Rapid diversification of five Oryza AA genomes associated with rice adaptation.

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.

Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships.

BACKGROUND: Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly difficult taxa in plants. Sequence comparisons of chloroplast (cp) genomes are of great interest to provide a robust evidence for taxonomic studies, species identification and understanding mechanisms that underlie the evolution of the Camellia species. RESULTS: The eight complete cp genomes and five draft cp genome sequences of Camellia species were determined using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. The Camellia cp genomes exhibited typical circular structure that was rather conserved in genomic structure and the synteny of gene order. Differences of repeat sequences, simple sequence repeats, indels and substitutions were further examined among five complete cp genomes, representing a wide phylogenetic diversity in the genus. A total of fifteen molecular markers were identified with more than 1.5% sequence divergence that may be useful for further phylogenetic analysis and species identification of Camellia. Our results showed that, rather than functional constrains, it is the regional constraints that strongly affect sequence evolution of the cp genomes. In a substantial improvement over prior studies, evolutionary relationships of the section Thea were determined on basis of phylogenomic analyses of cp genome sequences. CONCLUSIONS: Despite a high degree of conservation between the Camellia cp genomes, sequence variation among species could still be detected, representing a wide phylogenetic diversity in the genus. Furthermore, phylogenomic analysis was conducted using 18 complete cp genomes and 5 draft cp genome sequences of Camellia species. Our results support Chang's taxonomical treatment that C. pubicosta may be classified into sect. Thea, and indicate that taxonomical value of the number of ovaries should be reconsidered when classifying the Camellia species. The availability of these cp genomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of the genus Camellia.

Carcinosarcoma of common bile duct: A case report.

BACKGROUND: Carcinosarcomas of the common bile duct (CBD) are an extremely rare finding in the clinical setting. Based on a review of 12 literatures, 3 cases had the imaging features of ossification. Carcinosarcomas are prone to distant metastasis, as they possess clinical features of both carcinoma and sarcoma, and generally have with a poor prognosis. Due to the small number of cases reported, clinical experience in the diagnosis and treatment of the disease is lacking. CASE SUMMARY: The patient was a 75-year-old woman who had experienced recurrent chills with nausea and vomiting for 3 mo. Computed tomography, magnetic resonance imaging, endoscopic ultrasonography and endoscopic retrograde cholangiopancreatography led to the diagnosis of malignant tumor of the CBD. The patient ultimately underwent cholecystectomy, CBD resection, and choledochojejunostomy. Postoperative pathological examination revealed carcinosarcoma of the CBD, and the latest follow-up showed that the patient is recovering well. Based on previous case reports, some carcinosarcoma has ossification characteristics in imaging. If it is misdiagnosed as biliary calculi, the use of laser lithotripsy in surgery may lead to tumor diffusion. Choledochoscopy and narrow band staining of mucosa are very important for diagnosis. CONCLUSION: We herein present a rare case of carcinosarcomas of the CBD, we found the tumours may have imaging features of polypoid growth and ossification only when the sarcomal components are bone differentiation, while show soft tissue shadow when non bone differentiation. Confirmation of diagnosis depends greatly upon postoperative pathological examination and the adjuvant treatment has not been established, which leads to the poor prognosis.

Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating-system evolution.

Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.

Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata, from Illumina and PacBio sequencing reads.

African wild rice Oryza longistaminata, one of the eight AA- genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high-quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating Illumina and PacBio sequencing datasets. The final genome assembly comprised only 107 scaffolds and was approximately ∼363.5 Mb, representing ∼92.7% of the estimated African wild rice genome (∼392 Mb). The N50 lengths of the assembled contigs and scaffolds were ∼46.49 Kb and ∼6.83 Mb, indicating ∼3.72-fold and ∼18.8-fold improvement in length compared to the earlier released assembly (∼12.5 Kb and 364 Kb, respectively). Aided with Hi-C data and syntenic relationship with O. sativa, these assembled scaffolds were anchored into 12 pseudo-chromosomes. Genome annotation and comparative genomic analysis reveal that lineage-specific expansion of gene families that respond to biotic- and abiotic stresses are of great potential for mining novel alleles to overcome major diseases and abiotic adaptation in rice breeding programs. This reference genome of African wild rice will greatly enlarge the existing database of rice genome resources and unquestionably form a solid base to understand genomic basis underlying highly valued phenotypic traits and search for novel gene sources in O. longistaminata for the future rice breeding programs.

Water translocation between ramets of strawberry during soil drying and its effects on photosynthetic performance.

To explore the mechanisms underlying water regulation in clonal plants and its effects on carbon assimilation under water stress, we studied the responses of water status, gas exchange and abscisic acid (ABA) contents to water stress in leaves of pairs of strawberry ramets that consist of mother and daughter ramets. There was a greater decrease in photosynthetic rates (P(n)) and stomatal conductance (G(s)) in the disconnected mother ramets than the connected mother ramets upon exposure to water stress, indicating that water stress in mother ramets was alleviated by water translocation from the well-watered daughter ramets. Conversely, the connected mother ramets displayed enhanced symptoms of water stress when the connected daughter ramets were exposed to water deficit. The mother ramets had lower water potential (psi(w)) due to their stronger osmotic adjustment than in well-watered daughter ramets; this resulted in water flow from the connected daughter ramets to mother ramets, thus alleviating water stress of mother ramets. During soil drying, there was a striking increase in ABA concentrations in leaves of the disconnected mother ramets, whereas leaf bulk ABA was much lower in the connected and water-stressed mother ramets than that in the drought-affected mother ramets in the disconnected group. In this study, though G(s) was linearly correlated with leaf bulk ABA and psi(w), G(s) in water-stressed mother ramets in disconnected group exhibited less sensitivity to the variation in leaf bulk ABA and psi(w) than that in connected and water-stressed mother ramets. Taken together, these results indicate that: (1) the flux of water translocation between the connected ramets is determined by a water potential gradient; (2) water translocation between connected ramets helps to keep sensitivity of G(s) to ABA and psi(w) in drought-affected ramets, thereby benefit to effectively maintain the homeostasis of leaf water status and (3) the improvements in P(n) in water-stressed ramets due to water translocation from well-watered ramets suggest the advantages of physiological integration in clonal plants in environments with heterogeneous water distribution.

Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats.

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences.

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis.

Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.

[A rapid method for preparation of plasmid DNA for screening recombinant clones].

A simple and rapid method for preparation of plasmid DNA from overnight incubation was introduced. It does not require any additional reagents; the incubation mixture containing recombinant plasmid DNA was just mixed with H2O and phenol/chloroform/isoamyl alcohol in certain ratio. After vortexing and spinning of the mixture, the supernatant could be directly loaded onto agarose gel and analyzed using electrophoresis. The whole preparation requires only 3-5 minutes. So to quickly screen recombinant clones, this method is better compared with traditional methods.