Complete chloroplast genome sequence of the medicinal plant Arctium lappa

Genome ◽  
2020 ◽  
Vol 63 (1) ◽  
pp. 53-60 ◽  
Author(s):  
Liping Nie ◽  
Yingxian Cui ◽  
Xinlian Chen ◽  
Zhichao Xu ◽  
Wei Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Sequence Alignments ◽  
Protein Coding ◽  
Saussurea Involucrata ◽  
Arctium Lappa ◽  
Complete Chloroplast Genome ◽  
Centaurea Diffusa ◽  
Protein Coding Genes

Arctium lappa, commonly called burdock, has a long medicinal and edible history. It has recently gained increasing attention because of its economic value. In this study, we obtained the complete chloroplast genome of A. lappa by Illumina Hiseq. The complete chloroplast genome of A. lappa is a typical circular structure with 152 708 bp in length. The GC content in the whole chloroplast genome of A. lappa is 37.7%. A total of 37 tRNA genes, 8 rRNA genes, and 87 protein-coding genes were successfully annotated. And the chloroplast genome contains 113 unique genes, 19 of which are duplicated in the inverted repeat. The distribution of 39 simple sequence repeats was analysed, and most of them are in the large single-copy (LSC) sequence. An inversion comprising 16 genes was found in the LSC region, which is 26 283 bp long. We performed multiple sequence alignments using 72 common protein-coding genes of 29 species and constructed a Maximum Parsimony (MP) tree. The MP phylogenetic result shows that A. lappa grouped together with Carthamus tinctorius, Centaurea diffusa, and Saussurea involucrata. The chloroplast genome of A. lappa is a valuable resource for further studies in Asteraceae.

scholarly journals Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1354
Author(s):  
Slimane Khayi ◽  
Fatima Gaboun ◽  
Stacy Pirro ◽  
Tatiana Tatusova ◽  
Abdelhamid El Mousadik ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Important Species ◽  
Complete Chloroplast Genome ◽  
Argania Spinosa ◽  
Protein Coding Genes ◽  
Cp Genome

Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.

scholarly journals Comparative Complete Chloroplast Genome of Nine Species in Litsea (Lauraceae) and Uncover Evolutionary Dynamic Patterns

2021 ◽  
Author(s):  
Weicai Song ◽  
Zimeng Chen ◽  
Qi Feng ◽  
Chuxuan Ji ◽  
Chengbo Wei ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Structural Features ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Wide Range ◽  
High Consistency

Abstract Background: Litsea, Lauraceae, is a group of evergreen trees or shrubs that widely distributed in tropical and subtropical countries, such as Asia and America. Species in Litsea are spontaneously distributed at a maximum altitude of 2,700 m from sea level. Pants and its extractions from Litsea species cover a wide range of medicinal and industrial values. The aromatic oil extracted from Litsea is of great value with citral as its main component. At present, studies related to gene resources of Litsea are limited in the morphological analysis, while studies at the genetic level are insufficient. We therefore firstly assembled and annotated the complete chloroplast genome of nine species in Litsea, carried out a serious of comparative analysis, and completed the construction of phylogenetic tree within genus Litsea. Results: The genome length ranged from 152,051 to 152,717 bp. A total of 128 genes were identified, including 84 protein-coding genes, 36 rRNA genes and 8 tRNA genes. High consistency of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) revealed highly conserved chloroplast phenotypes in species within the genus Litsea. Changes in gene length and the present of pseudogene ycf1Ψ that caused by IR contraction and expansion were reported. The non-coding regions, especially atpF - atpH and ndhC - trnV-UAC presented high gene divergence. PsbJ - psbE regions showed remarkably high nucleotide diversity (Pi) values. Furthermore, we constructed two phylogenetic trees, demonstrating two dominant clades within genus Litsea. And the differences between trees constructed by full chloroplast (cp) genome and protein-coding genes were revealed. Conclusion: Overall, the evolutionary pattern of Litsea species regarding structural features, repeats sequences and variations presented high consistency. Valuable genomic resources and theoretical basis were also provided for further research of taxonomic discrepancies, molecular marker-assisted breeding and phylogenetic relationships of Litsea and other angiosperm species.

scholarly journals The complete chloroplast genome sequence of American elm (Ulmus americana) and comparative genomics of related species

2020 ◽  
Author(s):  
Aziz Ebrahimi ◽  
Jennifer D. Antonides ◽  
Cornelia C. Pinchot ◽  
James M. Slavicek ◽  
Charles E. Flower ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Natural Populations ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Ulmus Americana ◽  
Important Species ◽  
Complete Chloroplast Genome ◽  
American Elm ◽  
Chloroplast Genomes

