Karyotype analysis of Panax ginseng C.A.Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution

Disentangling Crocus Series Verni and Its Polyploids

Spring crocuses, the eleven species within Crocus series Verni (Iridaceae), consist of di- and tetraploid cytotypes. Among them is a group of polyploids from southeastern Europe with yet-unclear taxonomic affiliation. Crocuses are generally characterized by complex dysploid chromosome number changes, preventing a clear correlation between these numbers and ploidy levels. To reconstruct the evolutionary history of series Verni and particularly its polyploid lineages associated with C. heuffelianus, we used an approach combining phylogenetic analyses of two chloroplast regions, 14 nuclear single-copy genes plus rDNA spacers, genome-wide genotyping-by-sequencing (GBS) data, and morphometry with ploidy estimations through genome size measurements, analysis of genomic heterozygosity frequencies and co-ancestry, and chromosome number counts. Chromosome numbers varied widely in diploids with 2n = 8, 10, 12, 14, 16, and 28 and tetraploid species or cytotypes with 2n = 16, 18, 20, and 22 chromosomes. Crocus longiflorus, the diploid with the highest chromosome number, possesses the smallest genome (2C = 3.21 pg), while the largest diploid genomes are in a range of 2C = 7-8 pg. Tetraploid genomes have 2C values between 10.88 pg and 12.84 pg. Heterozygosity distribution correlates strongly with genome size classes and allows discernment of di- and tetraploid cytotypes. Our phylogenetic analyses showed that polyploids in the C. heuffelianus group are allotetraploids derived from multiple and partly reciprocal crosses involving different genotypes of diploid C. heuffelianus (2n = 10) and C. vernus (2n = 8). Dysploid karyotype changes after polyploidization resulted in the tetraploid cytotypes with 20 and 22 chromosomes. The multi-data approach we used here for series Verni, combining evidence from nuclear and chloroplast phylogenies, genome sizes, chromosome numbers, and genomic heterozygosity for ploidy estimations, provides a way to disentangle the evolution of plant taxa with complex karyotype changes that can be used for the analysis of other groups within Crocus and beyond. Comparing these results with morphometric analysis results in characters that can discern the different taxa currently subsumed under C. heuffelianus.

Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna

BACKGROUND

DNA tandem repeats (TRs) are often abundant and occupy discrete regions in eukaryotic genomes. These TRs often cause or generate chromosomal rearrangements, which, in turn, drive chromosome evolution and speciation. Tracing the chromosomal distribution of TRs could therefore provide insights into the chromosome dynamics and speciation among closely related taxa. The basic chromosome number in the genus Senna is 2n = 28, but dysploid species like Senna tora have also been observed.

OBJECTIVE

To understand the dynamics of these TRs and their impact on S. tora dysploidization.

METHODS

We performed a comparative fluorescence in situ hybridization (FISH) analysis among nine closely related Senna species and compared the chromosomal distribution of these repeats from a cytotaxonomic perspective by using the ITS1-5.8S-ITS2 sequence to infer phylogenetic relationships.

RESULTS

Of the nine S. tora TRs, two did not show any FISH signal whereas seven TRs showed similar and contrasting patterns to other Senna species. StoTR01_86, which was localized in the pericentromeric regions in all S. tora, but not at the nucleolar organizer region (NOR) site, was colocalized at the NOR site in all species except in S. siamea. StoTR02_7_tel was mostly localized at chromosome termini, but some species had an interstitial telomeric repeat in a few chromosomes. StoTR05_180 was distributed in the subtelomeric region in most species and was highly amplified in the pericentromeric region in some species. StoTR06_159 was either absent or colocalized in the NOR site in some species, and StoIGS_463, which was localized at the NOR site in S. tora, was either absent or localized at the subtelomeric or pericentromeric regions in other species.

CONCLUSIONS

These data suggest that TRs play important roles in S. tora dysploidy and suggest the involvement of 45S rDNA intergenic spacers in "carrying" repeats during genome reshuffling.

Dynamic evolution of Panax species

Background

Panax ginseng is one of the most valuable medicinal plants in Korea. However, deciphering its full genome sequence information for crop improvement has been hampered due to its complex genomic, genetic, and growth characteristics. Many efforts have been made in the past decade to overcome these limitations and understand the genome structure and the evolutionary history of P. ginseng.

Methods

This review aims to discuss the current status of genomic studies on P. ginseng and related species, and the experimental clues suggesting phylogenetic classification and evolutionary history of the genus Panax.

