Joo-Hwan Kim

Comparative genome analysis and phylogenetic relationship of order Liliales insight from the complete plastid genome sequences of two Lilies (Lilium longiflorum and Alstroemeria aurea).

Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Lilium longiflorum (Liliaceae) and 155,510bp in Alstroemeria aurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L . longflorum and L . superbum . Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria . IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria . Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium.

Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes

Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses.

Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. (Melanthiaceae)

The sequence of the chloroplast genome, which is inherited maternally, contains useful information for many scientific fields such as plant systematics, biogeography and biotechnology because its characteristics are highly conserved among species. There is an increase in chloroplast genomes of angiosperms that have been sequenced in recent years. In this study, the nucleotide sequence of the chloroplast genome (cpDNA) of Veratrum patulum Loes. (Melanthiaceae, Liliales) was analyzed completely. The circular double-stranded DNA of 153,699 bp consists of two inverted repeat (IR) regions of 26,360 bp each, a large single copy of 83,372 bp, and a small single copy of 17,607 bp. This plastome contains 81 protein-coding genes, 30 distinct tRNA and four genes of rRNA. In addition, there are six hypothetical coding regions (ycf1, ycf2, ycf3, ycf4, ycf15 and ycf68) and two open reading frames (ORF42 and ORF56), which are also found in the chloroplast genomes of the other species. The gene orders and gene contents of the V. patulum plastid genome are similar to that of Smilax china, Lilium longiflorum and Alstroemeria aurea, members of the Smilacaceae, Liliaceae and Alstroemeriaceae (Liliales), respectively. However, the loss rps16 exon 2 in V. patulum results in the difference in the large single copy regions in comparison with other species. The base substitution rate is quite similar among genes of these species. Additionally, the base substitution rate of inverted repeat region was smaller than that of single copy regions in all observed species of Liliales. The IR regions were expanded to trnH_GUG in V. patulum, a part of rps19 in L. longiflorum and A. aurea, and whole sequence of rps19 in S. china. Furthermore, the IGS lengths of rbcL-accD-psaI region were variable among Liliales species, suggesting that this region might be a hotspot of indel events and the informative site for phylogenetic studies in Liliales. In general, the whole chloroplast genome of V. patulum, a potential medicinal plant, will contribute to research on the genetic applications of this genus.

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries.

Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.

A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales).

The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 454 sequencing system and Sanger sequencing method to trace the evolutionary pattern in the tribe Parideae of the family Melanthiaceae (Liliales). The circular double-stranded cpDNA of P. verticillata (157,379 bp) consists of two inverted repeat regions each of 28,373 bp, a large single copy of 82,726 bp, and a small single copy of 17,907 bp. Gene content and order are generally similar to the previously reported cpDNA sequences within the order Liliales. However, we found that trnI_CAU was triplicated in P. verticillata. In addition, cemA is suspected to be a pseudogene due to the presence of internal stop codons created by poly(A) insertion and single small CA repeats. Such changes were not found in previously examined cpDNAs of the Melanthiaceae or other families of the Liliales, suggesting that such features are unique to the tribe Parideae of Melanthiaceae. The characteristics of P. verticillata cpDNA will provide useful information for uncovering the evolution within Paris and for further research of plastid genome evolution and phylogenetic studies in Liliales.

Complete Chloroplast Genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae): Comparative Genomics and Evaluation of Universal Primers for Liliales

The complete chloroplast genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae, Liliales) was mapped using polymerase chain reaction and the Sanger method. The circular double-stranded DNA was a typical quadripartite structure consisting of two inverted repeated regions (27,397 bp), a small single copy region (18,205 bp), and a large single-copy region (81,646 bp), with a total length of 154,645 bp. The genome consisted of 137 coding genes, including 91 protein-coding genes, 38 distinct tRNA, and 8 rRNA genes. The ycf15 and ycf68 genes had several internal stop codons interpreted as pseudogenes. The inverted repeat (IR) region expanded to part of the rps3 gene in the junction between large single-copy and IRA regions in C. japonica. We designed 785 primers, of which 481 were used to map the entire chloroplast genome of C. japonica. Primers were compared with the complete chloroplast sequence of Smilax china (Smilacaceae) to identify primers that could be used for other Liliales members and whole chloroplast genome sequencing. Of the primers used for C. japonica, 398 could be used with other smaller species within the order.

The complete chloroplast genome of colchicine plants (Colchicum autumnale L. and Gloriosa superba L.) and its application for identifying the genus

AbstractMain conclusionThe complete chloroplast genome of two colchicine medicinal plants is reported for the first time. Deletion ofycf15 gene occurred only inColchicumbut not inGloriosaand suggests this as a potential marker for delineating the two species.Colchicum autumnale L. and Gloriosa superba L. are well-known sources of colchicine, a type of alkaloid and an ancient anti-inflammatory drug used to prevent gout. Accordingly, this alkaloid has been used as a chemical marker for identifying the expanded Colchicaceae family. In the present study, we report the completen chloroplast genome (cpDNA) sequence of two colchicine medicinal plants (G. superba and C. autumnale) that belong to the tribe Colchiceae of the Colchicaceae family. In C. autumnale, the circular double-stranded cpDNA sequence of 156,462xa0bp consists of two inverted repeat (IR) regions of 27,741xa0bp each, a large single-copy region (LSC) of 84,246xa0bp, and a small single-copy region (SSC) of 16,734xa0bp. The cpDNA sequence of G. superba is longer than that of C. autumnale (157,924xa0bp), which consists of two IRs (28,063xa0bp), an SSC (16,786xa0bp), and an LSC (85,012xa0bp). Significant structural differences between them were observed in the ycf15 gene. ycf15 gene was absent from C. autumnale cpDNA and affected the length of the chloroplast genome between the species. Furthermore, this gene loss event was specific to the expanded genus of Colchicum sensu Vinnersten and Manning. Therefore, this gene may be an effective and powerful molecular marker for identifying the Colchicum genus within the family.

