The complete chloroplast genome of Glycyrrhiza uralensis Fisch. isolated in Korea (Fabaceae)

The chloroplast genome of Glycyrrhiza uralensis Fisch was sequenced to investigate intraspecific variations on the chloroplast genome. Its length is 127,689 bp long (34.3% GC ratio) with atypical structure of chloroplast genome, which is congruent to those of Glycyrrhiza genus. It includes 110 genes (76 protein-coding genes, four rRNAs, and 30 tRNAs). Intronic region of ndhA presented the highest nucleotide diversity based on the six G. uralenesis chloroplast genomes. A total of 150 single nucleotide polymorphisms and 10 insertion and deletion (INDEL) regions were identified from the six G. uralensis chloroplast genomes. Phylogenetic trees show that the six chloroplast genomes of G. uralensis formed the two clades, requiring additional studies to understand it.

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The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

Korean Journal of Plant Taxonomy ◽

10.11110/kjpt.2021.51.3.326 ◽

2021 ◽

Vol 51 (3) ◽

pp. 326-331

Author(s):

Sung-Dug OH ◽

Seong-Kon LEE ◽

Doh-Won YUN ◽

Hyeon-Jin SUN ◽

Hong-Gyu KANG ◽

...

Keyword(s):

Chloroplast Genome ◽

Species Delimitation ◽

Phylogenetic Trees ◽

Single Copy ◽

Phylogenetic Position ◽

Nucleotide Polymorphisms ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes ◽

Intraspecific Variations

The complete chloroplast genome of Zoysia macrostachya Franch. & Sav. isolated in Korea is 135,902 bp long (GC ratio is 38.4%) and has four subregions; 81,546 bp of large single-copy (36.3%) and 12,586 bp of small single-copy (32.7%) regions are separated by 20,885 bp of inverted repeat (44.1%) regions, including 130 genes (83 protein-coding genes, eight rRNAs, and 39 tRNAs). Thirty-nine single nucleotide polymorphisms and 11 insertions and deletion (INDEL) regions were identified from two Z. macrostachya chloroplast genomes, the smallest among other Zoysia species. Phylogenetic trees show that two Z. macrostachya chloroplast genomes are clustered into a single clade. However, we found some incongruency with regard to the phylogenetic position of the Z. macrostachya clade. Our chloroplast genome provides insights into intraspecific variations and species delimitation issues pertaining to the Zoysia species.

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Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

Scientific Reports ◽

10.1038/s41598-020-76699-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Qiu-jie Li ◽

Na Su ◽

Ling Zhang ◽

Ru-chang Tong ◽

Xiao-hui Zhang ◽

...

Keyword(s):

Molecular Markers ◽

Phylogenetic Trees ◽

Phylogenetic Signal ◽

Data Sets ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Variable Regions ◽

Chloroplast Genomes ◽

Medicinal Value ◽

Cp Genome

AbstractPulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.

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The complete chloroplast genome of Limonium tetragonum (Plumbaginaceae) isolated in Korea

Korean Journal of Plant Taxonomy ◽

10.11110/kjpt.2021.51.3.337 ◽

2021 ◽

Vol 51 (3) ◽

pp. 337-344

Author(s):

Yongsung KIM ◽

Hong XI ◽

Jongsun PARK

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Trees ◽

Sister Group ◽

Single Copy ◽

Nucleotide Polymorphisms ◽

Large Single Copy ◽

Single Nucleotide ◽

Complete Chloroplast Genome ◽

Cp Genome

The chloroplast genome of Limonium tetragonum (Thunb.) Bullock, a halophytic species, was sequenced to understand genetic differences based on its geographical distribution. The cp genome of L. tetragonum was 154,689 bp long (GC ratio is 37.0%) and has four subregions: 84,572 bp of large single-copy (35.3%) and 12,813 bp of small singlecopy (31.5%) regions were separated by 28,562 bp of inverted repeat (40.9%) regions. It contained 128 genes (83 proteincoding genes, eight rRNAs, and 37 tRNAs). Thirty-five single-nucleotide polymorphisms and 33 INDEL regions (88 bp in length) were identified. Maximum-likelihood and Bayesian inference phylogenetic trees showed that L. tetragonum formed a sister group with L. aureum, which is incongruent with certain previous studies, including a phylogenetic analysis.

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Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae

Chinese Medicine ◽

10.1186/s13020-019-0274-5 ◽

2019 ◽

Vol 14 (1) ◽

Cited By ~ 2

Author(s):

Tingting Zhang ◽

Yanping Xing ◽

Liang Xu ◽

Guihua Bao ◽

Zhilai Zhan ◽

...

