The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development.

BACKGROUND: Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. RESULTS: Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. CONCLUSIONS: We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms.

BACKGROUND: Several de novo transcriptome assemblers have been developed recently to assemble the short reads generated from the next-generation sequencing platforms and different strategies were employed for assembling transcriptomes of various eukaryotes without genome sequences. Though there are some comparisons among these de novo assembly tools for assembling transcriptomes of different eukaryotic organisms, there is no report about the relationship between assembly strategies and ploidies of the organisms. RESULTS: When we de novo assembled transcriptomes of sweet potato (hexaploid), Trametes gallica (a diploid fungus), Oryza meyeriana (a diploid wild rice), five assemblers, including Edena, Oases, Soaptrans, IDBA-tran and Trinity, were used in different strategies (Single-Assembler Single-Parameter, SASP; Single-Assembler Multiple-Parameters, SAMP; Combined De novo Transcriptome Assembly, CDTA, that is multiple assembler multiple parameter). It was found that CDTA strategy has the best performance compared with other two strategies for assembling transcriptome of the hexaploid sweet potato, whereas SAMP strategy with assembler Oases is better than other strategies for assembling transcriptomes of diploid fungus and the wild rice transcriptomes. CONCLUSION: Based on the results from ours and others, it is suggested that CDTA strategy is better used for transcriptome assembly of polyploidy organisms and SAMP strategy of Oases is outperformed for those diploid organisms without genome sequences.

De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification.

Ipomoea nil is widely used as an ornamental plant due to its abundance of flower color, but the limited transcriptome and genomic data hinder research on it. Using illumina platform, transcriptome profiling of I. nil was performed through high-throughput sequencing, which was proven to be a rapid and cost-effective means to characterize gene content. Our goal is to use the resulting information to facilitate the relevant research on flowering and flower color formation in I. nil. In total, 268 million unique illumina RNA-Seq reads were produced and used in the transcriptome assembly. These reads were assembled into 220,117 contigs, of which 137,307 contigs were annotated using the GO and KEGG database. Based on the result of functional annotations, a total of 89,781 contigs were assigned 455,335 GO term annotations. Meanwhile, 17,418 contigs were identified with pathway annotation and they were functionally assigned to 144 KEGG pathways. Our transcriptome revealed at least 55 contigs as probably flowering-related genes in I. nil, and we also identified 25 contigs that encode key enzymes in the phenylpropanoid biosynthesis pathway. Based on the analysis relating to gene expression profiles, in the phenylpropanoid biosynthesis pathway of I. nil, the repression of lignin biosynthesis might lead to the redirection of the metabolic flux into anthocyanin biosynthesis. This may be the most likely reason that I. nil has high anthocyanins content, especially in its flowers. Additionally, 15,537 simple sequence repeats (SSRs) were detected using the MISA software, and these SSRs will undoubtedly benefit future breeding work. Moreover, the information uncovered in this study will also serve as a valuable resource for understanding the flowering and flower color formation mechanisms in I. nil.

De Novo Transcriptome Sequencing of Oryza officinalis Wall ex Watt to Identify Disease-Resistance Genes.

Oryza officinalis Wall ex Watt is one of the most important wild relatives of cultivated rice and exhibits high resistance to many diseases. It has been used as a source of genes for introgression into cultivated rice. However, there are limited genomic resources and little genetic information publicly reported for this species. To better understand the pathways and factors involved in disease resistance and accelerating the process of rice breeding, we carried out a de novo transcriptome sequencing of O. officinalis. In this research, 137,229 contigs were obtained ranging from 200 to 19,214 bp with an N50 of 2331 bp through de novo assembly of leaves, stems and roots in O. officinalis using an Illumina HiSeq 2000 platform. Based on sequence similarity searches against a non-redundant protein database, a total of 88,249 contigs were annotated with gene descriptions and 75,589 transcripts were further assigned to GO terms. Candidate genes for plant-pathogen interaction and plant hormones regulation pathways involved in disease-resistance were identified. Further analyses of gene expression profiles showed that the majority of genes related to disease resistance were all expressed in the three tissues. In addition, there are two kinds of rice bacterial blight-resistant genes in O. officinalis, including two Xa1 genes and three Xa26 genes. All 2 Xa1 genes showed the highest expression level in stem, whereas one of Xa26 was expressed dominantly in leaf and other 2 Xa26 genes displayed low expression level in all three tissues. This transcriptomic database provides an opportunity for identifying the genes involved in disease-resistance and will provide a basis for studying functional genomics of O. officinalis and genetic improvement of cultivated rice in the future.

Assessing the suitable regions and the key factors for three Cd-accumulating plants (Sedum alfredii, Phytolacca americana, and Hylotelephium spectabile) in China using MaxEnt model.

