Sang Hyun Sung

Association of molecular markers derived from the BrCRISTO1 gene with prolycopene‑enriched orange‑colored leaves in Brassica rapa

AbstractKey messageSequence polymorphism inBrCRTISO1, encodingcarotenoid isomerase, is identified in orange-coloredB. rapa, and three resulting gene-based markers will be useful for marker-assisted breeding of OC cultivars.Abstract Carotenoids are color pigments that are important for protection against excess light in plants and essential sources of retinols and vitamin A for animals. We identified a single recessive gene that might cause orange-colored (OC) inner leaves in Brassica rapa. The inner leaves of the OC cultivar were enriched in lycopene-like compounds, specifically prolycopene and its isomers, which can be a useful functional trait for Kimchi cabbage. We used a candidate gene approach based on the 21 genes in the carotenoid pathway to identify a candidate gene responsible for the orange color. Among them, we focused on two carotenoid isomerase (CRTISO) genes, BrCRTISO1 and BrCRTISO2. The expression of BrCRTISO1 was higher than that of BrCRTISO2 in a normal yellow-colored (YE) cultivar, but full-length BrCRTISO1 transcripts were not detected in the OC cultivar. Genomic sequence analysis revealed that BrCRTISO1 of the OC cultivar had many sequence variations, including single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels), compared to that of the YE cultivar. We developed molecular makers for the identification of OC phenotype based on the polymorphic regions within BrCRTISO1 in B. rapa breeding. The BrCRTISO1 gene and its markers identified in this study are novel genetic resources and will be useful for studying the carotenoid biosynthesis pathway as well as developing new cultivars with unique carotenoid contents in Brassica species.

The complete chloroplast genome sequence of Zanthoxylum piperitum

Abstract The complete chloroplast genome sequence of Zanthoxylum piperitum, a plant species with useful aromatic oils in family Rutaceae, was generated in this study by de novo assembly with whole-genome sequence data. The chloroplast genome was 158 154 bp in length with a typical quadripartite structure containing a pair of inverted repeats of 27 644 bp, separated by large single copy and small single copy of 85 340 bp and 17 526 bp, respectively. The chloroplast genome harbored 112 genes consisting of 78 protein-coding genes 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis of the complete chloroplast genome sequences with those of known relatives revealed that Z. piperitum is most closely related to the Citrus species.

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

Summary 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.

The complete chloroplast genome sequence of an important medicinal plant Cynanchum wilfordii (Maxim.) Hemsl. (Apocynaceae).

Abstract Cynanchum wilfordii (Maxim.) Hemsl. is a traditional medicinal herb belonging to the Asclepiadoideae subfamily, whose dried roots have been used as traditional medicine in Asia. The complete chloroplast genome of C. wilfordii was generated by de novo assembly using the small amount of whole genome sequencing data. The chloroplast genome of C. wilfordii was 161 241 bp long, composed of large single copy region (91 995 bp), small single copy region (19 930 bp) and a pair of inverted repeat regions (24 658 bp). The overall GC contents of the chloroplast genome was 37.8%. A total of 114 genes were annotated, which included 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that C. wilfordii is most closely related to Asclepias nivea (Caribbean milkweed) and Asclepias syriaca (common milkweed) within the Asclepiadoideae subfamily.

The complete chloroplast genome sequence of Cynanchum auriculatum Royle ex Wight (Apocynaceae).

Abstract Cynanchum auriculatum is a climbing vine belonging to the Apocynaceae family and shows very similar morphology to Cynanchum wilfordii, a medicinal plant. The complete chloroplast genome of C. auriculatum was generated by de novo assembly using the small amount of whole genome sequencing data. The chloroplast genome of C. auriculatum was 160 840 bp in length and consisted of four distinct regions, such as large single copy region (91 973 bp), small single copy region (19 667 bp), and a pair of inverted repeat regions (24 600 bp). The overall GC contents of the chloroplast genome were 37.8%. A total of 114 genes were predicted and included 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that C. auriculatum is most closely related to Cynanchum wilfordii, a medicinal plant.

