The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations

Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

Euonymus maackii Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of E. maackii. By combining this genome with seven available cp genomes from Euonymus species, we performed plastome variation analysis of E. maackii and Euonymus. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of E. maackii. The newly assembled cp genome of E. maackii was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of E. maackii, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including trnV-UAC, petN, ycf1-ndhF, trnM-CAU-atpE, rpl2-rpl23, psbZ-trnG-GCC, trnY-GUA-trnE-UUC, trnW-CCA-trnP-UGG, rps16-trnQ-UUG, and psbC-trnS-UGA. The hypervariable coding and noncoding regions in E. maackii were not the same as those in Euonymus. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven Euonymus species formed a clade, which was sister to that formed with Catha edulis and Maytenus guangxiensis, and they separated 24.74 million years ago. E. maackii and E. hamiltonianus were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of E. maackii, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in Euonymus.

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.

The complete chloroplast genome of Abeliophyllum distichum f. lilacinum Nakai (Oleaceae) from the Chungbuk Province, Korea

The chloroplast genome of Abeliophyllum distichum f. lilacinum Nakai, classified to a monotypic in this genus, and an endemic species in Korea, was sequenced to understand the genetic differences among intraspecies and cultivars of A. distichum. The chloroplast genome length is 156,015 bp (GC ratio is 37.8%) and has a typical quadripartite structure: 86,779 bp large single copy (35.8%) and 17,828 bp small single copy (31.9%) regions separated by two 25,704 bp inverted repeat (43.2%) regions. The genome encodes for 133 genes (88 protein-coding genes, eight rRNAs, and 37 tRNAs). Six to 99 SNPs and seven to 18 INDEL regions (19 bp to 72 bp) were identified against available chloroplast genomes of A. distichum. Phylogenetic trees show that A. distichum f. lilacinum is clustered with the Dae Ryun cultivar which has a larger fruit body. Our analyses suggest additional research, such as Genotyping-By-Sequencing, for understanding relationship between morphology and genotype of A. distichum.

The complete mitochondrial genome of Douinia plicata (Lindb.) Konstant. et. Vilnet (Scapaniaceae, Jungermanniales)

Douinia plicata (Lindb.) Konstant. & Vilnet is the endemic species in Northeast Asia. Here, we reported complete mitochondrial genome of D. plicata. It is 144,206 bp long and includes 72 genes (42 protein-coding genes, three rRNAs, and 27 tRNAs). The overall GC content is 45.1%. Intergeneic variations against S. amplicata, which is slightly higher than intraspecific variations of S. ampliata and W. denudata. Phylogenetic trees show D. plicatum is clustered with three Scapania mitochondrial genomes with high supportive values, which is congruent with previous studies.

The complete chloroplast genome of Zoysia matrella (L.) Merr. isolated in Korea (Poaceae): investigation of intraspecific variations on chloroplast genomes

Completed chloroplast genome of Zoysia matrella (L.) Merr. isolated in Korea is 135,888 bp long (GC ratio is 38.4%) and has four subregions: 81,370 bp of large single copy (36.3%) and 12,594 bp of small single copy (32.7%) regions are separated by 20,962 bp of inverted repeat (44.1%) regions including 130 genes (83 protein-coding genes, eight rRNAs, 38 tRNAs, and one pseudogene). 28 SNPs and 57 INDELs were identified ss intraspecific variations against previously sequenced chloroplast genome. Phylogenetic trees show that Z. matrella and Z. tenuifolia (=Z. pacifica) are clustered in one clade with low level of variations on chloroplast genomes.

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.