Phytoremediation is an effective way to remove metals from contaminated soil, and selecting remediation plants suitable for climate conditions is a prerequisite for effective phytoremediation. In this study, a MaxEnt model was applied to investigate the potential distribution and habitat suitability of three Cd-accumulating plants in China- Sedum alfredii, Phytolacca americana, and Hylotelephium spectabile and explore the key environmental factors that affect their habitat suitability. A total of 44 environmental parameters, including bioclimatic variables, altitude, and soil property parameters were used. The results showed that: (1) For S. alfredii, suitable areas account for 14.9 % of the area of China, which are mainly distributed in the middle and lower reaches of the Yangtze River. (2) The suitable areas of P. americana account for 22.7 % of China and are mainly located in the regions of the Qinling Mountains and the south of China. (3) While that for H. spectabile are mainly located in the regions of northeastern China and certain regions of central China, with suitable areas account for 8.3 % of the area of China. (4) The distribution of these three plants is significantly affected by precipitation; specifically, solar radiation is an influential factor for the distribution of S. alfredii and H. spectabile, and temperature limits the distribution of P. americana. The selection and agronomic management of hyperaccumulators for phytoremediation requires multifactor consideration (e.g., climate, soil conditions and planting patterns). The results can provide guidance for identifying suitable areas for planting these three accumulating plants, which could not only prevent the unscientific cultivation of them in unsuitable habitats but also enhance the efficiency of phytoremediation. Meanwhile, these findings are expected to contribute to agronomic management for improved phytoremediation effects in different Cd-contaminated regions of China.

Spatial heterogeneity of human lifespan in relation to living environment and socio-economic polarization: a case study in the Beijing-Tianjin-Hebei region, China.

The spatial heterogeneity and influence factors of public lifespan have been reported worldwide at the national level or typical longevous areas. However, few sub-national studies considering the living environment and socio-economic level together have been explored in the imbalanced developed region with a huge population base and deteriorated air quality. In this paper, spatial heterogeneity of lifespan integrating environment and socio-economic influence factors was investigated in the Beijing-Tianjin-Hebei (BTH) region of China using geographically weighted regression (GWR). Five indicators were constructed to determine the lifespan based on the three national censuses (1990-2010) in the BTH region. The results showed that the areas with higher CH (centenarians per 100,000 inhabitants) and centenarity index (CI) exhibited changing distribution in the BTH region, whereas those with lower CH and CI and extreme value of the ultra-octogenarian index (UOI) and LI (> 90/ > 65) maintained a relatively stable feature through time. But as lifespan indicators increase overall, the differences between the counties/districts widen. Furthermore, remarkable spatial heterogeneity was detected for the associations between the significant environmental and socio-economic variables and lifespan indicators. Although the natural geographic condition (altitude) still exhibited a negative influence on the longevity of the population, the socio-economic factors (GDPpc and income level) showed a more dominant influence on the extension of the elderly and longevity population. Correspondingly, the widened unbalance of population lifespan (UOI, LI, CH) was considered closely related to the socio-economic polarization, and the adverse effects of air pollution on life expectancy at birth (LEB) have also emerged. To further improve the overall lifespan level and narrow the lifespan gap in the BTH region, future work on cleaner air and more balanced development is still needed.

Method on site-specific source apportionment of domestic soil pollution across China through public data mining: A case study on cadmium from non-ferrous industries.

The lack of emission data of major Cd-emitting enterprises has long limited the source apportionment of soil cadmium (Cd). Non-ferrous metal enterprises (NMEs) contribute the most Cd emissions in China in recent years. We estimated the cumulative Cd emission of 8750 NMEs across China through public data collection and material balance methods for the first time. The results showed that the total Cd emissions were estimated at 133,177 tons, of which 78.68% contributed by zinc primary smelting and mining. The emission hotspots are mainly concentrated in the south of the Yangtze River, such as Nanling Mountain areas, Nanpan River Basin, and Jincheng River Basin, as well as a few parts of the North and Northwest China. Then a significant positive spatial correlation was furtherly detected between NMEs and soil Cd, except for secondary smelting enterprises. Moreover, the hotspots of soil Cd pollution caused by NMEs were identified across China. By promoting the accounting calibrator from annual emission intensity of regional (mainly provincial) scale to the cumulative emission of site-specific enterprise in its entire life cycle, this study realized the finer description of the spatial heterogeneity of Cd emission from non-ferrous industry on a large scale and make it possible to refine the reliability of follow-up site-specific source apportionment, by introducing the emission intensity instead of the enterprise sites density. Finally, a modified approach for the regional source apportionment of soil pollution was proposed to obtain a more realistic and precise drawing. The results pointed out key NMEs subcategories and the affected hotspots which require continuous strengthening of Cd-related rectification. This methodological framework is expected to contribute to the precise management and differential sources control of Cd pollution and can be further extended to other pollutants for the precise targeting of key industries and hotspots during source pollution control in the future.

Transcriptome analysis reveals the effects of grafting on sweetpotato scions during the full blooming stages.