Conclusion

The development of sequencing technologies made genome sequencing of the large P. ginseng genome possible, providing fundamental information to deciphering the evolutionary history of P. ginseng and related species. P. ginseng went through two rounds of whole genome duplication events after diverging from the closest family Apiaceae, which was unveiled from complete whole genome sequences. Further in-depth comparative genome analysis with other related species and genera will uncover the evolutionary history as well as important morphological and ecological characteristics of Panax species.

Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy

Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant Senna tora dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the S. tora genome and compared the chromosomal distribution of these repeats between S. tora and a closely related euploid, Senna occidentalis. Using a read clustering algorithm, we identified the major S. tora tandem repeats and visualized their chromosomal distribution by fluorescence in situ hybridization. We identified eight independent repeats covering ~85 Mb or ~12% of the S. tora genome. The unit lengths and copy numbers had ranges of 7-5,833 bp and 325-2.89 × 10⁶, respectively. Three short duplicated sequences were found in the 45S rDNA intergenic spacer, one of which was also detected at an extra-NOR locus. The canonical plant telomeric repeat (TTTAGGG)_n was also detected as very intense signals in numerous pericentromeric and interstitial loci. StoTR05_180, which showed subtelomeric distribution in Senna occidentalis, was predominantly pericentromeric in S. tora. The unusual chromosomal distribution of tandem repeats in S. tora not only enabled easy identification of individual chromosomes but also revealed the massive chromosomal rearrangements that have likely played important roles in shaping its dysploid karyotype.

Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines

Long-term cultivation of Panax ginseng cell lines leads to a decreasing synthesis of the biologically active substances used in traditional medicine. To gain insight into the cellular mechanisms which may influence this process, we analyzed variations within the rDNA cluster of the Oriental ginseng cell lines. The cell lines were cultivated for 6 and 24 years; the number of nucleoli and chromosomes was analyzed. The complete 18S rDNA sequences were cloned and sequenced. The nucleotide polymorphism and phylogenetic relations of the sequences were analyzed, and the secondary structures for separate 18S rRNA regions were modeled. The 18S rDNA accumulated mutations during cell cultivation that correlate well with an increase in the number of chromosomes and nucleoli. The patterns of nucleotide diversity are culture-specific and the increasing polymorphism associates with cytosine methylation sites. The secondary structures of some 18S rRNA regions and their interaction can alter during cultivation. The phylogenetic tree topologies are particular for each cell line.The observed alterations in rDNA clusters are associated with a somaclonal variation, leading to changes in the pattern of intracellular synthesis during cell cultivation. The identified divergent rRNAs could provide additional gene expression regulation in P. ginseng cells by forming heterogeneous ribosomes.

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng

Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.

Characteristics of Panax ginseng Cultivars in Korea and China

Ginseng (Panax ginseng Meyer) is one of the most important medicinal herbs in Asia. Its pharmacological activity comes from ginsenosides, and its roots are produced commercially for traditional and Oriental medicine. Though 17 Panax species are available around the world, there was a need to develop cultivars adapted to different climatic conditions and resistant to various diseases while still producing high-quality, high-yield roots. Thus, 12 and 9 commercial P. ginseng cultivars have been registered in South Korea and China, respectively. Those varieties show superiority to local landraces. For example, Chunpoong is more highly resistant to rusty rot disease than the local Jakyungjong landrace and has a good root shape; it is highly cultivated to produce red ginseng. The Chinese cultivar Jilin Huangguo Renshen has higher ginsenoside content than its local landraces. This review provides information about P. ginseng cultivars and offers directions for future research, such as intra- and interspecific hybridization.

Genetic diversity among cultivated and wild Panax ginseng populations revealed by high-resolution microsatellite markers

Background

Ginseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood.

Methods

We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries.

Results

Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (H_e) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship.

Conclusion

Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.

Genome and evolution of the shade-requiring medicinal herb Panax ginseng

Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng

BACKGROUND

The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb.

DESCRIPTION

The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page.

CONCLUSION

This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

A refined Panax ginseng karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs

Background

Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification.

Methods

Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR.

Results

Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4′,6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype.

Conclusion

Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.

Comprehensive analysis of Panax ginseng root transcriptomes

BACKGROUND

Korean ginseng (Panax ginseng C.A. Meyer) is a highly effective medicinal plant containing ginsenosides with various pharmacological activities, whose roots are produced commercially for crude drugs.

RESULTS

Here, we used the Illumina platform to generate over 232 million RNA sequencing reads from four root samples, including whole roots from one-year-old plants and three types of root tissue from six-year-old plants (i.e., main root bodies, rhizomes, and lateral roots). Through de novo assembly and reference-assisted selection, we obtained a non-redundant unigene set consisting of 55,949 transcripts with an average length of 1,250 bp. Among transcripts in the unigene set, 94 % were functionally annotated via similarity searches against protein databases. Approximately 28.6 % of the transcripts represent novel gene sequences that have not previously been reported for P. ginseng. Digital expression profiling revealed 364 genes showing differential expression patterns among the four root samples. Additionally, 32 were uniquely expressed in one-year-old roots, while seven were uniquely expressed in six-year-old root tissues. We identified 38 transcripts encoding enzymes involved in ginsenoside biosynthesis pathways and 189 encoding UDP-glycosyltransferases.