Keyword(s):

Related Species ◽

Phylogenetic Trees ◽

Single Copy ◽

Nucleotide Polymorphisms ◽

Illumina Hiseq ◽

Closely Related Species ◽

Protein Coding ◽

Simple Sequence Repeat Analysis ◽

Chloroplast Genomes ◽

Cp Genome

Abstract Background Baitouweng is a traditional Chinese medicine with a long history of different applications. Although referred to as a single medicine, Baitouweng is actually comprised of many closely related species. It is therefore critically important to identify the different species that are utilized in these medicinal applications. Knowledge about their phylogenetic relationships can be derived from their chloroplast genomes and may provide additional insights into development of molecular markers. Methods Genomic DNA was extracted from six species of Pulsatilla and then sequenced on an Illumina HiSeq 4000. Sequences were assembled into contigs by SOAPdenovo 2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the cp genomes of the six species were analyzed and compared with closely related species. Additionally, phylogenetic trees were constructed, based on single nucleotide polymorphisms (SNPs) and 51 shared protein-coding gene sequences in the cp genome among all 31 species via maximum likelihood. Results The size of cp genomes of P. chinensis (Bge.) Regel, P. chinensis (Bge.) Regel var. kissii (Mandl) S. H. Li et Y. H. Huang, P. cernua (Thunb.) Bercht. et Opiz f. plumbea J. X. Ji et Y. T. zhao, P. dahurica (Fisch.) Spreng, P. turczaninovii Kryl. et Serg, and P. cernua (Thunb.) Bercht. et Opiz. were 163,851 bp, 163,756 bp, 162,481 bp, 162,450 bp, 162,795 bp, and 162,924 bp, respectively. Each species included two inverted repeat regions, a small single-copy region, and a large single-copy region. A total of 134 genes were annotated, including 90 protein-coding genes, 36 tRNAs, and eight rRNAs across all species. In simple sequence repeat analysis, only P. dahurica was found to contain hexanucleotide repeats. A total of 26, 39, 32, 37, 32 and 43 large repeat sequences were identified in the genic regions of the six Pulsatilla species. Nucleotide diversity analysis revealed that the rpl36 gene and ccsA-ndhD region have the highest Pi value. In addition, two phylogenetic trees of the cp genomes were constructed, which laced all Pulsatilla species into one branch within Ranunculaceae. Conclusions We identified and analyzed the cp genome features of six species of P. Miller, with implications for species identification and phylogenetic analysis.

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Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya)

BioMed Research International ◽

10.1155/2018/6293847 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 15

Author(s):

Junling Cao ◽

Dan Jiang ◽

Zhenyu Zhao ◽

Subo Yuan ◽

Yujun Zhang ◽

...

Keyword(s):

Chloroplast Genome ◽

Single Copy ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Complete Chloroplast Genome ◽

Genomic Resources ◽

Chinese Yam ◽

Chloroplast Genomes ◽

Chloroplast Genome Sequence ◽

Simple Sequence

Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs). Seventy simple sequence repeats (SSRs) were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

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Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae

PLoS ONE ◽

10.1371/journal.pone.0242591 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242591

Author(s):

Jie Li ◽

Guang-ying Ye ◽

Hai-lin Liu ◽

Zai-hua Wang

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Intergenic Spacer ◽

Nucleotide Polymorphisms ◽

Genome Sequences ◽

Protein Coding ◽

Important Species ◽

Coding Regions ◽

Chloroplast Genomes ◽

Mutational Hotspots

Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.

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The Comparative Analyses of Six Complete Chloroplast Genomes of Morphologically Diverse Chenopodium album L. (Amaranthaceae) Collected in Korea

International Journal of Genomics ◽

10.1155/2021/6643444 ◽

2021 ◽

Vol 2021 ◽

pp. 1-15

Author(s):

Jongsun Park ◽

Juhyeon Min ◽

Yongsung Kim ◽

Youngjae Chung

Keyword(s):

Chenopodium Album ◽

Sensu Stricto ◽

Morphological Features ◽

Nucleotide Polymorphisms ◽

Morphological Variations ◽

Insertion And Deletion ◽

Chloroplast Genomes ◽

Intraspecific Variations ◽

Angiosperm Species ◽

The Relationship

Chenopodium album sensu stricto belonging to C. album aggregate is an annual cosmopolitan weed displaying the diversity of morphologies. We completed the six chloroplast genomes of C. album s. str. collected in Korea to understand the relationship between the diversity of chloroplast genomes and their morphological variations. All six C. album chloroplast genomes have a typical quadripartite structure with length ranging from 151,906 bp to 152,199 bp, similar to the previously sequenced C. album chloroplast genome (NC_034950). In total, 56 single nucleotide polymorphisms (SNPs) and 26 insertion and deletion (INDEL) regions (308 bp in total) were identified from the six chloroplast genomes, presenting a low level of intraspecific variations in comparison to the other angiosperm species. 376 normal simple sequence repeats were identified in all seven C. album chloroplast genomes. The phylogenetic analysis based on all available complete Amaranthaceae chloroplast genomes presents phylogenetic positions of six C. album samples as well as correlation with one of C. album morphological features. Our results provide the way to investigate intraspecific features of C. album chloroplast genomes and also the insights of understanding various intraspecific characteristics including morphological features.

