Sweetpotato Genome Research Articles

Characterization of Nucleotide Binding ­Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses

Sweetpotato, Ipomoea batatas (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that IbNBS75, IbNBS219, and IbNBS256 respond to stem nematode infection; Ib­NBS240, IbNBS90, and IbNBS80 respond to cold stress, while IbNBS208, IbNBS71, and IbNBS159 respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.

QTL analysis of root diameter in a wild diploid relative of sweetpotato (Ipomoea batatas (L.) Lam.) using a SNP-based genetic linkage map generated by genotyping-by-sequencing

The complexity of sweetpotato genome, including hexaploidy and heterozygosity, has hindered genetic studies on agronomically important traits such as storage root formation and thickening. Ipomoea trifida (H. B. K.) G. Don. (2n = 2x = 30) is closely related to and cross-compatible with sweetpotato. The diploid I. trifida has been developed as a model plant for sweetpotato genetic research, due to its low ploidy and simple genetic background. In order to reveal the molecular mechanisms underlying storage root development in sweetpotato, F1 mapping population derived from diploid I. trifida was screened for root diameter by genotyping-by-sequencing method. A total of 11,555 raw polymorphic SNPs were identified, in which 8454 SNPs can be used in this F1 population. The SNP genotyping data was utilized to construct the genetic linkage map of I. trifida. The maternal and paternal linkage maps were produced, and 904 maternal and 2034 paternal markers resulted in 13 and 15 LGs respectively. The total length of the maternal maps covered 842.34 cM, while the paternal maps spanned 1540.98 cM. The integrated genetic map consisted of 2892 SNPs (average of 193 markers/linkage group) on 15 linkage groups (LGs) covering 1550.22 cM of the whole genome at an average inter marker distance of 0.55 cM. By using the phenotypic data obtained in this study, three significant QTL were detected for root diameter. These QTL were distributed among three LGs at three independent positions, and each QTL explained significant amount of phenotypic trait variation ranged from 6.1 to 12.0%. The qRD-2 QTL explained 12.0% of the phenotypic variation. This study results will assist in the map-based cloning of genes controlling storage root-related traits and further helps to reveal the genetic basis of root development in sweetpotato.

Discovery and analysis of NBS-LRR gene family in sweet potato genome

<p indent=0mm>The NBS-LRR gene families possess the most abundant resistance genes in plants. Members of the NBS-LRR gene families contain nucleotide-binding site (NBS) and leucine-leucine repeat (LRR) domains. The genome of sweet potato (<italic>Ipomoea batatas</italic>) cultivar has been sequenced but the genes have not been annotated yet. In this study, we predicted the exons of sweet potato genome and obtained the proteins sequences, which were then used to identify and analyze genes of NBS-LRR family. There were 379 genes within NBS-LRR family, amounting to 0.212% of the total genes of sweet potato. The number of the N type, NL type, CNL type, TNL type and PN type was 120, 103, 133, 22, and 1, respectively. All of the chromosomes had NBS-LRR family genes but varied in number and 60.9% of them were clustered. NBS-LRR genes included 15 conservative domains and the genes were conservative within N terminal domain. The results provide references for further studies on the function of NBS-LRR family genes and resistance breeding of sweet potato.

Badnaviruses of Sweet Potato: Symptomless Coinhabitants on a Global Scale.

Sweet potato is among the most important root crops worldwide, particularly in developing countries, and its production is affected severely by a variety of virus diseases. During the last decade, a number of new viruses have been discovered in sweet potatoes through next-generation sequencing studies. Among them are viruses belonging to the genus Badnavirus and collectively assigned to the species sweet potato pakakuy virus (SPPV). We determined the complete genome sequence of two SPPV isolates and show the ubiquitous presence of similar viruses in germplasm and field material from around the globe. We show that SPPV is not integrated into the sweet potato genome, occurs only at extremely low titers, and is efficiently transmitted through seeds and cuttings. They are unaffected by virus elimination therapy and do not induce discernible symptoms in sweet potatoes or indicator host plants. They show considerable variation in their nucleotide sequences and correspond to several genetic lineages. Studies of their interaction with the two most important sweet potato viruses showed only limited synergistic increase in the titers of one of two SPPV isolates. We contend that these viruses may pose little threat to sweet potato production and more likely represent a new type of persistent virus in sweet potato.

