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Dry rot caused by Diaporthe batatatis leads to the serious decay of sweetpotato storage roots during postharvest storage, which can result in considerable economic loss. Genomic research of the pathogen could provide a basis for study and prevention of sweetpotato dry rot. Herein, we report a high-quality draft genome sequence of D. batatatis CRI 302-4 isolated from infected sweetpotato storage roots in Taizhou City, Zhejiang Province, China. The size of the genome was 54.38 Mb and consisted of 36 scaffolds with a G+C content of 50.56% and an N50 of 2,950,914 bp. The information provided in this genome sequence will be an invaluable resource for molecular genetic research and disease control in sweetpotato production.

Elsinoë batatas is a phytopathogenic fungus causing stem and foliage scab disease of sweet potato. At present, there is no reference genome available for E. batatas, limiting basic research for the pathogen. The present study applied the Nanopore single-molecule sequencing technology to sequence the E. batatas genome. This study reports the first high-quality genome sequence of E. batatas, with a total contig size of 26.49 Mb, 50.8% GC content, and an N50 of 2,546,814 bp. The sequences obtained serve as a reference for analysis of E. batatas isolates and provide a resource to better understand the biology of stem and foliage scab disease of sweet potato.

Postharvest disease is an important limiting factor for sweetpotato production. Recently, a new green mold disease was found in sweetpotato storage roots. To investigate the mechanism underlying the pathogenesis of the disease, the pathogen was isolated and identified based on morphological and molecular features, and its characteristics were further analyzed by pathogenic and antagonistic evaluations. The results showed that the isolated pathogen (CRI-Ta1) was identified as Trichoderma asperellum based on the similar growth and morphological features with Trichoderma spp., 99% homology of internal transcribed spacer (ITS) sequence, and membership to the same phylogenetic group with the model strain of T. asperellum (CBS 433.97). The pathogenic analysis revealed that CRI-Ta1 could cause green mold disease through wound infection on the storage roots and the strains reisolated from infected storage roots could cause disease in different sweetpotato varieties, which was fulfilled in Koch’s postulate. Moreover, CRI-Ta1 could also infect other common crop species, including chestnut, carrot, apple, pear, and others. It indicated that CRI-Ta1 was the pathogen to the storage roots of sweetpotato and had a wide host range. Additionally, in vitro antagonistic evaluation showed that CRI-Ta1 effectively inhibited the growth of common sweetpotato pathogens, including Fusarium solani and Rhizopus nigricans. However, further research is needed on the potential of CRI-Ta1 to control sweetpotato diseases in vivo. Collectively, our findings provided valuable insights into the characteristics of the T. asperellum CRI-Ta1 in sweetpotato and would be helpful to the prevention and control of sweetpotato green mold disease.

Foot rot of sweet potato caused by Diaporthe destruens severely affects yield and quality worldwide. Research on this pathogen is limited due to nonavailability of genome resources. Here, we report a high-quality genome sequence of D. destruens isolate CRI 305-2, which was originally isolated from infected stem of sweet potato in Taizhou City, Zhejiang Province, China. The genome comprised a total length of 56,108,228 bp, consisted of 47 scaffolds with an overall G+C content of 48.7% and an N50 of 2,479,481 bp. This resource can be used as a reference for evolution mechanisms and comparative genomic research.

A new bacterial disease of sweetpotato was recently identified in Puning, Guangdong Province, China and is referred to bacterial internal browning of sweetpotato in this paper. One-third of the tubers of sweetpotato were infected in the field. These tubers in the field with bacterial inner brown displayed yellowing on the skin that turned into slightly roughened and cracked surface with progress in disease. Cross-sections of these roots revealed a yellowish brown or dark brown circle in the vascular cambium. Pathogenicity tests were conducted on different organs of two sweetpotato cultivars and revealed that the isolated bacteria are pathogenic on stems and roots. We confirmed the causal agent as Burkholderia gladioli based on biochemical and physiological characterization, carbon source utilization, and sequence analysis of partial 16S rDNA and 16S–23S rDNA internal transcribed spacer (ITS) region. To our knowledge, it is the first report on the occurrence of B. gladioli in sweetpotato as a pathogen.