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Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication

Frontiers in Genetics ◽

10.3389/fgene.2021.602528 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaolei Yu ◽

Wenxiu Wang ◽

Hongxia Yang ◽

Xiaoying Zhang ◽

Dan Wang ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Analysis ◽

Phylogenetic Trees ◽

Start Codon ◽

Adaptation Studies ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Original Plant ◽

Conserved Gene

Vincetoxicum versicolor (Bunge) Decne is the original plant species of the Chinese herbal medicine Cynanchi Atrati Radix et Rhizoma. The lack of information on the transcriptome and chloroplast genome of V. versicolor hinders its evolutionary and taxonomic studies. Here, the V. versicolor transcriptome and chloroplast genome were assembled and functionally annotated. In addition, the comparative chloroplast genome analysis was conducted between the genera Vincetoxicum and Cynanchum. A total of 49,801 transcripts were generated, and 20,943 unigenes were obtained from V. versicolor. One thousand thirty-two unigenes from V. versicolor were classified into 73 functional transcription factor families. The transcription factors bHLH and AP2/ERF were the most significantly abundant, indicating that they should be analyzed carefully in the V. versicolor ecological adaptation studies. The chloroplast genomes of Vincetoxicum and Cynanchum exhibited a typical quadripartite structure with highly conserved gene order and gene content. They shared an analogous codon bias pattern in which the codons of protein-coding genes had a preference for A/U endings. The natural selection pressure predominantly influenced the chloroplast genes. A total of 35 RNA editing sites were detected in the V. versicolor chloroplast genome by RNA sequencing (RNA-Seq) data, and one of them restored the start codon in the chloroplast ndhD of V. versicolor. Phylogenetic trees constructed with protein-coding genes supported the view that Vincetoxicum and Cynanchum were two distinct genera.

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Analysis of Inter-Chromosomal Distribution of Disease-Related Genes in Human Genome

Current Protein and Peptide Science ◽

10.2174/1389203721666200426233158 ◽

2020 ◽

Vol 21 (11) ◽

pp. 1068-1077

Author(s):

Xiaochao Sun ◽

Bin Yang ◽

Qunye Zhang

Keyword(s):

Spatial Distribution ◽

Model Organisms ◽

Nucleotide Polymorphisms ◽

Chromosomal Distribution ◽

Single Nucleotide ◽

Protein Coding ◽

Single Chromosome ◽

Deletion Mutations ◽

Protein Coding Genes ◽

Disease Related Genes

: Many studies have shown that the spatial distribution of genes within a single chromosome exhibits distinct patterns. However, little is known about the characteristics of inter-chromosomal distribution of genes (including protein-coding genes, processed transcripts and pseudogenes) in different genomes. In this study, we explored these issues using the available genomic data of both human and model organisms. Moreover, we also analyzed the distribution pattern of protein-coding genes that have been associated with 14 common diseases and the insert/deletion mutations and single nucleotide polymorphisms detected by whole genome sequencing in an acute promyelocyte leukemia patient. We obtained the following novel findings. Firstly, inter-chromosomal distribution of genes displays a nonstochastic pattern and the gene densities in different chromosomes are heterogeneous. This kind of heterogeneity is observed in genomes of both lower and higher species. Secondly, protein-coding genes involved in certain biological processes tend to be enriched in one or a few chromosomes. Our findings have added new insights into our understanding of the spatial distribution of genome and disease- related genes across chromosomes. These results could be useful in improving the efficiency of disease-associated gene screening studies by targeting specific chromosomes.

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Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽

10.3390/f12060744 ◽

2021 ◽

Vol 12 (6) ◽

pp. 744

Author(s):

Yunyan Zhang ◽

Yongjing Tian ◽

David Y. P. Tng ◽

Jingbo Zhou ◽

Yuntian Zhang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Eastern China ◽

Chloroplast Microsatellites ◽

Endangered Tree ◽

Protein Coding ◽

Intergenic Spacers ◽

Chloroplast Genomes ◽

Phylogenetic Implications ◽

Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

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