Identification and Analysis of &lt;i&gt;R2R3-MYB&lt;/i&gt; Genes in Sweet Potato Genome

The plant MYB is a transcription factor family large in number and with important functions. In this study, the MYB family genes were screened and identified via bioinformatic methods from the raw sequence of sweet potato ( Ipomoea batatas ) genome and the gene structure and function of R2R3-MYB were analyzed. The results showed that there were 88 R2R3-MYB genes with intact R2 and R3 conservative domains, which contained 8 and 9 highly conserved basic amino acids. The results of MEME analysis showed that there were 10 conserved motifs within the I. batatas R2R3-MYB protein sequences. For the I. batatas R2R3-MYB protein sequences, over 80% contained motif 1, motif 2, motif 3, motif 4, motif 5 and motif 7. The R2R3-MYB genes were distributed unevenly across the 15 chromosomes. The number of R2R3-MYB genes in chromosome No.5 was 15, which was the largest; the numbers of R2R3-MYB genes in chromosome No. 4 and 13 were both only 2, which was the smallest. Analysis of the sequence alignment showed that there were 6 pairs of interchromosomal duplication and there were 20 pairs of intrachromosomal duplication, 19 of which existed in clusters. The function prediction and categorization via sequence analysis showed that 44 R2R3-MYB genes of the I. batatas could be categorized to the 13 subgroups of the A. thaliana R2R3-MYB genes, which were involved in the responses to biotic stress and abiotic stress, anthocyanin biosynthesis, anther development, etc. Further analysis showed that 36 R2R3-MYB genes might play important roles in dealing with biotic stress and abiotic stress, 9 of which showed significant up/down-regulation under Fusarium oxysporum f. sp. batatas stress and 27 of which showed significant up/down-regulation under low temperature stress. The domains of I. batatas R2R3-MYB transcription factors were highly conservative, which contained highly conserved motifs within R2 and R3 domains. The phylogenetic tree and transcriptomics data analysis showed that some R2R3-MYB genes might play roles in growth and development, metabolism regulation, biotic stress and abiotic stress, which lent support to I. batatas breeding.

Methods for Optimization of Protein Extraction and Proteogenomic Mapping in Sweet Potato.

The complexity in chemical composition alongside the genomic complexity of crop plants poses significant challenges for the characterization of their proteomes. This chapter provides specific methods that can be used for the extraction and identification of proteins from sweet potato, and a proteogenomic method for the subsequent peptide mapping on the haplotype-derived sweet potato genome assembly. We outline two basic methods for extracting proteins expressed in root and leaf tissues for the label-free quantitative proteomics-one phenol-based procedure and one polyethylene glycol (PEG) 4000-based fractionation method-and discuss strategies for the organ-specific protein extraction and increased recovery of low-abundance proteins. Next, we describe computational methods for improved proteome annotation of sweet potato based on aggregated genomics and transcriptomics resources available in our and public databases. Lastly, we describe an easily customizable proteogenomics approach for mapping sweet potato peptides back to their genome location and exemplify its use in improving genome annotations using a mass spectrometry data set.

Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq

Sweetpotato (Ipomoea batatas L.) is one of the most important food and grain-forage crops globally. It has been planted in >100 countries. Due to the complexity of the sweetpotato genome, its research is far behind other major food crops. At present, limited information about the sweetpotato genome is available. Thus, it is central to find an efficient approach for the investigation of sweetpotato genome. In this study, RAD-seq (Restriction site-associated DNA sequencing) was used to evaluate sweetpotato genetic structure diversity and to develop relevant SSR markers. The study yielded >128 Gb reliable sequence data from 81 sweetpotato accessions. By analyzing polymorphic tags from each accession, a total of 55,622 restriction-site associated DNA sequencing tags (RAD-seq) were found, containing 907,010 SNP. Genetic analysis divided 81 accessions into five major clusters based on their SNP genotype, which matches the results of genetic analysis and the genetic family tree. In addition, 18,320 SSRs loci were detected and 9336 SSR primer pairs were developed. Eighty-three primer pairs were amplified in different sweetpotato genotypes, 76 of which successfully amplified polymorphism bands. These results provide significant information about sweetpotato genome, which can be used to identify novel gene and to further develop the gene chip. And more significant, clustering results based on the SNP genotype provide an essential reference for breeders to match parent plants in breeding program. Additionally, SSR markers developed in this study will supply a wealth of markers for marker-assisted selection in sweetpotato breeding.

Genome-Wide Association Studies (GWAS) for Yield and Weevil Resistance in Sweet potato (Ipomoea batatas (L.) Lam).

We apply the GWAS to sweet potato genome, and identified the SNPs associated with yield and weevil resistance. The sweet potato (Ipomoea batatas (L.) Lam) is a highly heterozygous, outcrossing, polyploid species, which presents challenges for genetic analysis. Therefore, we considered that genome-wide association studies (GWAS) may be applied to the study of the sweet potato genome. The yield of two sweet potato varieties [Purple Sweet Lord (PSL) and 90IDN-47] was assessed at two locations (Kumamoto and Okinawa prefectures) in Japan in 2013 and the yield scores were used for GWAS. The results showed that there were several single nucleotide polymorphisms (SNP) above the significance thresholds in PSL; two peaks were detected in Kumamoto and Okinawa on the Ib03-3 and Ib01-4 linkage groups of PSL, respectively. As for 90IDN-47, one relatively high peak was detected in Kumamoto on the Ib13-8 linkage group. Interestingly, although high peaks above significance thresholds were detected in Kumamoto and Okinawa in PSL, the peaks were located in different linkage groups. This result suggests that the genetic regions controlling yield may change in response to environmental conditions. Additionally, we investigated the degree of weevil damage to the plants, which is the greatest problem in sweet potato cultivation in Okinawa. In this experiment, no SNPs were identified above the significance thresholds. However, one relatively high peak was found in the 90IDN-47 genotype, which showed resistance to weevils. On the other hand, one relatively high peak was also detected in the PSL genotype, which showed susceptibility to weevils. These results suggest that two regions could affect weevil resistance and may contain the gene(s) controlling weevil resistance.

Genome-wide identification and expression analysis of glycine-rich RNA-binding protein family in sweet potato wild relative Ipomoea trifida

Glycine-rich RNA-binding proteins (GRPs) contain RNA recognition motif (RRM) and glycine-rich domains at the N- or C-terminus, respectively, and they participate in varied physiological and biochemical processes, as well as environmental stresses. Sweet potato from the genus Ipomoea is one of the most important crops. However, the role of the GRP gene family in Ipomoea plant species has not been reported yet. At the same time, the genome of sweet potato remains to be elucidated, but the genome of I. trifida which is most probably the progenitor of the sweet potato was released recently. In this regard, we carried out genome-wide analysis of GRP family members in I. trifida. Here, we identified nine GRP genes in I. trifida and investigated their motif distribution, promoters and gene structure. Subsequently, we performed phylogenetic analysis with the GRP genes from I. trifida, Arabidopsis thaliana, Zea mays L. and Oryza sativa to investigate their phylogenetic relationship. Moreover, we studied the expression patterns of ItGRPs in the roots, stems, young and mature leaves and flowers and found that ItGRP genes were tissue-specific. Meanwhile, the expression profiles under four abiotic stress conditions, including heat, cold, salt and drought stress treatments, revealed that some genes were markedly up-regulated or down-regulated. Taken together, our findings will provide reference to studies on the function of GRP genes in the development and stress response of I. trifida.

