Sang-Ho Kang

The complete chloroplast genome of two Brassica species, Brassica nigra and B. Oleracea

Abstract The two Brassica species, Brassica nigra and Brassica oleracea, are important agronomic crops. The chloroplast genome sequences were generated by de novo assembly using whole genome next-generation sequences. The chloroplast genomes of B. nigra and B. oleracea were 153u2009633u2009bp and 153u2009366u2009bp in size, respectively, and showed conserved typical chloroplast structure. The both chloroplast genomes contained a total of 114 genes including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis revealed that B. oleracea is closely related to B. rapa and B. napus but B. nigra is more diverse than the neighbor species Raphanus sativus.

Comparative transcriptome analysis reveals whole-genome duplications and gene selection patterns in cultivated and wild Chrysanthemum species

AbstractKey messageComparative transcriptome analysisnof wild and cultivated chrysanthemums provides valuablengenomic resources and helps uncover common andndivergent patterns of genome and gene evolution in these species.AbstractPlants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C. morifolium is an allohexaploid plant that is thought to have originated via the hybridization of several Chrysanthemum species, but the genomic and molecular evolutionary mechanisms remain poorly understood. In the present study, we sequenced and compared the transcriptomes of C. morifolium and the wild Korean diploid species, C. boreale. De novo transcriptome assembly revealed 11,318 genes in C. morifolium and 10,961 genes in C. boreale, whose functions were annotated by homology searches. An analysis of synonymous substitution rates (Ks) of paralogous and orthologous genes suggested that the two Chrysanthemum species commonly experienced the Asteraceae paleopolyploidization and recent genome duplication or triplication before the divergence of these species. Intriguingly, C. boreale probably underwent rapid diploidization, with a reduction in chromosome number, whereas C. morifolium maintained the original chromosome number. Analysis of the ratios of non-synonymous to synonymous nucleotide substitutions (Ka/Ks) between orthologous gene pairs indicated that 107 genes experienced positive selection, which may have been crucial for the adaptation, domestication, and speciation of Chrysanthemum.

Analysis of flavonoids in double haploid population derived from microspore culture of F1 hybrid of Brassica rapa

본 연구에서는 유지형 배추인 LP08과 청경채형 LP21을 교배한 교잡종

The complete chloroplast genome sequence of medicinal plant, Artemisia argyi

F_1

The complete chloroplast genome sequence of Coix lacryma-jobi L. (Poaceae), a cereal and medicinal crop

을 소포자 배양하여 유전적으로 고정된 계통을 획득하였다. 엽의 결각 유무 및 결각수에서 다양한 형태적 특징을 보이는 66개 고정계통을 대상으로 항암 및 항산화 물질로 알려진 플라보노이드의 함량을 분석하였다. 66개 고정 계통의 엽의 결각...

The complete mitochondrial genome of Wonwhang (Pyrus pyrifolia)

Abstract Artemisia argyi, called wormwood, is widely distributed in northeastern Asia. The complete chloroplast genome sequence of A. argyi was generated by de novo assembly using whole genome next generation sequences. The complete chloroplast genome sequence of A. argyi is 151u2009192u2009bp in size. It is composed of a large single-copy (LSC), a small single-copy (SSC) and two inverted repeat (IR) regions of 82u2009930u2009bp, 18u2009344u2009bp and 24u2009959u2009bp, respectively. Overall GC contents of the genome were 37.46%. The A. argyi chloroplast genome has a total of 114 genes including 80 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on the chloroplast genome demonstrated that A. argyi is most closely related to Artemisia montana.

The multipartite mitochondrial genome of Cynanchum wilfordii (Gentianales: Apocynaceae)

Abstract Coix lacryma-jobi is a cereal and medicinal crop belonging to the Poaceae family. This study characterized complete chloroplast genome sequence of a Korean cultivar Johyun of C. lacryma-jobi var. ma-yuen through the de novo hybrid assembly with Illumina and PacBio genomic reads. The chloroplast genome is 140,863u2009bp long and composed of large single copy (82,827u2009bp), small single copy (12,522u2009bp), and a pair of inverted repeats (each 22,757u2009bp). A total of 123 genes including 87 protein-coding genes, 32 tRNA genes, and four rRNA genes were predicted in the genome. Phylogenetic analysis confirmed a close relationship of C. lacryma-jobi with species in the Panicoideae subfamily of the Poaceae family.

Complete chloroplast genome and 45S nrDNA sequences of the medicinal plant species Glycyrrhiza glabra and Glycyrrhiza uralensis

Abstract This is a de novo assembly and annotation of a complete mitochondrial genome from Pyrus pyrifolia in the family Rosaceae. The complete mitochondrial genome of P. pyrifolia was assembled from PacBio RSII P6-C4 sequencing reads. The circular genome was 458,873u2009bp in length, containing 39 protein-coding genes, 23 tRNA genes and three rRNA genes. The nucleotide composition was A (27.5%), T (27.3%), G (22.6%) and C (22.6%) with GC content of 45.2%. Most of protein-coding genes use the canonical start codon ATG, whereas nad1, cox1, matR and rps4 use ACG, mttB uses ATT, rpl16 and rps19 uses GTG. The stop codon is also common in all mitochondrial genes. The phylogenetic analysis showed that P. pyrifolia was clustered with the Malus of Rosaceae family. Maximum-likelihood analysis suggests a clear relationship of Rosids and Asterids, which support the traditional classification.

Rediscovery of haploid breeding in the genomics era

Abstract Cynanchum wilfordii is a traditional herbal medicine and belongs to the family Apocynaceae. The C. wilfordii mitochondrial genome consists of three circular chromosomes (named chromosomes I-III), the lengths of which are 379,060, 352,767 and 111,332 nucleotides. The mitochondrial genome encodes 58 genes, including 38 protein-coding genes, 17 transfer RNA genes and three ribosomal RNA genes. Of these 58 genes, 37 are located in chromosome I, 35 in chromosome II and 15 in chromosome III. Phylogenetic analysis suggests that among the 14 reported species of Asterids, C. wilfordii is most closely related to Asclepias syriaca.

The Complete Chloroplast Genome of the Hare’s Ear Root, Bupleurum falcatum: Its Molecular Features

Glycyrrhiza uralensis and G. glabra, members of the Fabaceae, are medicinally important species that are native to Asia and Europe. Extracts from these plants are widely used as natural sweeteners because of their much greater sweetness than sucrose. In this study, the three complete chloroplast genomes and five 45S nuclear ribosomal (nr)DNA sequences of these two licorice species and an interspecific hybrid are presented. The chloroplast genomes of G. glabra, G. uralensis and G. glabra × G. uralensis were 127,895 bp, 127,716 bp and 127,939 bp, respectively. The three chloroplast genomes harbored 110 annotated genes, including 76 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The 45S nrDNA sequences were either 5,947 or 5,948 bp in length. Glycyrrhiza glabra and G. glabra × G. uralensis showed two types of nrDNA, while G. uralensis contained a single type. The complete 45S nrDNA sequence unit contains 18S rRNA, ITS1, 5.8S rRNA, ITS2 and 26S rRNA. We identified simple sequence repeat and tandem repeat sequences. We also developed four reliable markers for analysis of Glycyrrhiza diversity authentication.