CONCLUSION

Our analysis provides new insights into the role of the root transcriptome in development and secondary metabolite biosynthesis in P. ginseng.

Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy

Ginseng (Panax ginseng) is a famous medicinal herb, but the composition and structure of its genome are largely unknown. Here we characterized the major repeat components and inspected their distribution in the ginseng genome. By analyzing three repeat-rich bacterial artificial chromosome (BAC) sequences from ginseng, we identified complex insertion patterns of 34 long terminal repeat retrotransposons (LTR-RTs) and 11 LTR-RT derivatives accounting for more than 80% of the BAC sequences. The LTR-RTs were classified into three Ty3/gypsy (PgDel, PgTat and PgAthila) and two Ty1/Copia (PgTork and PgOryco) families. Mapping of 30-Gbp Illumina whole-genome shotgun reads to the BAC sequences revealed that these five LTR-RT families occupy at least 34% of the ginseng genome. The Ty3/Gypsy families were predominant, comprising 74 and 33% of the BAC sequences and the genome, respectively. In particular, the PgDel family accounted for 29% of the genome and presumably played major roles in enlargement of the size of the ginseng genome. Fluorescence in situ hybridization (FISH) revealed that the PgDel1 elements are distributed throughout the chromosomes along dispersed heterochromatic regions except for ribosomal DNA blocks. The intensity of the PgDel2 FISH signals was biased toward 24 out of 48 chromosomes. Unique gene probes showed two pairs of signals with different locations, one pair in subtelomeric regions on PgDel2-rich chromosomes and the other in interstitial regions on PgDel2-poor chromosomes, demonstrating allotetraploidy in ginseng. Our findings promote understanding of the evolution of the ginseng genome and of that of related species in the Araliaceae.

Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tag-simple sequence repeat bands in Panax ginseng Meyer

Background

Panax ginseng, the most famous medicinal herb, has a highly duplicated genome structure. However, the genome duplication of P. ginseng has not been characterized at the sequence level. Multiple band patterns have been consistently observed during the development of DNA markers using unique sequences in P. ginseng.

Methods

We compared the sequences of multiple bands derived from unique expressed sequence tag-simple sequence repeat (EST-SSR) markers to investigate the sequence level genome duplication.

Results

Reamplification and sequencing of the individual bands revealed that, for each marker, two bands around the expected size were genuine amplicons derived from two paralogous loci. In each case, one of the two bands was polymorphic, showing different allelic forms among nine ginseng cultivars, whereas the other band was usually monomorphic. Sequences derived from the two loci showed a high similarity, including the same primer-binding site, but each locus could be distinguished based on SSR number variations and additional single nucleotide polymorphisms (SNPs) or InDels. A locus-specific marker designed from the SNP site between the paralogous loci produced a single band that also showed clear polymorphism among ginseng cultivars.

Conclusion

Our data imply that the recent genome duplication has resulted in two highly similar paralogous regions in the ginseng genome. The two paralogous sequences could be differentiated by large SSR number variations and one or two additional SNPs or InDels in every 100 bp of genic region, which can serve as a reliable identifier for each locus.

Randomly detected genetically modified (GM) maize (Zea mays L.) near a transport route revealed a fragile 45S rDNA phenotype

Monitoring of genetically modified (GM) crops has been emphasized to prevent their potential effects on the environment and human health. Monitoring of the inadvertent dispersal of transgenic maize in several fields and transport routes in Korea was carried out by qualitative multiplex PCR, and molecular analyses were conducted to identify the events of the collected GM maize. Cytogenetic investigations through fluorescence in situ hybridization (FISH) of the GM maize were performed to check for possible changes in the 45S rDNA cluster because this cluster was reported to be sensitive to replication and transcription stress. Three GM maize kernels were collected from a transport route near Incheon port, Korea, and each was found to contain NK603, stacked MON863 x NK603, and stacked NK603 x MON810 inserts, respectively. Cytogenetic analysis of the GM maize containing the stacked NK603 x MON810 insert revealed two normal compact 5S rDNA signals, but the 45S rDNA showed a fragile phenotype, demonstrating a “beads-on-a-string” fragmentation pattern, which seems to be a consequence of genetic modification. Implications of the 45S rDNA cluster fragility in GM maize are also discussed.