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 and phylogenetic analysis of Primula stenocalyx Maxim.

ABSTRACT: Primula stenocalyx Maxim. is a perennial herb with purple umbel flowers. This alpine plant can survive at altitudes of 2700-4300 m. To explore the chloroplast genome, total DNA was extracted from a sample and sequenced, the reads of the chloroplast genome were assembled and annotated. The chloroplast genome of this plant has a circular form with a length of 153,678 bp comprising a large single-copy region (LSC, 84,236 bp), a small single-copy region (SSC, 17,746 bp), and two inverted repeats (IRs, 25,848 bp). The genome has a GC content of 37%. A total of 133 genes were predicted to contain 88 encoded proteins, 8 rRNAs and 37 tRNAs. The evolutionary history indicates that P. stenocalyx was grouped within Primula and formed a clade with Primula knuthiana with a 100% bootstrap support value. The complete cp genome of P. stenocalyx can serve as a reference for future studies on molecular biology, evolution, population genetics, taxonomy and resource protection.

SUBMITTER: Guo Y

PROVIDER: S-EPMC8526034 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome and phylogenetic analysis of Primula stenocalyx Maxim.

Guo Yupeng Y Ma Li L Li Junqiao J

Mitochondrial DNA. Part B, Resources 20211015 11

Primula stenocalyx Maxim. is a perennial herb with purple umbel flowers. This alpine plant can survive at altitudes of 2700-4300 m. To explore the chloroplast genome, total DNA was extracted from a sample and sequenced, the reads of the chloroplast genome were assembled and annotated. The chloroplast genome of this plant has a circular form with a length of 153,678 bp comprising a large single-copy region (LSC, 84,236 bp), a small single-copy region (SSC, 17,746 bp), and two inverted repe ...[more]

PMID: 34676298

Similar Datasets

The complete chloroplast genome of Zanthoxylum piasezkii Maxim. (Rutaceae) and its phylogenetic analysis.

Project description:Zanthoxylum piasezkii Maxim. is a widely distributed species of edible medicinal plant in China. It has been used for traditional spicy condiment and medicinal ingredients for quite a long time. In this study, the complete chloroplast genome sequence of Z. piasezkii was first reported and characterized from sequencing data. The complete chloroplast genome was determined to be 158,728 bp in length, consisting of a large single-copy (LSC) region (85,918 bp) and a small single copy (SSC) region (17,612 bp), which were separated by a pair of 27,599 bp inverted repeat (IR) regions. The chloroplast genome is predicted to contain 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of cpDNA is 38.4%. The phylogenetic analysis of 12 complete chloroplast genomes reveals that Z. piasezkii is mostly related to the congeneric Z. bungeanum.

| S-EPMC7872585 | biostudies-literature

Complete chloroplast genome and phylogenetic analysis of Meliosma oldhamii Miq. ex Maxim. (Sabiaceae).

Project description:Meliosma oldhamii Miq. is a deciduous arbor and a member of Sabiaceae. It is one of the rare and protected plants with outstanding ornamental and economic value in Jiangsu, China. In addition to the resource values indicated above, there are numerous other elements that require additional research, including the chloroplast (cp) genomic information. In this work, the complete cp genome sequence of M. oldhamii was assembled and characterized for the first time. The complete cp genome of M. oldhamii was 159,950 base pair (bp) in length, including a large single-copy (LSC) region of 87,147 bp, a small single-copy (SSC) region of 18,015 bp, and the inverted repeats (IRs) region of 27,394 bp. It contains 131 genes, including 37 tRNA genes, eight rRNA genes, 85 protein-coding genes, and one pseudogene. The overall GC content of M. oldhamii cp genome was 37.95%. The placement of M. oldhamii in the phylogenetic tree constructed using the complete cp genome is largely congruent with previous studies. The clustering of Meliosma is non-monophyletic, aligns more closely with existing morphological taxonomic studies, thereby enhancing the scholarly and scientific nature of this research.

| S-EPMC10769540 | biostudies-literature

The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses.

Project description:The six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.

| S-EPMC7699626 | biostudies-literature

The complete chloroplast genome of Primula obconica (Primulaceae).

Project description:We report the complete chloroplast genome of Primula obconica, a popular house-plant all over the world. The complete chloroplast genome of P. obconica was sequenced using an Illumina Miseq platform. The circular genome is 153,694 bp in length and comprises a large single copy (LSC, 84,485 bp) region and a small single copy (SSC, 17,689 bp) region, which are separated by a pair of inverted repeats (IRa and IRb, 25,760 bp each). The overall GC content is 37.2%. The P. obconica chloroplast genome encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Phylogenetic analysis based on 18 chloroplast genomes indicates that P. obconica is closely related to the clade of Primula sect. Carolinella, sect. Corusoides and sect. Monocarpicae.

| S-EPMC7687417 | biostudies-literature

The complete chloroplast genome of Spiraea mongolica Maxim.

Project description:The complete chloroplast genome of Spirea mongolica Maxim. was sequenced and assembled. It is a circular form of 155949 bp in length, which was separated into four distinct regions, a large single copy (LSC) of 84375 bp, a small single copy region (SSC) of 18894 bp, two inverted repeats (IR) of 26340 bp. After annotation, a total of 115 genes were predicted, of which, 70 encode proteins, 8 rRNA, 37 tRNA. The evolutionary history, inferred using Neighbour-Joining method, indicates that S. mongolica was grouped within Rosaceae, and comprised a clade with Spirea blumei G.Don, another species in Spirea, with 100% BS value.

| S-EPMC8118401 | biostudies-literature

The complete chloroplast genome of Primula odontocalyx, a heterostylous species.

