scholarly journals Characterization of the complete chloroplast genome sequence and phylogenetic analysis of B. oleracea var. italica

2020 ◽  
Author(s):  
Zhenchao Zhang ◽  
Zhongliang Dai ◽  
Yuemei Yao ◽  
Yongfei Pan ◽  
Guosheng Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Genomic Structure ◽  
Gc Content ◽  
Single Copy ◽  
Biological Research ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Functional Components

Abstract Backgrounds: Broccoli (Brassica. oleracea var. italica L.) is known as one of the most nutritionally rich vegetables, as well as rich in functional components that benefit to health. The main purposes of this research were sequencing, assembling and annotation of chloroplast genome of broccoli based on Illumina HiSeq2500 sequencing platform. Results: The size of the broccoli cp genome is 153,364 bp, including two inverted repeat (IR) regions of 26,197 bp each, separated by a small single copy (SSC) region of 17,834 bp and a large single copy (LSC) region of 83,136 bp. The GC content of the complete genome is 36.36%, while those of SSC, LSC, and IR are 29.1%, 34.15% and 42.35%, respectively. It harbors 134 functional genes, including 87 protein-coding genes, 39 tRNAs and 8 rRNAs, with 31 duplicates in the IRs. The most abundant amino acid in the protein-coding genes is leucine, while the least is cysteine. Codon usage frequency showed bias for A/T-ending codons in the cp genome. In the repeat structure analysis, a total of 34 repeat sequences and 291 simple sequence repeat (SSRs) were detected in the work. Although cp genomic structure and size are highly conserved, the SC-IR boundary regions are variable between the 7 cp genomes. The phylogenetic relationships based on complete cp genome from 9 species suggest that B. oleracea var. italica is closely related to Brassica juncea. Conclusions: The complete cp genome sequence was obtained and annotated for broccoli for the first time. The information acquired from this research will be useful for further species identification, population genetics and biological research of broccoli.

scholarly journals Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae

2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Samaila S. Yaradua ◽  
Dhafer A. Alzahrani ◽  
Enas J. Albokhary ◽  
Abidina Abba ◽  
Abubakar Bello
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Cp Genome

The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.

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 Complete Chloroplast Genome Sequence of Erigeron breviscapus and Characterization of Chloroplast Regulatory Elements

2021 ◽  
Vol 12 ◽  
Author(s):  
Yifan Yu ◽  
Zhen Ouyang ◽  
Juan Guo ◽  
Wen Zeng ◽  
Yujun Zhao ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Regulatory Elements ◽  
Rrna Genes ◽  
Expression Vectors ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flanking Sequences ◽  
Erigeron Breviscapus ◽  
Cp Genome

Erigeron breviscapus is a famous medicinal plant. However, the limited chloroplast genome information of E. breviscapus, especially for the chloroplast DNA sequence resources, has hindered the study of E. breviscapus chloroplast genome transformation. Here, the complete chloroplast (cp) genome of E. breviscapus was reported. This genome was 152,164bp in length, included 37.2% GC content and was structurally arranged into two 24,699bp inverted repeats (IRs) and two single-copy areas. The sizes of the large single-copy region and the small single-copy region were 84,657 and 18,109bp, respectively. The E. breviscapus cp genome consisted of 127 coding genes, including 83 protein coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For those genes, 95 genes were single copy genes and 16 genes were duplicated in two inverted regions with seven tRNAs, four rRNAs, and five protein coding genes. Then, genomic DNA of E. breviscapus was used as a template, and the endogenous 5' and 3' flanking sequences of the trnI gene and trnA gene were selected as homologous recombinant fragments in vector construction and cloned through PCR. The endogenous 5' flanking sequences of the psbA gene and rrn16S gene, the endogenous 3' flanking sequences of the psbA gene, rbcL gene, and rps16 gene and one sequence element from the psbN-psbH chloroplast operon were cloned, and certain chloroplast regulatory elements were identified. Two homologous recombination fragments and all of these elements were constructed into the cloning vector pBluescript SK (+) to yield a series of chloroplast expression vectors, which harbored the reporter gene EGFP and the selectable marker aadA gene. After identification, the chloroplast expression vectors were transformed into Escherichia coli and the function of predicted regulatory elements was confirmed by a spectinomycin resistance test and fluorescence intensity measurement. The results indicated that aadA gene and EGFP gene were efficiently expressed under the regulation of predicted regulatory elements and the chloroplast expression vector had been successfully constructed, thereby providing a solid foundation for establishing subsequent E. breviscapus chloroplast transformation system and genetic improvement of E. breviscapus.

