Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The characteristics of the chloroplast genome of the Michelia chartacea (Magnoliaceae).

ABSTRACT: In this study, the complete chloroplast genome of Michelia chartacea B. L. Chen & S. C. Yang was 160,138 bp in length. It includes a large single-copy (LSC) region of 88,164 bp, a small single-copy region (SSC) of 18,824 bp, and with a pair of inverted repeats (IRs) of 26,575 bp. The GC content in the chloroplast genome was 39.23%. In total, 130 genes in the chloroplast genome of Michelia chartacea were annotated, including 83 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that M. chartacea was closely related with M. martini and M. maudiae, forming a clade included in Michelia.

SUBMITTER: Li Y

PROVIDER: S-EPMC7889203 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of Michelia maudiae (Magnoliaceae).

Project description:Michelia maudiae is an evergreen ornamental shrub with strong aromatic flowers with great important for horticulture. In this study, the complete chloroplast genome of M. maudiae was assembled based on the Illumina sequences. The genome was 160,154 bp in length presenting a typical quadripartite structure and contains an inverted repeat region (IR, 26,575 bp), a large single copy region (LSC, 88,200 bp) and a small single copy region (SSC, 18,804 bp). The overall GC content was 39.24%. A total of 130 genes were identified, including 83 protein-coding genes, 38 transfer RNA genes, and eight rRNA genes. Twelve gene species contained one or two introns. The maximum-likelihood phylogenetic analysis revealed that M. maudiae was closely related with Manglietia insignis.

| S-EPMC7687539 | biostudies-literature

The chloroplast genome sequence of Michelia alba (Magnoliaceae), an ornamental tree species.

Project description:Magnoliaceae are both economically and ornamentally important trees. Despite extensive studies in this family, the taxonomy of Michelia L. remains unclear, as well as the taxonomical status of Michelia alba. Herein, we report the complete chloroplast genome of M. alba DC. The chloroplast genome was 159,789?bp in length, with a large single-copy (LSC) region of 87,951?bp and a small single-copy (SSC) region of 18,798?bp, separated by two inverted repeat (IRs) regions of 26,570?bp. It contained 156 genes, including 83 coding genes, 68 tRNA genes, and 8 rRNA genes. The overall GC content was 39.3%, and 43.2%, 38.0%, 34.3%, in the IRs, LSC, and SSC regions, respectively. A phylogenetic analysis showed that M. alba is closely related to M. odora, with the genus Michelia nested inside Magnolia.

| S-EPMC7800174 | biostudies-literature

The complete chloroplast genome sequence of Michelia macclurei (Dandy, 1928) (Magnoliaceae), an important fire-resistant tree species.

Project description:Michelia macclurei (Dandy, 1928) is an evergreen broad-leaved tree species native to South China. This species has great ecological and economic importance. However, the genomic study of M. macclurei has lagged far behind. Here, we reported the complete chloroplast genome sequence of M. macclurei. The chloroplast genome size of M. macclurei was 160,139 bp, consisting of a pair of inverted repeat (IR) regions (26,575 bp), which was separated by a large single copy (LSC) region (88,167 bp) and a small single copy (SSC) region (18,822 bp). A total of 113 unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The overall GC content was 39.2%. Phylogenetic analysis based on 16 whole chloroplast genome sequences of Michelia species suggested that M. macclurei and M. maudiae are sister to each other, and jointly sister to M. chapensis.

| S-EPMC9661983 | biostudies-literature

Complete chloroplast genome sequence of Michelia champaca var. champaca Linnaeus, an ornamental tree species of Magnoliaceae.

Project description:Michelia champaca var. champaca is an ornamentally important tree in Magnoliaceae. The paper reported the complete chloroplast genome (cpDNA) of M. champaca var. champaca and its basic annotated information. The size of cpDNA is 160,008 bp, with a typical quadripartite structure of a large single-copy (LSC) region of 88,037 bp and a small single-copy (SSC) region of 18,809 bp separated by a pair identical inverted repeat regions (IRs) of 26,581 bp each. The genome contained 131 genes (113 unique), including 86 protein-coding genes (80 unique), 37 tRNA genes (29 unique), and eight rRNA genes (four unique). Phylogenetic analysis showed that M. champaca var. champaca is affinal to M. baillonii and they form a nomophyletic group with other eight Michelia species. This Michelia clade is sister to the Aromadendron cathcartii clade with high support. All genera mentioned in this analysis are nomophyletic under the system of Magnoliaceae by Sima and Lu.

| S-EPMC7782985 | biostudies-literature

Inferring Genetic Variation and Demographic History of Michelia yunnanensis Franch. (Magnoliaceae) from Chloroplast DNA Sequences and Microsatellite Markers.