The phylogenetic relationships of Asparagales in Korea based on five plastid DNA regions

We performed a phylogenetic analysis of 13 families of Asparagales sensu APG III, including 59 Korean taxa representing 10 families based on five plastid regions sequences (matK, rbcL, rpoC1, rps3, and atpF-H intergenic spacer). Parsimony and Bayesian analyses were conducted to clarify the relationships among Korean Asparagales. Among the five regions, matK and atpF-H were the most informative. The most congruent phylogenetic trees were obtained from the combinations of four regions excluding atpF-H. Although both the matK and rbcL gene trees implied that the family system of Asparagales sensu APG III should be modified to include three expanded families, our combined four-regions data set resulted in a highly resolved topology with strong support for the following: (1) Asparagaceae s.l.; (2) Amaryllidaceae s.l.; (3) Hemerocallidoideae of Xanthorrhoeaceae s.l.; (4) Iridaceae; (5) Hypoxidaceae; and (6) Orchidaceae. However, the position of Scilla (Scilloideae of Asparagaceae s.l.) was ambiguous. Hemerocallidoideae was a sister group of both the expanded families of Asparagaceae s.l. and Amaryllidaceae s.l., which are considered the core asparagoids, while Orchidaceae was sister to all other Asparagales. We discuss differentiation of the morphological character within the Korean Asparagales, which clearly suggests that the subfamily Nolinoideae of Asparagaceae s.l. exhibits different character states than the other subfamilies. We compared 10 representative morphological characters to the molecular phylogenetic relationships, and propose that the circumscription within Asparagales sensu APG III needs to be reconsidered.

Flavonoids from Litsea japonica Inhibit AGEs Formation and Rat Lense Aldose Reductase In Vitro and Vessel Dilation in Zebrafish.

In our ongoing efforts to identify effective naturally sourced agents for the treating of diabetic complications, two new (1 and 2) and 11 known phenolic compounds (3-13) were isolated from an 80u200a% ethanol extract of Litsea japonica leaves. The structures of the new compounds were established by spectroscopic and chemical studies. These isolates (1-13) were subjected to an in vitro bioassay evaluating their inhibitory activity on advanced glycation end products formation and rat lens aldose reductase activity. Of the compounds evaluated, the flavonoids (3, 4, 6-8, 11, and 12) markedly inhibited advanced glycation end products formation, with IC50 values of 7.4-72.0u2009µM, compared with the positive control, aminoguanidine (IC50u2009=u2009975.9u2009µM). In the rat lens aldose reductase assay, consistent with the inhibition of advanced glycation end products formation, the flavonoids (3, 4, 6-8, 11, and 12) exhibited considerable inhibition of rat lens aldose reductase activity, with IC50 values of 1.1-12.5u2009µM. In addition, the effects of kaempferol (4) and tiliroside (7) on the dilation of hyaloid-retinal vessels induced by high glucose in larval zebrafish were investigated. Only kaempferol significantly reduced the diameters of high glucose-induced hyaloid-retinal vessels, by 52.2u200a% at 10u2009µM, compared with those in the high glucose-treated control group.

Molecular identification of Schisandra chinensis and its allied species using multiplex PCR based on SNPs

Schisandra chinensis (Turcz.) Baill. is a climbing woody vine found over a wide geographical range in northeast Asia. Its red five-flavored fruits have been used as drugs and food. In China and Korea, the dried fruit of S. chinensis has been used for a long time as a traditional medicine. Three species of the family Schisandraceae, S. chinensis, S. repanda, and Kadsura japonica, are distributed mainly in southern Korea. While S. chinensis is broadly distributed, S. repanda and K. japonica are restricted to the southern islands of Korea, especially Jeju. The amplification refractory mutation system (ARMS), one of molecular genotyping technique, is a simple and rapid method for detecting point mutations, restriction fragment length polymorphisms, and small deletions or insertions in a DNA sequence. This PCR-based technique utilizes a primer designed to react only when it anneals to specific target sequences in a DNA sample. In the present study, we analyzed rbcL of the chloroplast gene and ITS from S. chinensis and two related taxa, S. repanda and K. japonica, and developed a specific marker for distinguishing S. chinensis from the related taxa based on SNPs using multiplex PCR. Result showed that two species-specific fragments with 230 bp of rbcL and 278 bp of ITS region were additionally amplified only in all of individuals of S. chinenesis using multiplex PCR method. Here, we describe the details of the protocol for the molecular identification of S. chinensis and other related species. Our results cover five populations of S. chinensis in Korea.