floral regulators. Phylogenetic analysis indicated that H. mutabilis was closely related to H. syriacus, from which it diverged approximately 15.3 million years ago. The availability of cotton rose genome data increases our understanding of the species' genetic evolution and will support further biological research and breeding in cotton rose, as well as other Malvaceae species.

Chromosome-Scale Reference Genome of Amphicarpaea edgeworthii: A New Resource for Amphicarpic Plants Research and Complex Flowering Pattern

Amphicarpaea edgeworthii, an annual twining herb, is a widely distributed species and an attractive model for studying complex flowering types and evolutionary mechanisms of species. Herein, we have generated a high-quality assembly of A. edgeworthii by using a combination of PacBio, 10× Genomics libraries, and Hi-C mapping technologies. The final 11 chromosome-level scaffolds covered 90.61% of the estimated genome (343.78Mb), which is a chromosome-scale assembled genome of an amphicarpic plant. Subsequently, we characterized the genetic diversity and population structure of A. edgeworthii species by resequencing individuals collected from their natural area of distribution. Using transcriptome profiling, we observed that specific phenotypes are regulated by a complex network of light, hormones, and MADS-box gene families. These data are beneficial for the discovery of genes that control major agronomic traits and spur genetic improvement of and functional genetic studies in legumes, as well as supply comparative genetic resources for other amphicarpic plants.

Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan

Pecan (Carya illinoinensis) is a tree nut crop of worldwide economic importance that is rich in health-promoting factors. However, pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal diseases. Here, we report a high-quality, chromosome-scale genome assembly of the controlled-cross pecan cultivar 'Pawnee' constructed by integrating Nanopore sequencing and Hi-C technologies. Phylogenetic and evolutionary analyses reveal two whole-genome duplication (WGD) events and two paleo-subgenomes in pecan and walnut. Time estimates suggest that the recent WGD event and considerable genome rearrangements in pecan and walnut account for expansions in genome size and chromosome number after the divergence from bayberry. The two paleo-subgenomes differ in size and protein-coding gene sets. They exhibit uneven ancient gene loss, asymmetrical distribution of transposable elements (especially LTR/Copia and LTR/Gypsy), and expansions in transcription factor families (such as the extreme pecan-specific expansion in the far-red impaired response 1 family), which are likely to reflect the long evolutionary history of species in the Juglandaceae. A whole-genome scan of resequencing data from 86 pecan scab-associated core accessions identified 47 chromosome regions containing 185 putative candidate genes. Significant changes were detected in the expression of candidate genes associated with the chitin response pathway under chitin treatment in the scab-resistant and scab-susceptible cultivars 'Excell' and 'Pawnee'. These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in pecan. The high-quality sequences are valuable resources for pecan breeders and will provide a foundation for the production and quality improvement of tree nut crops.

Molecular Characteristics of Novel Phage vB_ShiP-A7 Infecting Multidrug-Resistant Shigella flexneri and Escherichia coli, and Its Bactericidal Effect in vitro and in vivo

In recent years, increasing evidence has shown that bacteriophages (phages) can inhibit infection caused by multidrug-resistant (MDR) bacteria. Here, we isolated a new phage, named vB_ShiP-A7, using MDR Shigella flexneri as the host. vB_ShiP-A7 is a novel member of Podoviridae, with a latency period of approximately 35 min and a burst size of approximately 100 phage particles/cell. The adsorption rate constant of phage vB_ShiP-A7 to its host S. flexneri was 1.405 × 10^–8 mL/min. The vB_ShiP-A7 genome is a linear double-stranded DNA composed of 40,058 bp with 177 bp terminal repeats, encoding 43 putative open reading frames. Comparative genomic analysis demonstrated that the genome sequence of vB_ShiP-A7 is closely related to 15 different phages, which can infect different strains. Mass spectrometry analysis revealed that 12 known proteins and 6 hypothetical proteins exist in the particles of phage vB_ShiP-A7. Our results confirmed that the genome of vB_ShiP-A7 is free of lysogen-related genes, bacterial virulence genes, and antibiotic resistance genes. vB_ShiP-A7 can significantly disrupt the growth of some MDR clinical strains of S. flexneri and Escherichia coli in liquid culture and biofilms in vitro. In addition, vB_ShiP-A7 can reduce the load of S. flexneri by approximately 3–10 folds in an infection model of mice. Therefore, vB_ShiP-A7 is a stable novel phage with the potential to treat infections caused by MDR strains of S. flexneri and E. coli.

Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd

The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long-read-based, high-quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390-fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one-step geometric morphometrics-based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well-known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.

Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication

A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1.47 Gb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.

Chromosome-Scale Genome Assembly of the Resurrection Plant Acanthochlamys bracteata (Velloziaceae)

Acanthochlamys bracteata (Velloziaceae) is a resurrection plant with cold tolerance. Herein, a chromosome-level reference genome of A. bracteata based on Nanopore, Illumina, and Hi-C data is reported. The high-quality assembled genome was 197.97 Mb, with a scaffold N50 value of 8.64 Mb and a contig N50 value of 6.96 Mb. We annotated 23,509 protein-coding genes. Eight contracted gene families and three expanded gene families were detected. Repeat sequences accounted for approximately 28.63% of the genome. The LEA1 and Dehydrin gene families, which are involved in desiccation resistance, expanded in A. bracteata. We identified genes involved in chilling tolerance, COLD1.

Chromosomal-scale genome assembly of Eleutherococcus senticosus provides insights into chromosome evolution in Araliaceae

Siberian ginseng (Eleutherococcus senticosus, also known as ciwujia) belongs to the Araliaceae family, which contains more than 1,500 species in 41 genera with diverse chromosome numbers and genome sizes. General consensus posits that ancient whole-genome duplication events and rapid evolutionary radiation are the driving forces for this variation in genome properties. In an attempt to generate more genomic information for the Araliaceae family, we report a 1.30 Gb high-quality draft genome assembly (contig N50 = 309.43 kb) of E. senticosus via PacBio long reads and Hi-C chromatin interaction maps. We found that transposable elements accounted for 72.82% of the genome and a total of 36,372 protein-coding genes were predicted. Comparative analyses of the E. senticosus, Panax notoginseng and Daucus carota genomes revealed a burst expansion of Tekay chromoviral elements in Araliaceae after its divergence with Apiaceae. We also found that E. senticosus underwent a lineage-specific whole-genome duplication event Es-α and a whole-genome duplication event Araliaceae-β that was probably shared by all Araliaceae species. Even though the rediploidization of the E. senticosus genome is evident, pathway analyses show that these two whole-genome duplication events may have contributed to the adaptation of E. senticosus to a cold environment. Taken together, the high-quality genome assembly of E. senticosus provides a valuable genomic resource for future research on the evolution of Araliaceae.

Whole-genome sequence data of Hypericum perforatum and functional characterization of melatonin biosynthesis by N-acetylserotonin O-methyltransferase

Hypericum perforatum is among the most commonly used herbal remedies and supplements. The aerial plant parts are often used to treat depression. Due to the lack of genomic information of H. perforatum, the gene networks regulating secondary metabolite synthesis remain unclear. Here, we present a high-quality genome for H. perforatum with a 2.3-Mb scaffold N50. The draft assembly covers 91.9% of the predicted genome and represents the fourth sequenced genus in the order Malpighiales. Comparing this sequence with model or related species revealed that Populus trichocarpa and Hevea brasiliensis could be grouped into one branch, while H. perforatum and Linum usitatissimum are grouped in another branch. Combined with transcriptome data, 40 key genes related to melatonin, hyperforin, and hypericin synthesis were screened and analyzed. Five N-acetylserotonin O-methyltransferases (HpASMT1-HpASMT5) were cloned and functionally characterized. Purified HpASMT3 protein converted N-acetylserotonin into melatonin with a V_max of about 1.35 pkat/mg protein. HpASMT1 and HpASMT3 overexpression in Arabidopsis mutants caused 1.5-2-fold higher melatonin content than in mutant and wild-type plants. The endogenous reactive oxygen species (ROS) in transgenic plants was significantly lower than ROS in mutant and wild-type plants, suggesting higher drought tolerance. The obtained genomic data offer new resources for further study on the evolution of Hypericaceae family, but also provide a basis for further study of melatonin biosynthetic pathways in other plants.

Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis

Akebia trifoliata subsp. australis is a well-known medicinal and potential woody oil plant in China. The limited genetic information available for A. trifoliata subsp. australis has hindered its exploitation. Here, a high-quality chromosome-level genome sequence of A. trifoliata subsp. australis is reported. The de novo genome assembly of 682.14 Mb was generated with a scaffold N50 of 43.11 Mb. The genome includes 25,598 protein-coding genes, and 71.18% (485.55 Mb) of the assembled sequences were identified as repetitive sequences. An ongoing massive burst of long terminal repeat (LTR) insertions, which occurred ~1.0 million years ago, has contributed a large proportion of LTRs in the genome of A. trifoliata subsp. australis. Phylogenetic analysis shows that A. trifoliata subsp. australis is closely related to Aquilegia coerulea and forms a clade with Papaver somniferum and Nelumbo nucifera, which supports the well-established hypothesis of a close relationship between basal eudicot species. The expansion of UDP-glucoronosyl and UDP-glucosyl transferase gene families and β-amyrin synthase-like genes and the exclusive contraction of terpene synthase gene families may be responsible for the abundant oleanane-type triterpenoids in A. trifoliata subsp. australis. Furthermore, the acyl-ACP desaturase gene family, including 12 stearoyl-acyl-carrier protein desaturase (SAD) genes, has expanded exclusively. A combined transcriptome and fatty-acid analysis of seeds at five developmental stages revealed that homologs of SADs, acyl-lipid desaturase omega fatty acid desaturases (FADs), and oleosins were highly expressed, consistent with the rapid increase in the content of fatty acids, especially unsaturated fatty acids. The genomic sequences of A. trifoliata subsp. australis will be a valuable resource for comparative genomic analyses and molecular breeding.

The Acer truncatum genome provides insights into nervonic acid biosynthesis

Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole-genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.

A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of ~1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). The S. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using the S. melongena-HQ reference genome and detected a QTL interval of 71.29-78.26 Mb on chromosome E03. The gene Smechr0301963, which belongs to the SUN gene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.

The chromosome-level draft genome of Dalbergia odorifera

BACKGROUND

Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation.

FINDINGS

We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ∼92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan.

CONCLUSIONS

We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.

Chromosome Level Genome Assembly of Andrographis paniculata

Andrographis paniculata (Chinese name: Chuanxinlian) is an annual dicotyledonous medicinal plant widely grown in China and Southeast Asia. The dried plant has a highly acclaimed usage in the traditional Chinese medicine for its antipyretic, anti-inflammatory, and analgesic effects. In order to help delineate the biosynthetic pathways of various secondary metabolites, we report in this study a high-quality reference genome for A. paniculata. With the help of both PacBio single molecule real time sequencing and Illumina sequencing reads for error correction, the A. paniculata genome was assembled into a total size of 284 Mb with a contig N50 size of 5.14 Mb. The contigs were further assembled into 24 pseudo-chromosomes by the Hi-C technique. We also analyzed the gene families (e.g., KSL, and CYP450) whose protein products are essential for synthesizing bioactive compounds in A. paniculata. In conclusion, the high-quality A. paniculata genome assembly builds the foundation for decoding the biosynthetic pathways of various medicinal compounds.

Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh

BACKGROUND

Due to its rapid lethal effect in the early development stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) has been causing great economic losses, since its first outbreak in southeast China in 2009. Vibrio parahaemolyticus, carrying the pirA and pirB toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence the whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp (Peneaus monodon) of the south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen.

RESULTS

Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh, AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of a total of 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type III secretion system-1 (T3SS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~ 69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pirA and pirB. Antibiotic resistance genes were predicted against β-lactam, fluoroquinolone, tetracycline and macrolide groups in both MSR16 and MSR17 strains.