Project description:Michelia yunnanensis Franch., is a traditional ornamental, aromatic, and medicinal shrub that endemic to Yunnan Province in southwest China. Although the species has a large distribution pattern and is abundant in Yunnan Province, the populations are dramatically declining because of overexploitation and habitat destruction. Studies on the genetic variation and demography of endemic species are necessary to develop effective conservation and management strategies. To generate such knowledge, we used 3 pairs of universal cpDNA markers and 10 pairs of microsatellite markers to assess the genetic diversity, genetic structure, and demographic history of 7 M. yunnanensis populations. We calculated a total of 88 alleles for 10 polymorphic loci and 10 haplotypes for a combined 2,089 bp of cpDNA. M. yunnanensis populations showed high genetic diversity (Ho = 0.551 for nuclear markers and Hd = 0.471 for cpDNA markers) and low genetic differentiation (FST = 0.058). Geographical structure was not found among M. yunnanensis populations. Genetic distance and geographic distance were not correlated (P > 0.05), which indicated that geographic isolation is not the primary cause of the low genetic differentiation of M. yunnanensis. Additionally, M. yunnanensis populations contracted ~20,000-30,000 years ago, and no recent expansion occurred in current populations. Results indicated that the high genetic diversity of the species and within its populations holds promise for effective genetic resource management and sustainable utilization. Thus, we suggest that the conservation and management of M. yunnanensis should address exotic overexploitation and habitat destruction.

| S-EPMC5399939 | biostudies-literature

The complete chloroplast genome sequence of Michelia balansae var. balansae (Aug. Candolle) Dandy, a timber and spices species in Magnoliaceae.

Project description:Michelia balansae var. balansae (Aug. Candolle) Dandy is a timber and spices species in Magnoliaceae, native to China and Vietnam. In this paper, the complete chloroplast genome (cpDNA) and basic annotated information were reported and its phylogenetic relationship with other species in Magnoliaceae was analyzed. The size of chloroplast genome of M. balansae var. balansae is 160,134 bp, which exhibited a typical quadripartite structure comprising a large single-copy (LSC) region of 88,161 bp and a small single-copy (SSC) region of 18,845 bp separated by a pair identical inverted repeat regions (IRs) of 26,564 bp each. The chloroplast genome contains 131 genes, including 86 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that M. balansae var. balansae is most affinal to M. montana and they form a nomophyletic group with other 14 Michelia species. This Michelia clade is sister to the Aromadendron clade with high support. All genera mentioned in this analysis are nomophyletic under the system of Magnoliaceae by Sima and Lu.

| S-EPMC7889223 | biostudies-literature

The complete chloroplast genome sequence of Michelia floribunda.

Project description:The first complete chloroplast genome (cpDNA) sequence of Michelia floribunda was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,049 bp in length, contains a large single-copy region (LSC) of 88,140 bp and a small single-copy region (SSC) of 18,773 bp, which were separated by a pair of inverted repeats (IR) regions of 26,568 bp. The genome contains 132 genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further phylogenomic analysis showed that M. floribunda was closely related to Michelia yunnanensis in Michelieae tribe.

| S-EPMC7510816 | biostudies-literature

The complete chloroplast genome sequence of Michelia compressa.

Project description:Michelia compressa is an evergreen ornamental tree species. The high-throughput sequencing technology was used to sequence and assemble the chloroplast genome of Michelia compressa. Results showed that the chloroplast genome is 160,061 bp in length, of which the inverted repeats sequence (IRs) is 26,581 bp, the large single-copy region (LSC) and the small single copy region (SSC) are 88,097 bp and 18,802 bp, respectively. The GC content of the plastome was 39.2%, with 43.2%, 37.9% and 34.2% in IRs, LSC and SSC, respectively. A total of 132 genes are annotated, 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This study enriched the Michelia compressa genomic information which provides the basis for rational exploitation and utilization of germplasm resources.

| S-EPMC7782975 | biostudies-literature

The chloroplast genome sequence of Magnolia kobus DC. (Magnoliaceae).

Project description:As an endangered species, Magnolia kobus is distributed in Jeju island in Korea with only about 500-1000 individuals. In this study, we presented a complete chloroplast genome of M. kobus which is 159,443 bp and has four sub-regions: 87,484 bp of large single copy and 18,783 bp of small single copy regions are separated by 26,588 bp of inverted repeat regions including 113 genes (79 unique genes, four rRNAs and 30 tRNAs). Phylogenetic analysis using chloroplast genomes showed that M. kobus is a sister of M. insignis and M. laevifolia clade.

| S-EPMC7800189 | biostudies-literature

The complete chloroplast genome sequence of Manglietia yuyuanensis (Magnoliaceae).

Project description:Manglietia yuyuanensis is an important afforestation and excellent broad-leaved tree species in southern China. In this study, we assembled the complete chloroplast genome of M. yuyuanensis based on the Illumina sequences, sequence analysis showed the genome was 160,078 bp in length presenting a typical quadripartite structure and contains an inverted repeat region (IR, 26,467 b), a small single-copy (SSC) region, and a large single-copy (LSC) region (18,785 and 88,359 bp, respectively). The overall GC content was 39.27%. The sequence contained 128 unique genes, including 81 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The maximum-likelihood (ML) phylogenetic analysis revealed that M. maudiae was closely related to Manglietia insignis. A phylogenetic analysis revealed that M. yuyuanensis is closely related to Manglietia glaucifolia, with the genus Manglietia.

| S-EPMC7748696 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data