EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

The advancement of invasive plant species in a particular environment is threatening across Asia. When they are introduced, they could have a variety of different negative effects, either as minor inconveniences or a severe problem. The aim of this review is to compile a list of invasive plant species across Asia and organize a set of data according to their reproduction rates, growth rates, dispersal rates, and characterize the allelochemicals they produce and allelopathic effects they have on their environment. The target is to know the extent of their spread ability in the area that they inhibit and know what control measures can be done with that specific species. The data has been gathered by compiling research articles and obtaining pertinent data relating to the objective. This review also utilized the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist to confirm the credibility of the collected references. To achieve the needed references, keywords such as "distribution", "invasive", and "Asia" have been used to search for these on search engines and research journals such as Google Scholar, ScienceDirect, ResearchGate, and Directory for Open Access Journals, to be then compiled in spreadsheets and document files. The results show that the growth rate of these species varies from 7.5-60 cm per year, where Ipomoea eberhardtii has the highest growth rate of 60 cm per year. The dispersal rates of the species ranges from 0.002-2592 km from the parent plant, where animal mediated, water, and wind dispersal methods are the primary vector to spread. Allelopathic effects produced by the allelochemicals present mostly inhibit growth and seed germination. There are already implemented approaches to control these species, where biological control, physical means, and the use of chemicals are the most used strategies. In different dynamic processes, physical and chemical control measures are most utilized in this case. 

A Systematic Review on the Distribution of Invasive Plant Species Across Asia: Assessing the Rates of Invasion Success and Management

Biodiversity science in China has seen rapid growth over recent decades, ranging from baseline biodiversity studies to understanding the processes behind evolution across dynamic regions such as the Qinghai-Tibetan Plateau. We review research, including species catalogues; biodiversity monitoring; the origins, distributions, maintenance and threats to biodiversity; biodiversity-related ecosystem function and services; and species and ecosystems' responses to global change. Next, we identify priority topics and offer suggestions and priorities for future biodiversity research in China. These priorities include (i) the ecology and biogeography of the Qinghai-Tibetan Plateau and surrounding mountains, and that of subtropical and tropical forests across China; (ii) marine and inland aquatic biodiversity; and (iii) effective conservation and management to identify and maintain synergies between biodiversity and socio-economic development to fulfil China's vision for becoming an ecological civilization. In addition, we propose three future strategies: (i) translate advanced biodiversity science into practice for biodiversity conservation; (ii) strengthen capacity building and application of advanced technologies, including high-throughput sequencing, genomics and remote sensing; and (iii) strengthen and expand international collaborations. Based on the recent rapid progress of biodiversity research, China is well positioned to become a global leader in biodiversity research in the near future.

The global significance of biodiversity science in China: an overview.

Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum is challenging due to its complex genetic background. Here, we report a near-complete assembly and annotation for C. morifolium comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative and evolutionary analyses reveal a whole-genome triplication (WGT) event shared by Chrysanthemum species approximately 6 million years ago (Mya) and the possible lineage-specific polyploidization of C. morifolium approximately 3 Mya. Multilevel evidence suggests that C. morifolium is likely a segmental allopolyploid. Furthermore, a combination of genomics and transcriptomics approaches demonstrate the C. morifolium genome can be used to identify genes underlying key ornamental traits. Phylogenetic analysis of CmCCD4a traces the flower colour breeding history of cultivated chrysanthemum. Genomic resources generated from this study could help to accelerate chrysanthemum genetic improvement. 