CONCLUSIONS

The findings of this research may facilitate the tracking of pathogenic and/or antibiotic-resistant V. parahaemolyticus isolates between production sites, and the identification of candidate strains for the production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.

Improving Silkworm Genome Annotation Using a Proteogenomics Approach

The silkworm genome has been deeply sequenced and assembled, but accurate genome annotation, which is important for modern biological research, remains far from complete. To improve silkworm genome annotation, we carried out a proteogenomics analysis using 9.8 million mass spectra collected from different tissues and developmental stages of the silkworm. The results confirmed the translational products of 4307 existing gene models and identified 1701 novel genome search-specific peptides (GSSPs). Using these GSSPs, 74 novel gene-coding sequences were identified, and 121 existing gene models were corrected. We also identified 1182 novel junction peptides based on an exon-skipping database that resulted in the identification of 973 alternative splicing sites. Furthermore, we performed RNA-seq analysis to improve silkworm genome annotation at the transcriptional level. A total of 1704 new transcripts and 1136 new exons were identified, 2581 untranslated regions (UTRs) were revised, and 1301 alternative splicing (AS) genes were identified. The transcriptomics results were integrated with the proteomics data to further complement and verify the new annotations. In addition, 14 incorrect genes and 10 skipped exons were verified using the two analysis methods. Altogether, we identified 1838 new transcripts and 1593 AS genes and revised 5074 existing genes using proteogenomics and transcriptome analyses. Data are available via ProteomeXchange with identifier PXD009672. The large-scale proteogenomics and transcriptome analyses in this study will greatly improve silkworm genome annotation and contribute to future studies.

The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition

BACKGROUND

Pecan (Carya illinoinensis) and Chinese hickory (C. cathayensis) are important commercially cultivated nut trees in the genus Carya (Juglandaceae), with high nutritional value and substantial health benefits.

RESULTS

We obtained >187.22 and 178.87 gigabases of sequence, and ∼288× and 248× genome coverage, to a pecan cultivar ("Pawnee") and a domesticated Chinese hickory landrace (ZAFU-1), respectively. The total assembly size is 651.31 megabases (Mb) for pecan and 706.43 Mb for Chinese hickory. Two genome duplication events before the divergence from walnut were found in these species. Gene family analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids, and B vitamins. Further analyses of reduced-coverage genome sequences of 16 Carya and 2 Juglans species provide additional phylogenetic perspective on crop wild relatives.

CONCLUSIONS

Cooperative characterization of these valuable resources provides a window to their evolutionary development and a valuable foundation for future crop improvement.

Prediction of Sphingosine protein-coding regions with a self adaptive spectral rotation method

Identifying protein coding regions in DNA sequences by computational methods is an active research topic. Welan gum produced by Sphingomonas sp. WG has great application potential in oil recovery and concrete construction industry. Predicting the coding regions in the Sphingomonas sp. WG genome and addressing the mechanism underlying the explanation for the synthesis of Welan gum metabolism is an important issue at present. In this study, we apply a self adaptive spectral rotation (SASR, for short) method, which is based on the investigation of the Triplet Periodicity property, to predict the coding regions of the whole-genome data of Sphingomonas sp. WG without any previous training process, and 1115 suspected gene fragments are obtained. Suspected gene fragments are subjected to a similarity search against the non-redundant protein sequences (nr) database of NCBI with blastx, and 762 suspected gene fragments have been labeled as genes in the nr database.

Classifying the Unclassified: A Phage Classification Method

This work reports the method ClassiPhage to classify phage genomes using sequence derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov Models (HMMs) generated from clusters of related proteins. The method was validated on all publicly available genomes of phages that are known to infect Vibrionaceae. The phages belong to the well-described phage families of Myoviridae, Podoviridae, Siphoviridae, and Inoviridae. The achieved classification is consistent with the assignments of the International Committee on Taxonomy of Viruses (ICTV), all tested phages were assigned to the corresponding group of the ICTV-database. In addition, 44 out of 58 genomes of Vibrio phages not yet classified could be assigned to a phage family. The remaining 14 genomes may represent phages of new families or subfamilies. Comparative genomics indicates that the ability of the approach to identify and classify phages is correlated to the conserved genomic organization. ClassiPhage classifies phages exclusively based on genome sequence data and can be applied on distinct phage genomes as well as on prophage regions within host genomes. Possible applications include (a) classifying phages from assembled metagenomes; and (b) the identification and classification of integrated prophages and the splitting of phage families into subfamilies.

Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species

Cauliflower is an important variety of Brassica oleracea and is planted worldwide. Here, the high-quality genome sequence of cauliflower was reported. The assembled cauliflower genome was 584.60 Mb in size, with a contig N50 of 2.11 Mb, and contained 47,772 genes; 56.65% of the genome was composed of repetitive sequences. Among these sequences, long terminal repeats (LTRs) were the most abundant (32.71% of the genome), followed by transposable elements (TEs) (12.62%). Comparative genomic analysis confirmed that after an ancient paleohexaploidy (γ) event, cauliflower underwent two whole-genome duplication (WGD) events shared with Arabidopsis and an additional whole-genome triplication (WGT) event shared with other Brassica species. The present cultivated cauliflower diverged from the ancestral B. oleracea species ~3.0 million years ago (Mya). The speciation of cauliflower (~2.0 Mya) was later than that of B. oleracea L. var. capitata (approximately 2.6 Mya) and other Brassica species (over 2.0 Mya). Chromosome no. 03 of cauliflower shared the most syntenic blocks with the A, B, and C genomes of Brassica species and its eight other chromosomes, implying that chromosome no. 03 might be the most ancient one in the cauliflower genome, which was consistent with the chromosome being inherited from the common ancestor of Brassica species. In addition, 2,718 specific genes, 228 expanded genes, 2 contracted genes, and 1,065 positively selected genes in cauliflower were identified and functionally annotated. These findings provide new insights into the genomic diversity of Brassica species and serve as a valuable reference for molecular breeding of cauliflower.

Characterization and Genomic Study of Phage vB_EcoS-B2 Infecting Multidrug-Resistant Escherichia coli

The potential of bacteriophage as an alternative antibacterial agent has been reconsidered for control of pathogenic bacteria due to the widespread occurrence of multi-drug resistance bacteria. More and more lytic phages have been isolated recently. In the present study, we isolated a lytic phage named vB_EcoS-B2 from waste water. VB_EcoS-B2 has an icosahedral symmetry head and a long tail without a contractile sheath, indicating that it belongs to the family Siphoviridae. The complete genome of vB_EcoS-B2 is composed of a circular double stranded DNA of 44,283 bp in length, with 54.77% GC content. vB_EcoS-B2 is homologous to 14 relative phages (such as Escherichia phage SSL-2009a, Escherichia phage JL1, and Shigella phage EP23), but most of these phages exhibit different gene arrangement. Our results serve to extend our understanding toward phage evolution of family Siphoviridae of coliphages. Sixty-five putative open reading frames were predicted in the complete genome of vB_EcoS-B2. Twenty-one of proteins encoded by vB_EcoS-B2 were determined in phage particles by Mass Spectrometry. Bacteriophage genome and proteome analysis confirmed the lytic nature of vB_EcoS-B2, namely, the absence of toxin-coding genes, islands of pathogenicity, or genes through lysogeny or transduction. Furthermore, vB_EcoS-B2 significantly reduced the growth of E. coli MG1655 and also inhibited the growth of several multi-drug resistant clinical stains of E. coli. Phage vB_EcoS-B2 can kill some of the MRD E. coli entirely, strongly indicating us that it could be one of the components of phage cocktails to treat multi-drug resistant E. coli. This phage could be used to interrupt or reduce the spread of multi-drug resistant E. coli.

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.

Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen-Isolated Amycolatopsis Strains

Actinomycetes have been extensively exploited as one of the most prolific secondary metabolite-producer sources and continue to be in the focus of interest in the constant search of novel bioactive compounds. The availability of less expensive next generation genome sequencing techniques has not only confirmed the extraordinary richness and broad distribution of silent natural product biosynthetic gene clusters among these bacterial genomes, but also has allowed the incorporation of genomics in bacterial taxonomy and systematics. As part of our efforts to isolate novel strains from unique environments, we explored lichen-associated microbial communities as unique assemblages to be studied as potential sources of novel bioactive natural products with application in biotechnology and drug discovery. In this work, we have studied the whole genome sequences of two new Amycolatopsis strains (CA-126428 and CA-128772) isolated from tropical lichens, and performed a comparative genomic analysis with 41 publicly available Amycolatopsis genomes. This work has not only permitted to infer and discuss their taxonomic position on the basis of the different phylogenetic approaches used, but has also allowed to assess the richness and uniqueness of the biosynthetic pathways associated to primary and secondary metabolism, and to provide a first insight on the potential role of these bacteria in the lichen-associated microbial community.

A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus

The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239^T was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs). Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17^T, Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the A. methanolica genome, 12 gene clusters related to the biosynthesis of other specialized (secondary) metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of A. methanolica strain 239^T, including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452, a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic A. orientalis subclade (AOS), the mesophilic Amycolatopsis taiwanensis subclade (ATS) and the thermophilic A. methanolica subclade (AMS). The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.

Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus

Myxobacteria, a group of Gram-negative aerobes, belong to the class δ-proteobacteria and order Myxococcales. Unlike anaerobic δ-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of Myxococcus hansupus that encodes 7,753 proteins. Phylogenomic and genome-genome distance based analysis suggest that Myxococcus hansupus is a novel member of the genus Myxococcus. Comparative genome analysis with other members of the genus Myxococcus was performed to explore their genome diversity. The variation in number of unique proteins observed across different species is suggestive of diversity at the genus level while the overrepresentation of several Pfam families indicates the extent and mode of genome expansion as compared to non-Myxococcales δ-proteobacteria.

Genomic factors related to tissue tropism in Chlamydia pneumoniae infection

BACKGROUND

Chlamydia pneumoniae (Cpn) are obligate intracellular bacteria that cause acute infections of the upper and lower respiratory tract and have been implicated in chronic inflammatory diseases. Although of significant clinical relevance, complete genome sequences of only four clinical Cpn strains have been obtained. All of them were isolated from the respiratory tract and shared more than 99% sequence identity. Here we investigate genetic differences on the whole-genome level that are related to Cpn tissue tropism and pathogenicity.

RESULTS

We have sequenced the genomes of 18 clinical isolates from different anatomical sites (e.g. lung, blood, coronary arteries) of diseased patients, and one animal isolate. In total 1,363 SNP loci and 184 InDels have been identified in the genomes of all clinical Cpn isolates. These are distributed throughout the whole chlamydial genome and enriched in highly variable regions. The genomes show clear evidence of recombination in at least one potential region but no phage insertions. The tyrP gene was always encoded as single copy in all vascular isolates. Phylogenetic reconstruction revealed distinct evolutionary lineages containing primarily non-respiratory Cpn isolates. In one of these, clinical isolates from coronary arteries and blood monocytes were closely grouped together. They could be distinguished from all other isolates by characteristic nsSNPs in genes involved in RB to EB transition, inclusion membrane formation, bacterial stress response and metabolism.

CONCLUSIONS

This study substantially expands the genomic data of Cpn and elucidates its evolutionary history. The translation of the observed Cpn genetic differences into biological functions and the prediction of novel pathogen-oriented diagnostic strategies have to be further explored.

Genome Sequence of the Oleaginous Yeast Rhodotorula glutinis ATCC 204091

Rhodotorula glutinis ATCC 204091 is an oleaginous oxidative red yeast that can accumulate lipids to >50% of its biomass when grown with appropriate carbon and nitrogen ratios. It produces a red pigment consisting of useful antioxidants, such as carotenoids, torulene, and torularhodin, when cultivated under carbon-deficient conditions.

Complete Genome Sequence of Mannheimia haemolytica Strain 42548 from a Case of Bovine Respiratory Disease

Mannheimia haemolytica is the major bacterial component in the bovine respiratory disease complex, which accounts for considerable economic losses to the cattle industry worldwide. The complete genome sequence of M. haemolytica strain 42548 was determined. It has a size of 2.73 Mb and contains 2,888 genes, including several antibiotic resistance genes.