scholarly journals The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1405
Author(s):  
Gurusamy Raman ◽  
SeonJoo Park
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Gene Evolution ◽  
Single Copy ◽  
Specific Marker ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genome Sequence

The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

scholarly journals Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

2021 ◽  
Vol 11 ◽  
Author(s):  
Yongtan Li ◽  
Yan Dong ◽  
Yichao Liu ◽  
Xiaoyue Yu ◽  
Minsheng Yang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Evolutionary Relationships ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Cp Genome

In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.

scholarly journals Complete chloroplast genome sequence and structural analysis of the medicinal plant Lycium chinense Mill

2018 ◽  
Author(s):  
Zerui Yang ◽  
Yuying Huang ◽  
Xiasheng Zheng ◽  
Song Huang ◽  
Lingling Liang
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Start Codon ◽  
Lycium Chinense ◽  
Protein Coding ◽  
Engineering Research ◽  
Complete Sequences ◽  
Chloroplast Genome Sequence ◽  
Cp Genome

Lycium chinense Mill, an important Chinese herbal medicine, is emphasized as a healthy food and is widely used as a dietary supplement. Here we sequenced and analyzed the complete chloroplast (CP) genome of the L. chinense, which is 155,756 bp in length and with 37.8% GC content. This CP genome consists of a pair of inverted repeat regions (IRa and IRb) of 25,476 bp, separated by a large single-copy region (LSC) and a small single-copy region (SSC), with length of 86,595 and 18,209 bp, respectively. Annotation results revealed that the L. chinense CP genome contains 114 genes, 16 of which are duplicated genes. Most of the 85 protein-coding genes have a usual ATG start codon, except for 3 genes including rps12, psbL and ndhD. Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to the high AT content of the chloroplast genome. Revealing of the complete sequences and annotation of the L. chinense chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.

scholarly journals Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome

Plants ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 89 ◽  
Author(s):  
Yuying Huang ◽  
Zerui Yang ◽  
Song Huang ◽  
Wenli An ◽  
Jing Li ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Sister Relationship ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Plastid Genomes ◽  
Cp Genome ◽  
Rhodomyrtus Tomentosa

In the last decade, several studies have relied on a small number of plastid genomes to deduce deep phylogenetic relationships in the species-rich Myrtaceae. Nevertheless, the plastome of Rhodomyrtus tomentosa, an important representative plant of the Rhodomyrtus (DC.) genera, has not yet been reported yet. Here, we sequenced and analyzed the complete chloroplast (CP) genome of R. tomentosa, which is a 156,129-bp-long circular molecule with 37.1% GC content. This CP genome displays a typical quadripartite structure with two inverted repeats (IRa and IRb), of 25,824 bp each, that are separated by a small single copy region (SSC, 18,183 bp) and one large single copy region (LSC, 86,298 bp). The CP genome encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes and three pseudogenes (ycf1, rps19, ndhF). A considerable number of protein-coding genes have a universal ATG start codon, except for psbL and ndhD. Premature termination codons (PTCs) were found in one protein-coding gene, namely atpE, which is rarely reported in the CP genome of plants. Phylogenetic analysis revealed that R. tomentosa has a sister relationship with Eugenia uniflora and Psidium guajava. In conclusion, this study identified unique characteristics of the R. tomentosa CP genome providing valuable information for further investigations on species identification and the phylogenetic evolution between R. tomentosa and related species.

scholarly journals Complete chloroplast genome sequence and structural analysis of the medicinal plant Lycium chinense Mill