Project description:Primula odontocalyx (Franch.) Pax (1905) is a perennial herb of the genus Primula in Primulaceae with heterostyly and ornamental value. Here, the chloroplast genome of P. odontocalyx was sequenced, assembled, and annotated. The complete chloroplast genome was a closed-circular molecule of 151,738 bp in length, containing a large single-copy region (LSC) of 83,817 bp, a small single-copy region (SSC) of 17,529 bp, and two inverted repeat (IR) regions of 25,196 bp. A total of 115 unique genes were annotated in the whole cp genome, including 81 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Phylogenetic analysis confirmed the close relationship between P. odontocalyx and Primula moupinensis, and both species belong to Sect. Petiolares Pax.

| S-EPMC9673793 | biostudies-literature

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii.

Project description:Paeonia ostii, a common oil-tree peony, is important ornamentally and medicinally. However, there are few studies on the chloroplast genome of Paeonia ostii. We sequenced and analyzed the complete chloroplast genome of P. ostii. The size of the P. ostii chloroplast genome is 152,153 bp, including a large single-copy region (85,373 bp), a small single-copy region (17,054 bp), and a pair of inverted repeats regions (24,863 bp). The P. ostii chloroplast genome encodes 111 genes, including 77 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The genome contains forward repeats (22), palindromic repeats (28), and tandem repeats (24). The presence of rich simple-sequence repeat loci in the genome provides opportunities for future population genetics work for breeding new varieties. A phylogenetic analysis showed that P. ostii is more closely related to Paeonia delavayi and Paeonialudlowii than to Paeoniaobovata and Paeoniaveitchii. The results of this study provide an assembly of the whole chloroplast genome of P. ostii, which may be useful for future breeding and further biological discoveries. It will provide a theoretical basis for the improvement of peony yield and the determination of phylogenetic status.

| S-EPMC6017096 | biostudies-literature

Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'.

Project description:Spathiphyllum is a very important tropical plant used as a small, potted, ornamental plant in South China, with an annual output value of hundreds of millions of yuan. In this study, we sequenced and analyzed the complete nucleotide sequence of the Spathiphyllum 'Parrish' chloroplast genome. The whole chloroplast genome is 168,493 bp in length, and includes a pair of inverted repeat (IR) regions (IRa and IRb, each 31,600 bp), separated by a small single-copy (SSC, 15,799 bp) region and a large single-copy (LSC, 89,494 bp) region. Our annotation revealed that the S. 'Parrish' chloroplast genome contained 132 genes, including 87 protein coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. In the repeat structure analysis, we detected 281 simple sequence repeats (SSRs) which included mononucleotides (223), dinucleotides (28), trinucleotides (12), tetranucleotides (11), pentanucleotides (6), and hexanucleotides (1), in the S. 'Parrish' chloroplast genome. In addition, we identified 50 long repeats, comprising 18 forward repeats, 13 reverse repeats, 17 palindromic repeats, and 2 complementary repeats. Single nucleotide polymorphism (SNP) and insertion/deletion (indel) analyses of the chloroplast genome of the S. 'Parrish' relative S. cannifolium revealed 962 SNPs in S. 'Parrish'. There were 158 indels (90 insertions and 68 deletions) in the S. 'Parrish' chloroplast genome relative to the S. cannifolium chloroplast genome. Phylogenetic analysis of five species found S. 'Parrish' to be more closely related to S. kochii than to S. cannifolium. This study identified the characteristics of the S. 'Parrish' chloroplast genome, which will facilitate species identification and phylogenetic analysis within the genus Spathiphyllum.

| S-EPMC6808432 | biostudies-literature

The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis.

Project description:Carya cathayensis, an important economic nut tree, is narrowly endemic to eastern China in the wild. The complete cp genome of C. cathayensis was sequenced with NGS using an Illumina HiSeq2500, analyzed, and compared to its closely related species. The cp genome is 160,825 bp in length with an overall GC content of 36.13%, presenting a quadripartite structure comprising a large single copy (LSC; 90,115 bp), a small single copy (SSC; 18,760 bp), and a pair of inverted repeats (IRs; 25,975 bp). The genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 252 simple sequence repeats (SSRs) and 55 long repeats were identified. Gene selective pressure analysis showed that seven genes (rps15, rpoA, rpoB, petD, ccsA, atpI, and ycf1-2) were possibly under positive selection compared with the other Juglandaceae species. Phylogenetic relationships of 46 species inferred that Juglandaceae is monophyletic, and that C. cathayensis is sister to Carya kweichowensis and Carya illinoinensis. The genome comparison revealed that there is a wide variability of the junction sites, and there is higher divergence in the noncoding regions than in coding regions. These results suggest a great potential in phylogenetic research. The newly characterized cp genome of C. cathayensis provides valuable information for further studies of this economically important species.

| S-EPMC8871582 | biostudies-literature

The complete chloroplast genome sequence of Rubus peltatus Maxim. (Rosaceae).

Project description:Rubus peltatus Maxim. (Bull. Acad. Imp. 1871) is a wild species endemic to East and Southeast China. However, genetic resources were unavailable for this species. It holds great potential for domestication or other breeding purposes with the extraordinary large yellow fruits. The complete chloroplast genome sequence of R. peltatus, assembled with Illumina Hiseq X Ten platform sequencing data, was reported. The chloroplast genome was 155,582 bp in length. The large single-copy (LSC) and small single-copy (SSC) of 85,329 bp and 18,779 bp were separated by two inverted repeats (IRs) of 25,737 bp. The chloroplast genome of R. peltatus contains 130 genes, including eight transfer RNA genes, 36 ribosomal RNA genes, and 86 protein-coding genes. Phylogenetic analysis supports R. peltatus has a close relationship with the R. cochinchinensis and R. takesimensis.

| S-EPMC9248939 | biostudies-literature