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Dry rot caused by

Cross-incompatibility, frequently happening in intraspecific varieties, has seriously restricted sweetpotato breeding. However, the mechanism of sweetpotato intraspecific cross-incompatibility (ICI) remains largely unexplored, especially for molecular mechanism. Treatment by inducible reagent developed by our lab provides a method to generate material for mechanism study, which could promote incompatible pollen germination and tube growth in the ICI group. Based on the differential phenotypes between treated and untreated samples, transcriptome and metabolome were employed to explore the molecular mechanism of sweetpotato ICI in this study, taking varieties ‘Guangshu 146’ and ‘Shangshu 19’, a typical incompatible combination, as materials. The results from transcriptome analysis showed oxidation–reduction, cell wall metabolism, plant–pathogen interaction, and plant hormone signal transduction were the essential pathways for sweetpotato ICI regulation. The differentially expressed genes (DEGs) enriched in these pathways were the important candidate genes to response ICI. Metabolome analysis showed that multiple differential metabolites (DMs) involved oxidation–reduction were identified. The most significant DM identified in comparison between compatible and incompatible samples was vitexin-2-O-glucoside, a flavonoid metabolite. Corresponding to it, cytochrome P450s were the most DEGs identified in oxidation–reduction, which were implicated in flavonoid biosynthesis. It further suggested oxidation–reduction play an important role in sweetpotato ICI regulation. To validate function of oxidation–reduction, reactive oxygen species (ROS) was detected in compatible and incompatible samples. The green fluorescence was observed in incompatible but not in compatible samples. It indicated ROS regulated by oxidation–reduction is important pathway to response sweetpotato ICI. The results in this study would provide valuable insights into molecular mechanisms for sweetpotato ICI.

Foot rot of sweet potato caused by

Postharvest disease is an important limiting factor for sweetpotato production. Recently, a new green mold disease was found in sweetpotato storage roots. To investigate the mechanism underlying the pathogenesis of the disease, the pathogen was isolated and identified based on morphological and molecular features, and its characteristics were further analyzed by pathogenic and antagonistic evaluations. The results showed that the isolated pathogen (CRI-Ta1) was identified as

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Additional file 1:Table S1. The most abundant unigenes in Illumina sequencing data. (DOC 58 KB)

Additional file of De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

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The complete chloroplast genome of a novel chlorophyll-deficient mutant (clm) and its wild type (WT) in sweetpotato (Ipomoea batatas L.) was sequenced. The complete chloroplast genome of clm and WT was 161,393 bp and 161,429 bp in length, containing a large single copy (LSC) region of 87,561 bp and 87,597 bp, respectively, a small single copy (SSC) region with the same length of 30,890 bp and a pair of inverted repeat regions (IRs) with the same length of 12,052 bp. Both of them contained 132 genes including 87 protein-coding sequences, 37 tRNA, and eight rRNA. Comparing to the WT, four SNPs and three INDELs were detected and only one INDEL in the exon affecting the translation of rpoA gene. Phylogenetic analysis showed that clm and WT were closely related to Ipomoea tabascana. The complete chloroplast genome of clm and its WT will play a role in understanding the molecular mechanism of chlorophyll deficiency and developing molecular markers in sweetpotato.

Nitrogen (N) could affect storage root growth and development of sweet potato. To manage external N concentration fluctuations, plants have developed a wide range of strategies, such as growth changes and gene expression. Five sweet potato cultivars were used to analyse the functions of N in regulating storage root growth. Growth responses and physiological indicators were measured to determine the physiological changes regulated by different N concentrations. Expression profiles of related genes were analysed via microarray hybridization data and qRT-PCR analysis to reveal the molecular mechanisms of storage root growth regulated by different N concentrations. The growth responses and physiological indicators of the five cultivars were changed by N concentration. The root fresh weight of two of the sweet potato cultivars, SS19 and GS87, was higher under low N concentrations compared with the other cultivars. SS19 and GS87 were found to be having greater tolerance to low N concentration. The expression of N metabolism and storage root growth related genes was regulated by N concentration in sweet potato. These results reveal that N significantly regulated storage root growth. SS19 and GS87 were more tolerant to low N concentration and produced greater storage root yield (at 30 days). Furthermore, several N response genes were involved in both N metabolism and storage root growth.