Elevated carbon dioxide and drought modulate physiology and storage-root development in sweet potato by regulating microRNAs.

Elevated CO2 along with drought is a serious global threat to crop productivity. Therefore, understanding the molecular mechanisms plants use to protect these stresses is the key for plant growth and development. In this study, we mimicked natural stress conditions under a controlled Soil-Plant-Atmosphere-Research (SPAR) system and provided the evidence for how miRNAs regulate target genes under elevated CO2 and drought conditions. Significant physiological and biomass data supported the effective utilization of source-sink (leaf to root) under elevated CO2. Additionally, elevated CO2 partially rescued the effect of drought on total biomass. We identified both known and novel miRNAs differentially expressed during drought, CO2, and combined stress, along with putative targets. A total of 32 conserved miRNAs belonged to 23 miRNA families, and 25 novel miRNAs were identified by deep sequencing. Using the existing sweet potato genome database and stringent analyses, a total of 42 and 22 potential target genes were predicted for the conserved and novel miRNAs, respectively. These target genes are involved in drought response, hormone signaling, photosynthesis, carbon fixation, sucrose and starch metabolism, etc. Gene ontology and KEGG ontology functional enrichment revealed that these miRNAs might target transcription factors (MYB, TCP, NAC), hormone signaling regulators (ARF, AP2/ERF), cold and drought factors (corA), carbon metabolism (ATP synthase, fructose-1,6-bisphosphate), and photosynthesis (photosystem I and II complex units). Our study is the first report identifying targets of miRNAs under elevated CO2 levels and could support the molecular mechanisms under elevated CO2 in sweet potato and other crops in the future.

Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes.

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.

Disentangling a polyploid genome.

The sequencing and draft assembly of the sweet potato genome has resolved much of its complex genetic redundancies, allowing a better inference of the botanical origin of the staple crop.

Haplotype-resolved sweet potato genome traces back its hexaploidization history.

Here we present the 15 pseudochromosomes of sweet potato, Ipomoea batatas, the seventh most important crop in the world and the fourth most significant in China. By using a novel haplotyping method based on genome assembly, we have produced a half haplotype-resolved genome from ~296 Gb of paired-end sequence reads amounting to roughly 67-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two recent whole-genome duplication events as occurring about 0.8 and 0.5 million years ago. This half haplotype-resolved hexaploid genome represents the first successful attempt to investigate the complexity of chromosome sequence composition directly in a polyploid genome, using sequencing of the polyploid organism itself rather than any of its simplified proxy relatives. Adaptation and application of our approach should provide higher resolution in future genomic structure investigations, especially for similarly complex genomes.

Challenges to genome sequence dissection in sweetpotato.

The development of next generation sequencing (NGS) technologies has enabled the determination of whole genome sequences in many non-model plant species. However, genome sequencing in sweetpotato (Ipomoea batatas (L.) Lam) is still difficult because of the hexaploid genome structure. Previous studies suggested that a diploid wild relative, I. trifida (H.B.K.) Don., is the most possible ancestor of sweetpotato. Therefore, the genetic and genomic features of I. trifida have been studied as a potential reference for sweetpotato. Meanwhile, several research groups have begun the challenging task of directly sequencing the sweetpotato genome. In this manuscript, we review the recent results and activities of large-scale genome and transcriptome analysis related to genome sequence dissection in sweetpotato under the sections as follows: I. trifida genome and transcript sequencing, genome sequences of I. nil (Japanese morning glory), transcript sequences in sweetpotato, chloroplast sequences, transposable elements and transfer DNA. The recent international activities of de novo whole genome sequencing in sweetpotato are also described. The large-scale publically available genome and transcript sequence resources and the international genome sequencing streams are expected to promote the genome sequence dissection in sweetpotato.