Draft genome sequence of Streptomyces acidiscabies 84-104, an emergent plant pathogen

A draft genome sequence of the plant pathogen Streptomyces acidiscabies 84-104, an emergent plant pathogen, is presented here. The genome is among the largest of streptomycetes, at more than 11 Mb, and encodes a 100-kb pathogenicity island (PAI) shared with other plant-pathogenic streptomycetes. The presence of this conserved PAI, and the remnants of a conserved integrase/recombinase at its 3' end, supports the hypothesis that S. acidiscabies emerged as a plant pathogen as a result of this acquisition.

Identification of new meningococcal serogroup B surface antigens through a systematic analysis of neisserial genomes

The difficulty of inducing an effective immune response against the Neisseria meningitidis serogroup B capsular polysaccharide has lead to the search for vaccines for this serogroup based on outer membrane proteins. The availability of the first meningococcal genome (MC58 strain) allowed the expansion of high-throughput methods to explore the protein profile displayed by N. meningitidis. By combining a pan-genome analysis with an extensive experimental validation to identify new potential vaccine candidates, genes coding for antigens likely to be exposed on the surface of the meningococcus were selected after a multistep comparative analysis of entire Neisseria genomes. Eleven novel putative ORF annotations were reported for serogroup B strain MC58. Furthermore, a total of 20 new predicted potential pan-neisserial vaccine candidates were produced as recombinant proteins and evaluated using immunological assays. Potential vaccine candidate coding genes were PCR-amplified from a panel of representative strains and their variability analyzed using maximum likelihood approaches for detecting positive selection. Finally, five proteins all capable of inducing a functional antibody response vs N. meningitidis strain CU385 were identified as new attractive vaccine candidates: NMB0606 a potential YajC orthologue, NMB0928 the neisserial NlpB (BamC), NMB0873 a LolB orthologue, NMB1163 a protein belonging to a curli-like assembly machinery, and NMB0938 (a neisserial specific antigen) with evidence of positive selection appreciated for NMB0928. The new set of vaccine candidates and the novel proposed functions will open a new wave of research in the search for the elusive neisserial vaccine.

Estimating the size of the bacterial pan-genome

The 'pan-genome' denotes the set of all genes present in the genomes of a group of organisms. Here, we extend the pan-genome concept to higher taxonomic units. Using 573 sequenced genomes, we estimate the size of the bacterial pan-genome based on the frequency of occurrences of genes among sampled genomes. Using gene- and genome-centered approaches, we characterize three distinct pools of gene families that comprise the bacterial pan-genome, each evolving under different evolutionary constraints. Our findings indicate that the pan-genome of the bacterial domain is of infinite size (the Bacteria as a whole have an open pan-genome) and that approximately 250 genes per genome belong to the extended bacterial core genome.

Strategies for reliable exploitation of evolutionary concepts in high throughput biology

The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogeny-based inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting), interactomes (based on the presence and degree of conservation of interacting proteins), and in comparisons of transcriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression). Here we review the recent developments aimed at making automatic, reliable phylogeny-based inference feasible in large-scale projects. We also discuss how evolutionary concepts and phylogeny-based inference strategies are now being exploited in order to understand the evolution and function of biological systems. Such advances will be fundamental for the success of the emerging disciplines of systems biology and synthetic biology, and will have wide-reaching effects in applied fields such as biotechnology, medicine and pharmacology.