Since 2006, stem and root rot of sweetpotato has been observed in fields at a number of sweetpotato-production areas in Huidong, Haifeng, Puning, and Zhanjiang counties and Guangzhou City in Guangdong Province of China. Initially, the leaves turn yellow, and a black, water-soaked rot occurs on the bottom of the stems that gradually extends to the top of the stems. Finally, the entire plant collapses and dies. Bacteria were consistently isolated from stems of diseased seedlings by streaking on nutrient agar. Twelve representative isolates were chosen for further characterization. All strains grew at 37°C, were gram negative, facultatively anaerobic, and rod shaped with peritrichous flagella. The strains were negative for oxidase and positive for catalase and tryptophanase (indole production) They fermented glucose, reduced nitrates to nitrites, degraded pectate, produced phosphatase and lecithinase, and utilized citrate, tartrate, malonate, glucose, sucrose, fructose, and maltose, but not trehalose and lactose. These characteristics were similar to those of Erwinia chrysanthemi (Pectobacterium chrysanthemi) (1). PCR was performed on the 16S rDNA gene from isolate H12 (1,503 bp; GenBank Accession No. GU252371) with primers 27f (5′-GAGAGTTTGATCCTGGCTCAG-3′) and reverse primer (5′-GGCTACCTTGTTACGACTTC-3′). Subsequently, PCR products were sequenced. Results of sequence analysis showed the sequence of isolated strain H12 was 99% identical to that of E. chrysanthemi, 99% identical to that of type strain CFBP 1269T of Dickeya dadantii (Accession No. AF520707), and 98% identical to that of type strain CFBP 1200T of D. dianthicola (Accession No. AF520708). Recently, E. chrysanthemi was transferred to Dickeya gen. nov., but it was difficult to identify the species within the genus Dickeya. Seedlings (20 to 30 cm) were planted in 10-cm-diameter plastic pots containing sterilized field soil at room temperature. Four days later, five stem tops of sweetpotato were injected with a bacteria suspension (108 CFU/ml) of approximately 100 μl to fulfill Koch's postulates. Five control plants were inoculated with sterile distilled water. The experiment was conducted three times. All plants were incubated in a chamber at 30°C with high humidity. One to two days after inoculation, symptoms were observed in all inoculated plants and appeared to be identical to those observed in the field. No symptoms were noted on the control plants. The bacterium was reisolated from symptomatic stems of sweetpotato plants. This pathogen was previously reported on sweetpotato in the United States in 1974 (2). To our knowledge, this is the first report of a Dickeya sp. (E. chrysanthemi) causing bacterial stem and root rot of sweetpotato in China. References: (1) D. J. Brenner et al. Page 670 in: Bergey's Manual of Systematic Bacteriology. 2nd ed. Springer, New York, 2005. (2) N. W. Schaad et al. Phytopathology 67:302, 1977.

Elucidating the chemical composition and health benefits of specially bred leaf-vegetable sweet potato (Ipomoea batatas L.) can provide a basis for improving their utilization and commercialization and also inform effective breeding strategies. In this study, the nutritional and health-related parameters of different-colored leaf tips (green and purplish-green types) from 11 leafy cultivars of sweet potatoes were determined. The results showed that the tip tissue possessed a wide range of nutritional compounds, and the contents of all of these compounds differed significantly between cultivars (p

Background Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. Results In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. Conclusion This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.

Background The tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweetpotato root for gene discovery and molecular marker development. Results In this study, more than 59 million sequencing reads were generated using Illumina paired-end sequencing technology. De novo assembly yielded 56,516 unigenes with an average length of 581 bp. Based on sequence similarity search with known proteins, a total of 35,051 (62.02%) genes were identified. Out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 17,598 (31.14%) unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways, which were well represented by carbohydrate metabolism and biosynthesis of secondary metabolite. In addition, 4,114 cDNA SSRs (cSSRs) were identified as potential molecular markers in our unigenes. One hundred pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests. Conclusion This study generated a substantial fraction of sweetpotato transcript sequences, which can be used to discover novel genes associated with tuberous root formation and development and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Thousands of cSSR markers identified in the present study can enrich molecular markers and will facilitate marker-assisted selection in sweetpotato breeding. Overall, these sequences and markers will provide valuable resources for the sweetpotato community. Additionally, these results also suggested that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for gene discovery and molecular marker development for non-model species, especially those with large and complex genome.

Background The tuberous root of sweetpotato is undisputedly an important organ from agronomic and biological perspectives. Little is known regarding the regulatory networks programming tuberous root formation and development. Results Here, as a first step toward understanding these networks, we analyzed and characterized the genome-wide transcriptional profiling and dynamics of sweetpotato root in seven distinct developmental stages using a customized microarray containing 39,724 genes. Analysis of these genes identified temporal programs of gene expression, including hundreds of transcription factor (TF) genes. We found that most genes active in roots were shared across all developmental stages, although significant quantitative changes in gene abundance were observed for 5,368 (including 435 TFs) genes. Clustering analysis of these differentially expressed genes pointed out six distinct expression patterns during root development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that genes involved in different processes were enriched at specific stages of root development. In contrast with the large number of shared expressed genes in root development, each stage or period of root development has only a small number of specific genes. In total, 712 (including 27 TFs) and 1,840 (including 115 TFs) genes were identified as root-stage and root-period specific, respectively at the level of microarray. Several of the specific TF genes are known regulators of root development, including DA1-related protein, SHORT-ROOT and BEL1-like. The remaining TFs with unknown roles would also play critical regulatory roles during sweetpotato tuberous root formation and development. Conclusions The results generated in this study provided spatiotemporal patterns of root gene expression in support of future efforts for understanding the underlying molecular mechanism that control sweetpotato yield and quality. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0567-5) contains supplementary material, which is available to authorized users.