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition.

BackgroundSweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species.ResultsThe BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93–10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana.ConclusionsThe first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3302-1) contains supplementary material, which is available to authorized users.

The P1N-PISPO trans-Frame Gene of Sweet Potato Feathery Mottle Potyvirus Is Produced during Virus Infection and Functions as an RNA Silencing Suppressor.

The positive-sense RNA genome of Sweet potato feathery mottle virus (SPFMV) (genus Potyvirus, family Potyviridae) contains a large open reading frame (ORF) of 3,494 codons translatable as a polyprotein and two embedded shorter ORFs in the -1 frame: PISPO, of 230 codons, and PIPO, of 66 codons, located in the P1 and P3 regions, respectively. PISPO is specific to some sweet potato-infecting potyviruses, while PIPO is present in all potyvirids. In SPFMV these two extra ORFs are preceded by conserved G2A6 motifs. We have shown recently that a polymerase slippage mechanism at these sites could produce transcripts bringing these ORFs in frame with the upstream polyprotein, thus leading to P1N-PISPO and P3N-PIPO products (B. Rodamilans, A. Valli, A. Mingot, D. San Leon, D. B. Baulcombe, J. J. Lopez-Moya, and J.A. Garcia, J Virol 89:6965-6967, 2015, doi:10.1128/JVI.00337-15). Here, we demonstrate by liquid chromatography coupled to mass spectrometry that both P1 and P1N-PISPO are produced during viral infection and coexist in SPFMV-infected Ipomoea batatas plants. Interestingly, transient expression of SPFMV gene products coagroinfiltrated with a reporter gene in Nicotiana benthamiana revealed that P1N-PISPO acts as an RNA silencing suppressor, a role normally associated with HCPro in other potyviruses. Moreover, mutation of WG/GW motifs present in P1N-PISPO abolished its silencing suppression activity, suggesting that the function might require interaction with Argonaute components of the silencing machinery, as was shown for other viral suppressors. Altogether, our results reveal a further layer of complexity of the RNA silencing suppression activity within the Potyviridae family. Gene products of potyviruses include P1, HCPro, P3, 6K1, CI, 6K2, VPg/NIaPro, NIb, and CP, all derived from the proteolytic processing of a large polyprotein, and an additional P3N-PIPO product, with the PIPO segment encoded in a different frame within the P3 cistron. In sweet potato feathery mottle virus (SPFMV), another out-of-frame element (PISPO) was predicted within the P1 region. We have shown recently that a polymerase slippage mechanism can generate the transcript variants with extra nucleotides that could be translated into P1N-PISPO and P3N-PIPO. Now, we demonstrate by mass spectrometry analysis that P1N-PISPO is indeed produced in SPFMV-infected plants, in addition to P1. Interestingly, while in other potyviruses the suppressor of RNA silencing is HCPro, we show here that P1N-PISPO exhibited this activity in SPFMV, revealing how the complexity of the gene content could contribute to supply this essential function in members of the Potyviridae family.

Current status of sweetpotato genomics research

Sweetpotato [Ipomoea batatas (L.) Lam] grows well in harsh environmental conditions, and is cultivated as one of the top seven food crops in the world. Recently, sweetpotato is drawing interest from people as a healthy food because it is high in dietary fiber, vitamins, carotenoids and overall nutrition value. However, few studies have been conducted on sweetpotato genome sequencing in spite of its importance. This review is aimed at increasing the efficiency of sweetpotato genome sequencing research as well as establishing a base for gene utilization in order to control useful traits. Recently, animal and plant genome sequencing projects increased significantly. However, sweetpotato genome sequencing has not been performed due to polyploidy and heterogeneity problems in its genome. Meanwhile research on its transcriptome has been conducted actively. Recently, a draft of the diploid sweetpotato genome was reported in 2015 by Japanese researchers. In addition, the Korea-China-Japan Trilateral Research Association of Sweetpotato (TRAS) has conducted research on gene map construction and genome sequencing of the hexaploid sweetpotato Xushu 18 since 2014. The Bill & Melinda Gates Foundation launched the 'sweetpotato genomic sequencing to develop genomic tools for Sub-Sahara Africa breeding program'. The chloroplast genome sequence acquired during sweetpotato genome sequencing is used in evolutionary analyses. In this review, the trend of research in the sweetpotato genome sequencing was analyzed. Research trend analysis like this will provide researchers working toward sweetpotato productivity and nutrient improvement with information on the status of sweetpotato genome research. This will contribute to solving world food, energy and environmental problems.