ABSTRACTAmerican elm, Ulmus americana L., was cultivated widely in USA and Canada as a landscape tree, but the genome of this important species is poorly characterized. For the first time, we describe the sequencing and assembly of the chloroplast genomes of two American elm genotypes (RV16 and Am57845). The complete chloroplast genome of U. americana ranged from 158,935-158,993 bp. The genome contains 127 genes, including 85 protein-coding genes, 34 tRNA genes and 8 rRNA genes. Between the two American elm chloroplasts we sequenced, we identified 240 sequence variants (SNPs and indels). To evaluate the phylogeny of American elm, we compared the chloroplast genomes of two American elms along with seven Asian elm species and twelve other chloroplast genomes available through the NCBI database. As expected, Ulmus was closely related to Morus and Cannabis, as all three genera are assigned to the Urticales. Comparison of American elm with Asian elms revealed that trnH was absent from the chloroplast of American elm but not most Asian elms; conversely, petB, petD, psbL, trnK, and rps16 are present in the American elm but absent from all Asian elms. The complete chloroplast genome of U. americana will provide useful genetic resources for characterizing the genetic diversity of U. americana and potentially help to conserve natural populations of American elm.

scholarly journals Application of chloroplast genome to resolve the taxonomy and phylogenetic relationships of invasive dioecious weeds in Amaranthus (Amaranthaceae)

2019 ◽  
Author(s):  
Han Xu
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Rrna Genes ◽  
Alien Invasive Species ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Intergenic Spacers ◽  
Phylogenetic Studies ◽  
Hybrid Complex

Abstract Backgroud: Amaranthus palmeri, A. tuberculatus and A. arenicola are alien invasive dioecious amaranths originated from North America which have similar morphology and complex taxonomic relationship with their relatives. To search for effective molecular methods and accurate species boundary for detecting the alien invasive species, we sequenced whole chloroplast genome of 6 amaranths species, of which A. palmeri , A. arenicola , A. retroflexus and A. dubius are the first reports.Results: The complete chloroplast genome of 6 species has a circular molecular structure of 150,454 to 150,939 bp in length with 36.6% of GC content and contains a total of 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. There are a total of 802 parsimony-informative (PI) sites within genes and intergenic spacers. The rpl22-rps19 , ndhG-I , rpl 32- trnLUAG , trnPUGG-psaJ and ccsA - ndhD are the hotspots in the genus. And the 1,601 bp fragment from rpl32 to psaC has contained maximum variants with 82 PI sites. A. arenicola differs from A. tuberculatus with 19 PI sites located in 14 genes and spacers separately. The regions for differentiate A. dubius , A. hypochondriacus and A. caudatus of the Hybrid complex only fasten on 2 coding genes and 5 intergenic spacers. The patristic distances (0.00001-0.00005) among the three species are approximate to the distance (0.00005) between individuals of A. tuberculatus . Conformed to dioecious and monoecious distinctions but different with previous phylogenetic studies, A. palmeri clustered with A. arenicola and A. tuberculatus and formed a stable clade of subgen. Acnida .Conclusion: The chloroplast genome has played a role in offering enough information for discrimination and phylogenetic relationship among the Amaranthus subgen. Acnida . The most valuable regions of chloroplast genome in Amaranthus are intergenic spacers and could differentiate A. arenicola from A. tuberculatus better. Subsequently, much more Amaranthus species should be sequenced and analyzed complementally in the future.

scholarly journals The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2734 ◽  
Author(s):  
Xin Yao ◽  
Ying-Ying Liu ◽  
Yun-Hong Tan ◽  
Yu Song ◽  
Richard T. Corlett
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Phylogenomic Analysis ◽  
Trna Genes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genome Sequence

Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome forHelwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels. TheHelwingiagenome consists of 158,362 bp containing a pair of inverted repeat (IR) regions of 25,996 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

scholarly journals Complete Genome Sequence of Cupriavidus necator H16 (DSM 428)

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Gareth T. Little ◽  
Muhammad Ehsaan ◽  
Christian Arenas-López ◽  
Kamran Jawed ◽  
Klaus Winzer ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cupriavidus Necator ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Cupriavidus Necator H16

The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing. Annotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.

scholarly journals The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

2018 ◽  
Vol 94 ◽  
Author(s):  
P. Zhang ◽  
R.K. Ran ◽  
A.Y. Abdullahi ◽  
X.L. Shi ◽  
Y. Huang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Squirrel Monkey ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Rrna Genes ◽  
Saimiri Sciureus ◽  
Trna Genes ◽  
Loop Structure ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractDipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

scholarly journals The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242541
Author(s):  
Lvpei Du ◽  
Shanya Cai ◽  
Jun Liu ◽  
Ruoyu Liu ◽  
Haibin Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Cold Seep ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
High Support

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

scholarly journals Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8450 ◽  
Author(s):  
Sunan Huang ◽  
Xuejun Ge ◽  
Asunción Cano ◽  
Betty Gaby Millán Salazar ◽  
Yunfei Deng
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Variable Regions ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

2021 ◽  
Vol 46 (1) ◽  
pp. 162-174
Author(s):  
Ming-Hui Yan ◽  
Chun-Yang Li ◽  
Peter W. Fritsch ◽  
Jie Cai ◽  
Heng-Chang Wang
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

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