/pdf/analyses-of-a-chromosome-scale-genome-assembly-reveal-the-frvvdrnf.pdf

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

Summary Artemisia argyi, as famous as Artemisia annua, is a medicinal plant with huge economic value in the genus of Artemisia and has been widely used in the world for about 3000 years. However, a lack of the reference genome severely hinders the understanding of genetic basis for the active ingredient synthesis of A. argyi. Here, we firstly report a complex chromosome‐level genome assembly of A. argyi with a large size of 8.03 Gb, with features of high heterozygosity (2.36%), high repetitive sequences (73.59%) and a huge number of protein‐coding genes (279 294 in total). The assembly reveals at least three rounds of whole‐genome duplication (WGD) events, including a recent WGD event in the A. argyi genome, and a recent burst of transposable element, which may contribute to its large genome size. The genomic data and karyotype analyses confirmed that A. argyi is an allotetraploid with 34 chromosomes. Intragenome synteny analysis revealed that chromosomes fusion event occurred in the A. argyi genome, which elucidates the changes in basic chromosome numbers in Artemisia genus. Significant expansion of genes related to photosynthesis, DNA replication, stress responses and secondary metabolism were identified in A. argyi, explaining the extensive environmental adaptability and rapid growth characteristics. In addition, we analysed genes involved in the biosynthesis pathways of flavonoids and terpenoids, and found that extensive gene amplification and tandem duplication contributed to the high contents of metabolites in A. argyi. Overall, the reference genome assembly provides scientific support for evolutionary biology, functional genomics and breeding in A. argyi and other Artemisia species.

Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi

Mikania micrantha is one of the top 100 worst invasive species that can cause serious damage to natural ecosystems and substantial economic losses. Here, we present its 1.79 Gb chromosome-scale reference genome. Half of the genome is composed of long terminal repeat retrotransposons, 80% of which have been derived from a significant expansion in the past one million years. We identify a whole genome duplication event and recent segmental duplications, which may be responsible for its rapid environmental adaptation. Additionally, we show that M. micrantha achieves higher photosynthetic capacity by CO2 absorption at night to supplement the carbon fixation during the day, as well as enhanced stem photosynthesis efficiency. Furthermore, the metabolites of M. micrantha can increase the availability of nitrogen by enriching the microbes that participate in nitrogen cycling pathways. These findings collectively provide insights into the rapid growth and invasive adaptation. Mikania micrantha is an extremely fast-growing invasive plant species that can cause serious damage to natural ecosystems. Here, the authors assemble its chromosome-scale reference genome and explore possible mechanisms that contribute to its rapid growth.

/pdf/mikania-micrantha-genome-provides-insights-into-the-15e9v2ulmk.pdf

Mikania micrantha genome provides insights into the molecular mechanism of rapid growth.

Background Portulaca oleracea L., common purslane, is an insecticidal plant that has been documented as a 'Chinese indigenous pesticide', and it is seldom visited by insects in the field. However, identification of anti-insect compounds and mechanisms of action are still unclear. Results Interplanting purslane with Chinese cabbage demonstrated that purslane may contain secondary compounds that S. litura avoids eating. Four compounds were isolated from P. oleracea by directed anti-insect activity, and their chemical structures were identified by NMR spectra as (9Z,11E,15Z)-13-hydroxyoctadeca-9,11,15-trienoic acid (1), portulacanone A (2), portulacanone D (3), and a new natural product 2,4'-dihydroxy-3',5'-dimethoxychalcone (4). A combination of compound 1 and 2 possessed stronger activity than other combinations (compounds 1 + 3; 1 + 4; 2 + 3; 2 + 4; 3 + 4). Both active compounds were detected in all samples from 23 regions in China, and concentrations in samples collected from 17 regions were generally above 500 μg/kg. Concentrations of compounds 1 and 2 fluctuated greatly from April to November, and reached maximum concentrations of 45 951.44 μg/kg for compound 1 and 3739.09 μg/kg for compound 2 in November. The combination of these compounds (1 + 2) caused mid-gut structural deformation and tissue decay as determined by mid-gut histopathology of S. litura. Conclusion In general, these active compounds coexisting contributed to partly protect purslane from insects. This research also provides new insights into the use of purslane as important ingredient of botanical pesticide alternatives to traditional chemical pesticides. © 2019 Society of Chemical Industry.

A homoisoflavonoid and a fatty acid in common purslane (Portulaca oleracea L.) synergistically inhibit growth of Spodoptera litura larvae.

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Mikania micrantha genome provides insights into the molecular mechanism of rapid growth.

A homoisoflavonoid and a fatty acid in common purslane (Portulaca oleracea L.) synergistically inhibit growth of Spodoptera litura larvae.