The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop.

Agrobacterium rhizogenes and Agrobacterium tumefaciens are plant pathogenic bacteria capable of transferring DNA fragments [transfer DNA (T-DNA)] bearing functional genes into the host plant genome. This naturally occurring mechanism has been adapted by plant biotechnologists to develop genetically modified crops that today are grown on more than 10% of the world's arable land, although their use can result in considerable controversy. While assembling small interfering RNAs, or siRNAs, of sweet potato plants for metagenomic analysis, sequences homologous to T-DNA sequences from Agrobacterium spp. were discovered. Simple and quantitative PCR, Southern blotting, genome walking, and bacterial artificial chromosome library screening and sequencing unambiguously demonstrated that two different T-DNA regions (IbT-DNA1 and IbT-DNA2) are present in the cultivated sweet potato (Ipomoea batatas [L.] Lam.) genome and that these foreign genes are expressed at detectable levels in different tissues of the sweet potato plant. IbT-DNA1 was found to contain four open reading frames (ORFs) homologous to the tryptophan-2-monooxygenase (iaaM), indole-3-acetamide hydrolase (iaaH), C-protein (C-prot), and agrocinopine synthase (Acs) genes of Agrobacterium spp. IbT-DNA1 was detected in all 291 cultigens examined, but not in close wild relatives. IbT-DNA2 contained at least five ORFs with significant homology to the ORF14, ORF17n, rooting locus (Rol)B/RolC, ORF13, and ORF18/ORF17n genes of A. rhizogenes. IbT-DNA2 was detected in 45 of 217 genotypes that included both cultivated and wild species. Our finding, that sweet potato is naturally transgenic while being a widely and traditionally consumed food crop, could affect the current consumer distrust of the safety of transgenic food crops.

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.

Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don.

Ipomoea trifida (H. B. K.) G. Don. is the most likely diploid ancestor of the hexaploid sweet potato, I. batatas (L.) Lam. To assist in analysis of the sweet potato genome, de novo whole-genome sequencing was performed with two lines of I. trifida, namely the selfed line Mx23Hm and the highly heterozygous line 0431-1, using the Illumina HiSeq platform. We classified the sequences thus obtained as either ‘core candidates’ (common to the two lines) or ‘line specific’. The total lengths of the assembled sequences of Mx23Hm (ITR_r1.0) was 513 Mb, while that of 0431-1 (ITRk_r1.0) was 712 Mb. Of the assembled sequences, 240 Mb (Mx23Hm) and 353 Mb (0431-1) were classified into core candidate sequences. A total of 62,407 (62.4 Mb) and 109,449 (87.2 Mb) putative genes were identified, respectively, in the genomes of Mx23Hm and 0431-1, of which 11,823 were derived from core sequences of Mx23Hm, while 28,831 were from the core candidate sequence of 0431-1. There were a total of 1,464,173 single-nucleotide polymorphisms and 16,682 copy number variations (CNVs) in the two assembled genomic sequences (under the condition of log2 ratio of >1 and CNV size >1,000 bases). The results presented here are expected to contribute to the progress of genomic and genetic studies of I. trifida, as well as studies of the sweet potato and the genus Ipomoea in general.