Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Cannabis sativa variety Yunma 7.

ABSTRACT: Cannabis sativa variety Yunma 7 has been widely cultivated for hemp fiber production in Yunnan Province of China. In the present study, we have successfully sequenced the chloroplast genome of Yunma 7. The complete chloroplast genome size is 153,899 bp in length with a GC content of 36.67%. The genome contains a large single copy region (LSC) of 84,046 bp, a small single copy region (SSC) of 17,831 bp, and a pair of inverted repeat regions (IR) of 26,011 bp. A total of 74 protein-coding genes are annotated in the chloroplast genome, together with 37 tRNAs and 8 rRNAs. Phylogenetic tree reveals that Yunma 7 is closely related to Cannabis hybrid AK Royal Automatic reported by Matielo et al.

SUBMITTER: Deng G

PROVIDER: S-EPMC7889209 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Cannabis sativa variety Yunma 7.

Deng Gang G Yang Mei M Zhao Kaiyuan K Yang Yang Y Huang Xing X Cheng Xia X

Mitochondrial DNA. Part B, Resources 20210211 2

Cannabis sativa variety Yunma 7 has been widely cultivated for hemp fiber production in Yunnan Province of China. In the present study, we have successfully sequenced the chloroplast genome of Yunma 7. The complete chloroplast genome size is 153,899 bp in length with a GC content of 36.67%. The genome contains a large single copy region (LSC) of 84,046 bp, a small single copy region (SSC) of 17,831 bp, and a pair of inverted repeat regions (IR) of 26,011 bp. A total of 74 protein-coding g ...[more]

PMID: 33628916

Similar Datasets

The complete chloroplast genome sequence of Oryza sativa aus-type variety Nagina-22 (Poaceae).

Project description:Rice (Oryza sativa) is the predominant staple food crop belonging to the Poaceae family. In this study, complete chloroplast genome sequence of O. sativa aus-type variety Nagina-22 was characterized through de novo assembly. The genome is a circular DNA molecule of 134,503 bp and has typical quadripartite structures including large single copy region (80,548 bp), small single copy region (12,347 bp), and a pair of inverted repeats (20,804 bp). A total of 120 genes were predicted in the genome, including 77 protein-coding genes, 8 open reading frame genes, 31 tRNA genes, and 4 rRNA genes. Phylogenetic analysis confirmed a close taxonomical relationship with O. sativa ssp. Indica species.

| S-EPMC7800824 | biostudies-literature

The complete mitochondrial genome for Cannabis sativa.

Project description:The following report details the first annotated mitochondrial genome for the Carmagnola variety of Cannabis sativa, the first reference genome for the Cannabaceae family. The total length is 415,499 bp and contains 54 genes, which sub-divide into 38 protein-coding genes, 15 tRNA genes, and 3 rRNA genes.

| S-EPMC7871862 | biostudies-literature

Non-cannabinoid constituents from a high potency Cannabis sativa variety.

Project description:Six new non-cannabinoid constituents were isolated from a high potency Cannabis sativa L. variety, namely 5-acetoxy-6-geranyl-3-n-pentyl-1,4-benzoquinone (1), 4,5-dihydroxy-2,3,6-trimethoxy-9,10-dihydrophenanthrene (2), 4-hydroxy-2,3,6,7-tetramethoxy-9,10-dihydrophenanthrene (3), 4,7-dimethoxy-1,2,5-trihydroxyphenanthrene (4), cannflavin C (5) and beta-sitosteryl-3-O-beta-d-glucopyranoside-2'-O-palmitate (6). In addition, five known compounds, alpha-cannabispiranol (7), chrysoeriol (8), 6-prenylapigenin (9), cannflavin A (10) and beta-acetyl cannabispiranol (11) were identified, with 8 and 9 being reported for the first time from cannabis. Some isolates displayed weak to strong antimicrobial, antileishmanial, antimalarial and anti-oxidant activities. Compounds 2-4 were inactive as analgesics.

| S-EPMC4888767 | biostudies-other

Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae).

Project description:Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.

| S-EPMC7954331 | biostudies-literature

The complete chloroplast genome sequence of the Alstroemeria hybrid variety 'Hanhera'.

Project description:Alstroemeria, a member of the Alstroemeriaceae family, is a species from South America. The chloroplast genome of Alstroemeria spp. was completed by de novo assembly using a small amount of whole genome sequencing data. The chloroplast genome of Alstroemeria spp. was 155,672 bp in length consisting of 84,379 bp of large single copy, 17,815 bp of small single copy, and 26,739 bp of a pair of inverted repeat regions. A total of 157 genes were annotated including 103 protein-coding genes (PCGs), 46 tRNA genes, and eight rRNA genes. Maximum likelihood phylogenetic analysis with seven species belonging to the Alstroemeriaceae or Liliaceae family revealed that Alstroemeria spp. is grouped with the species in the Alstroemeriaceae family.

| S-EPMC7759260 | biostudies-literature

The complete chloroplast genome sequence of Oryza sativa Temperate japonica.