BACKGROUND: Sweetpotato (Ipomoea batatas) is a hexaploid plant and generally most genotypes do not flower at all in sub-tropics. Heterografting was carried out between sweetpotato cultivar 'Xushu 18' and Japanese morning glory (Ipomoea nil). With sweetpotato as 'scion' and I. nil as 'rootstock', sweetpotato was induced flowering in the autumn. However, little is known about the molecular mechanisms underlying sweetpotato responses to grafting, especially during the full blooming stages. OBJECTIVES: To investigate the poorly understood molecular responses underlying the grafting-induced phenotypic processes in sweetpotato at full anthesis. METHODS: In this study, to explore the transcriptome diversity and complexity of sweetpotato, PacBio Iso-Seq and Illumina RNA-seq analysis were combined to obtain full-length transcripts and to profile the changes in gene expression of five tissues: scion flowers (SF), scion leaves (SL), scion stems (SS), own-rooted leaves (OL) and own-rooted stems (OS). RESULTS: A total of 138,151 transcripts were generated with an average length of 2255 bp, and more than 72% (100,396) of the transcripts were full-length. During full blooming, to examine the difference in gene expression of sweetpotato under grafting and natural growth conditions, 7905, 7795 and 15,707 differentially expressed genes were detected in pairwise comparisons of OS versus SS, OL versus SL and SL versus SF, respectively. Moreover, differential transcription of genes associated with anthocyanin biosynthesis, light pathway and photosynthesis, ethylene signal transduction pathway was observed in scion responses to grafting. CONCLUSION: Our study is useful in understanding the molecular basis of grafting-induced flowering in grafted sweetpotatoes, and will lay a foundation for further research on sweetpotato breeding in the future.

Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.

Oryza meyeriana (O. meyeriana), with a GG genome type (2n = 24), accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. It is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq and obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (japonica-type Nipponbare and indica-type 93-11) genomes revealed that 13% of the O. meyeriana contigs had not been detected in O. sativa. Many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. There are two kinds of rice bacterial blight-resistant genes (Xa1 and Xa26) differentially or specifically expressed in O. meyeriana. The 4 Xa1 contigs were all only expressed in root, while three of Xa26 contigs have the highest expression level in leaves, two of Xa26 contigs have the highest expression profile in stems and one of Xa26 contigs was expressed dominantly in roots. The transcriptomic database of O. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease resistance in O. meyeriana.

Analyses of the complete genome and gene expression of chloroplast of sweet potato [Ipomoea batata].

Sweet potato [Ipomoea batatas (L.) Lam] ranks among the top seven most important food crops cultivated worldwide and is hexaploid plant (2n=6x=90) in the Convolvulaceae family with a genome size between 2,200 to 3,000 Mb. The genomic resources for this crop are deficient due to its complicated genetic structure. Here, we report the complete nucleotide sequence of the chloroplast (cp) genome of sweet potato, which is a circular molecule of 161,303 bp in the typical quadripartite structure with large (LSC) and small (SSC) single-copy regions separated by a pair of inverted repeats (IRs). The chloroplast DNA contains a total of 145 genes, including 94 protein-encoding genes of which there are 72 single-copy and 11 double-copy genes. The organization and structure of the chloroplast genome (gene content and order, IR expansion/contraction, random repeating sequences, structural rearrangement) of sweet potato were compared with those of Ipomoea (L.) species and some basal important angiosperms, respectively. Some boundary gene-flow and gene gain-and-loss events were identified at intra- and inter-species levels. In addition, by comparing with the transcriptome sequences of sweet potato, the RNA editing events and differential expressions of the chloroplast functional-genes were detected. Moreover, phylogenetic analysis was conducted based on 77 protein-coding genes from 33 taxa and the result may contribute to a better understanding of the evolution progress of the genus Ipomoea (L.), including phylogenetic relationships, intraspecific differentiation and interspecific introgression.

Adjuvant effects of recombinant giant panda (Ailuropoda melanoleuca) IL-18 on the canine distemper disease vaccine in mice.

Canine distemper virus (CDV) is a morbillivirus known to cause morbidity and mortality in a broad range of animals. Giant pandas (Ailuropoda melanoleuca), especially captive ones, are susceptible to natural infection with CDV. Interleukin-18 (IL-18) is a powerful adjuvant molecule that can enhance the development of antigen-specific immunity and vaccine efficacy. In this study, a giant panda IL-18 gene eukaryotic expression plasmid (pcAmIL-18) was constructed. Female BALB/c mice were muscularly inoculated with the plasmids pcAmIL-18, pcDNA3.1 and PBS, respectively. They were subsequently injected with an attenuated CDV vaccine for dogs, and the induced humoral and cellular responses were evaluated. The results showed that pcAmIL-18 remarkably improved the level of specific antibody, IFN-γ and IL-2 in mice sera, the T lymphocyte proliferation index and the percentage of CD4(+) and CD8(+) cells. These data indicated that pcAmIL-18 is a potential adjuvant that promotes specific immunity.