The complete chloroplast genome sequence of the Taraxacum officinale F.H.Wigg (Asteraceae)

Abstract Taraxacum officinale is a distributed weedy plant used as a traditional medicinal herb belonging to the family Asteraceae. The complete chloroplast genome of T. officinale was generated by de novo assembly with whole genome sequence data. The chloroplast genome was 151 324 bp in length, which consisted of a large single copy region of 83 895 bp and a short single copy region of 18 549 bp separated by a pair of inverted repeat regions of 24 440 bp. The chloroplast genome contained 79 protein-coding genes, 29 tRNA genes and four rRNA genes. Phylogenetic analysis revealed that T. officinale was closely related to Lactuca sativa.

The complete chloroplast genome sequence of Ligularia fischeri (Ledeb.) Turcz. (Asteraceae)

Abstract We characterized the complete chloroplast genome sequence of Ligularia fischeri, a collection from Halla Mountain in Jeju Island, Korea. The plants are utilized as edible functional plant species harbouring useful antioxidant compounds in family Asteraceae. De novo assembly with whole genome sequencing data of L. fischeri completed the chloroplast genome of 151 133 bp long, which included two inverted repeats (IRs) blocks of 24 831 bp, separated by the large single-copy block of 83 238 bp and small single-copy block of 18 233 bp. The genome encoded 113 genes consisting of 80 protein-coding genes, 29 tRNA genes and 4 rRNA genes. Phylogenetic analysis with protein coding gene sequences of reported Asteraceae chloroplast genomes revealed a close relationship of L. fischeri with Jacobaea vulgaris, a weed species world-widely distributed.

The complete chloroplast genomes of two Taraxacum species, T. platycarpum Dahlst. and T. mongolicum Hand.-Mazz. (Asteraceae)

Abstract Taraxacum platycarpum and Taraxacum mongolicum are perennial plants utilized for medicinal purposes in the family Asteraceae. The complete chloroplast genome sequences of the two species were characterized by de novo assembly with whole genome sequencing data. The chloroplast genomes of T. platycarpum and T. mongolicum were 151,307 and 151,451 bp in length, respectively, and showed a typical quadripartite structure. The chloroplast genomes of both species contained the same number of genes, 79 protein-coding genes, 29 tRNA genes and 4 rRNA genes. Phylogenetic analysis indicated that the two Taraxacum species were grouped with T. officinale, all of which showed sister relationship with Lactuca sativa.

Complete chloroplast genome sequence of Artemisia fukudo Makino (Asteraceae)

Abstract In this study, a complete chloroplast genome sequence of Artemisia fukudo (Asteraceae family) was characterized by de novo assembly using whole genome sequence data. The chloroplast genome was 151,011 bp in length, comprising a large single-copy region of 82,751 bp, a small single copy region of 18,348 bp and a pair of inverted repeats of 24,956 bp. The genome contained 80 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Phylogenetic tree revealed that A. fukudo was closely located in other Artemisia species, Artemisia montana and Artemisia frigida.

The complete chloroplast genome of Eclipta prostrata L. (Asteraceae)

Abstract Eclipta prostrata is an herbal medicinal plant belonging to the Asteraceae family. In this study, complete chloroplast genome sequence of the E. prostrata was characterized by de novo assembly using whole genome sequence data. The genome of E. prostrata was 151,757 bp in length, which was composed of large single copy region of 83,285 bp, small single copy region of 18,346 bp and a pair of inverted repeat regions of 25,063 bp. The genome harboured 80 protein coding sequences, 30 tRNA genes and 4 rRNA genes. We confirmed close taxonomic relationship between E. prostrata and Helianthus annuus through phylogenetic analysis with chloroplast protein-coding genes.