Project description:In this study, the complete chloroplast genome of O. sativa Temperate Japonica YunJing-24 was assembled using Illumina sequencing data. The complete chloroplast (cp) genome is 134,556 bp in length, including a pair of invert repeats (IRA and IRB) regions of 20,797 bp, large single-copy (LSC) region of 80,615 bp, and small single-copy (SSC) region of 12,347 bp. A total of 129 genes were predicted in the genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis confirmed the phylogenetic relationship between O. sativa Temperate Japonica and other representative species.

| S-EPMC7971287 | biostudies-literature

The complete chloroplast genome of Castanea sativa, an endemic to Europe.

Project description:Sweet chestnut (Castanea sativa) is an endemic species of genus Castanea in Europe, which is widespread in the southern part of continental Europe. The complete genome sequence of chloroplast was determined through Illumina NovaSeq platform. Totally the genome of chloroplast was 160,938 bp in length, GC rich (36.8%), comprising a pair of 25,726 bp inverted repeat sequences, separated by a 90,519 bp large and 18,967 bp small single-copy regions. There were 129 genes, including 37 transfer RNA genes, 8 ribosomal RNA genes, and 84 protein-coding genes. The phylogenetic tree analysis showed that C. sativa exhibited the closest relationship with Castanea henryi.

| S-EPMC8018368 | biostudies-literature

Massively parallel sequencing of Cannabis sativa chloroplast hotspots for forensic typing.

Project description:BackgroundMarijuana (Cannabis sativa) is the most commonly used illicit drug in the USA, and the use of DNA barcodes could assist drug trafficking investigations by indicating the biogeographical origin and crop type of a sample and providing a means for linking cases. Additionally, the legality of marijuana in the USA remains complicated with some states fully legalizing marijuana for recreational use while federally marijuana remains completely illegal. Massively parallel sequencing (MPS) offers distinct advantages over capillary electrophoresis (CE), including more comprehensive coverage of target loci, analysis of hundreds of markers simultaneously, and high throughput capabilities.MethodsThis study reports on the development of a MiSeq FGx® assay targeting seven "hotspot" regions in the Cannabis sativa chloroplast genome that are highly polymorphic and informative in attempts to determine biogeographical origin and distinguishing between marijuana and hemp. Sequencing results were compared to previous studies that used CE-based genotyping methods.ResultsA total of 49 polymorphisms were observed, 16 of which have not been previously reported. Additionally, sequence data revealed isoalleles at one locus, which were able to differentiate two samples that had the same haplotype using CE-based methods. This study reports preliminary results from sequencing 14 hemp and marijuana samples from different countries using the developed MPS assay.ConclusionFuture studies should genotype a more comprehensive sample set from around the world to build a haplotype database, which could be used to provide investigative leads for law enforcement agencies investigating marijuana trafficking.

| S-EPMC8928601 | biostudies-literature

The complete chloroplast genome of Catalpa 'Bairihua', a hybrid variety with multi season flowering.

Project description:The complete chloroplast genome of Catalpa 'Bairihua' a hybrid variety with multi season flowering obtained from hybrid progeny of C. bungei 'Luoqiu Sihao' (C. bungei '01' × C. bungei 'Changguo Qiu') and C. fargesii f. duclouxii was first sequenced with the Illumina HiSeq 2000 platform. Which was 158,210 bp in length with a typical quadruple structure and contained a large single copy (LSC: 84,928 bp) region and a small single copy (SSC: 12,664 bp) region that were separated by a pair of inverted repeats (IRa, b: 30,309 bp) region. The GC content of the whole chloroplast genome is 38.1%. A total of 130 genes was annotated in the complete chloroplast genome, including 85 protein-coding genes, 37 tRNA genes and 8rRNA genes. ML phylogenetic analysis by comparing with 39 chloroplast genomes of the Bignoniaceae indicated that Catalpa 'Bairihua' was close to Tecomaria capensis.

| S-EPMC7782214 | biostudies-literature

The complete chloroplast genome of weedy rice Oryza sativa f. spontanea.

Project description:The emergence of weedy rice (Oryza sativa f. spontanea) has been considered as a serious global agricultural problem in recent decades. To better understand its speciation, here we assembled the complete chloroplast genome of O. sativa f. spontanea with the length of 134,502 bp. The assembly contains a large single-copy (LSC, 80,549 bp), a small single-copy (SSC, 12,347 bp) and a pair of inverted repeats (IRa and IRb, 20,803 bp each). A total of 132 unique genes were annotated, including 82 protein-coding genes, 42 tRNA genes and eight rRNA genes. Phylogenetic analysis showed that O. sativa f. spontanea (indica type) appears closely related to cultivated indica rice rather than wild rice, supporting the hypothesis that weedy rice originated from cultivated rice.

| S-EPMC8462929 | biostudies-literature