The complete genome sequence of Mycobacterium avium subspecies paratuberculosis

We describe here the complete genome sequence of a common clone of Mycobacterium avium subspecies paratuberculosis (Map) strain K-10, the causative agent of Johne's disease in cattle and other ruminants. The K-10 genome is a single circular chromosome of 4,829,781 base pairs and encodes 4,350 predicted ORFs, 45 tRNAs, and one rRNA operon. In silico analysis identified >3,000 genes with homologs to the human pathogen, M. tuberculosis (Mtb), and 161 unique genomic regions that encode 39 previously unknown Map genes. Analysis of nucleotide substitution rates with Mtb homologs suggest overall strong selection for a vast majority of these shared mycobacterial genes, with only 68 ORFs with a synonymous to nonsynonymous substitution ratio of >2. Comparative sequence analysis reveals several noteworthy features of the K-10 genome including: a relative paucity of the PE/PPE family of sequences that are implicated as virulence factors and known to be immunostimulatory during Mtb infection; truncation in the EntE domain of a salicyl-AMP ligase (MbtA), the first gene in the mycobactin biosynthesis gene cluster, providing a possible explanation for mycobactin dependence of Map; and Map-specific sequences that are likely to serve as potential targets for sensitive and specific molecular and immunologic diagnostic tests. Taken together, the availability of the complete genome sequence offers a foundation for the study of the genetic basis for virulence and physiology in Map and enables the development of new generations of diagnostic tests for bovine Johne's disease.

Metagenomic gene discovery: past, present and future

It is now widely accepted that the application of standard microbiological methods for the recovery of microorganisms from the environment has had limited success in providing access to the true extent of microbial biodiversity. It follows that much of the extant microbial genetic diversity (collectively termed the metagenome) remains unexploited, an issue of considerable relevance to a wider understanding of microbial communities and of considerable importance to the biotechnology industry. The recent development of technologies designed to access this wealth of genetic information through environmental nucleic acid extraction has provided a means of avoiding the limitations of culture-dependent genetic exploitation.

Sequence finishing and gene mapping for Candida albicans chromosome 7 and syntenic analysis against the Saccharomyces cerevisiae genome

The size of the genome in the opportunistic fungus Candida albicans is 15.6 Mb. Whole-genome shotgun sequencing was carried out at Stanford University where the sequences were assembled into 412 contigs. C. albicans is a diploid basically, and analysis of the sequence is complicated due to repeated sequences and to sequence polymorphism between homologous chromosomes. Chromosome 7 is 1 Mb in size and the best characterized of the 8 chromosomes in C. albicans. We assigned 16 of the contigs, ranging in length from 7309 to 267,590 bp, to chromosome 7 and determined sequences of 16 regions. These regions included four gaps, a misassembled sequence, and two major repeat sequences (MRS) of >16 kb. The length of the continuous sequence attained was 949,626 bp and provided complete coverage of chromosome 7 except for telomeric regions. Sequence analysis was carried out and predicted 404 genes, 11 of which included at least one intron. A 7-kb indel, which might be caused by a retrotransposon, was identified as the largest difference between the homologous chromosomes. Synteny analysis revealed that the degree of synteny between C. albicans and Saccharomyces cerevisiae is too weak to use for completion of the genomic sequence in C. albicans.

Comparative analysis of the Borrelia garinii genome

Three members of the genus Borrelia (B.burgdorferi, B.garinii, B.afzelii) cause tick-borne borreliosis. Depending on the Borrelia species involved, the borreliosis differs in its clinical symptoms. Comparative genomics opens up a way to elucidate the underlying differences in Borrelia species. We analysed a low redundancy whole-genome shotgun (WGS) assembly of a B.garinii strain isolated from a patient with neuroborreliosis in comparison to the B.burgdorferi genome. This analysis reveals that most of the chromosome is conserved (92.7% identity on DNA as well as on amino acid level) in the two species, and no chromosomal rearrangement or larger insertions/deletions could be observed. Furthermore, two collinear plasmids (lp54 and cp26) seem to belong to the basic genome inventory of Borrelia species. These three collinear parts of the Borrelia genome encode 861 genes, which are orthologous in the two species examined. The majority of the genetic information of the other plasmids of B.burgdorferii is also present in B.garinii although orthology is not easy to define due to a high redundancy of the plasmid fraction. Yet, we did not find counterparts of the B.burgdorferi plasmids lp36 and lp38 or their respective gene repertoire in the B.garinii genome. Thus, phenotypic differences between the two species could be attributable to the presence or absence of these two plasmids as well as to the potentially positively selected genes.