2018 ◽  
Author(s):  
Zerui Yang ◽  
Yuying Huang ◽  
Xiasheng Zheng ◽  
Song Huang ◽  
Lingling Liang
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Start Codon ◽  
Lycium Chinense ◽  
Protein Coding ◽  
Engineering Research ◽  
Complete Sequences ◽  
Chloroplast Genome Sequence ◽  
Cp Genome

Lycium chinense Mill, an important Chinese herbal medicine, is emphasized as a healthy food and is widely used as a dietary supplement. Here we sequenced and analyzed the complete chloroplast (CP) genome of the L. chinense, which is 155,756 bp in length and with 37.8% GC content. This CP genome consists of a pair of inverted repeat regions (IRa and IRb) of 25,476 bp, separated by a large single-copy region (LSC) and a small single-copy region (SSC), with length of 86,595 and 18,209 bp, respectively. Annotation results revealed that the L. chinense CP genome contains 114 genes, 16 of which are duplicated genes. Most of the 85 protein-coding genes have a usual ATG start codon, except for 3 genes including rps12, psbL and ndhD. Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to the high AT content of the chloroplast genome. Revealing of the complete sequences and annotation of the L. chinense chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.

scholarly journals Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

2018 ◽  
Vol 19 (8) ◽  
pp. 2443 ◽  
Author(s):  
Xuan Li ◽  
Yongfu Li ◽  
Mingyue Zang ◽  
Mingzhi Li ◽  
Yanming Fang
Keyword(s):  
Chloroplast Genome ◽  
Simple Sequence Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Biological Research ◽  
Sequence Repeat ◽  
Quercus Acutissima ◽  
Cp Genome ◽  
Rna Genes ◽  
Simple Sequence

Quercus acutissima, an important endemic and ecological plant of the Quercus genus, is widely distributed throughout China. However, there have been few studies on its chloroplast genome. In this study, the complete chloroplast (cp) genome of Q. acutissima was sequenced, analyzed, and compared to four species in the Fagaceae family. The size of the Q. acutissima chloroplast genome is 161,124 bp, including one large single copy (LSC) region of 90,423 bp and one small single copy (SSC) region of 19,068 bp, separated by two inverted repeat (IR) regions of 51,632 bp. The GC content of the whole genome is 36.08%, while those of LSC, SSC, and IR are 34.62%, 30.84%, and 42.78%, respectively. The Q. acutissima chloroplast genome encodes 136 genes, including 88 protein-coding genes, four ribosomal RNA genes, and 40 transfer RNA genes. In the repeat structure analysis, 31 forward and 22 inverted long repeats and 65 simple-sequence repeat loci were detected in the Q. acutissima cp genome. The existence of abundant simple-sequence repeat loci in the genome suggests the potential for future population genetic work. The genome comparison revealed that the LSC region is more divergent than the SSC and IR regions, and there is higher divergence in noncoding regions than in coding regions. The phylogenetic relationships of 25 species inferred that members of the Quercus genus do not form a clade and that Q. acutissima is closely related to Q. variabilis. This study identified the unique characteristics of the Q. acutissima cp genome, which will provide a theoretical basis for species identification and biological research.

scholarly journals The complete chloroplast genome ofColobanthus apetalus(Labill.) Druce: genome organization and comparison with related species

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4723 ◽  
Author(s):  
Piotr Androsiuk ◽  
Jan Paweł Jastrzębski ◽  
Łukasz Paukszto ◽  
Adam Okorski ◽  
Agnieszka Pszczółkowska ◽  
...  
Keyword(s):  
Gc Content ◽  
Large Family ◽  
Detailed Comparison ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Unique Genes

Colobanthus apetalusis a member of the genusColobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genusColobanthusconsists of 25 species, includingColobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome ofC. apetalus.The complete cp genome ofC. apetalushas the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison ofC. apetalusandC. quitensiscp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae andC. apetalus,and it revealed thatC. apetalusandC. quitensisform a clade that is closely related toSilenespecies andAgrostemma githago. Moreover, the genusSileneappeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae.

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