Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete plastid genome sequence of Phyllodium pulchellum (L.) Desv. (Leguminosae).

ABSTRACT: This study investigated the complete plastid genome of Phyllodium pulchellum, which represents the first report of the complete plastome for the genus Phyllodium in the tribe Desmodieae of the subfamily Papilionoideae. De novo assembly and annotation showed that the plastid genome is a typical quadripartite structure consisting of two inverted repeats (IR = 24,286?bp), one small single copy (SSC = 18,334?bp), and one large single copy (LSC = 82,715?bp). We found 111 unique genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis based on the newly sequenced plastid genome of Ph. pulchellum and 11 plastomes obtained from GenBank recovered a strongly supported phylogenetic backbone of the tribe Desmodieae and a sister-relationship between Phyllodium and Ohwia.

SUBMITTER: Wu M

PROVIDER: S-EPMC7707775 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete plastid genome sequence of Phyllodium pulchellum (L.) Desv. (Leguminosae).

Wu Mingsong M Qin Ming M Qian Xin X Zhang Kai K Tu Tieyao T

Mitochondrial DNA. Part B, Resources 20191122 2

This study investigated the complete plastid genome of Phyllodium pulchellum, which represents the first report of the complete plastome for the genus Phyllodium in the tribe Desmodieae of the subfamily Papilionoideae. De novo assembly and annotation showed that the plastid genome is a typical quadripartite structure consisting of two inverted repeats (IR = 24,286 bp), one small single copy (SSC = 18,334 bp), and one large single copy (LSC = 82,715 bp). We found 111 unique genes, i ...[more]

PMID: 33366385

Similar Datasets

The complete plastid genome of Zenia insignis Chun (Leguminosae).

Project description:Zenia insignis Chun is a rare and threatened species of the monotypic genus Zenia Chun in the subfamily Dialioideae of Leguminosae. The complete plastid genome of Zenia insignis was sequenced for the first time which also represents the first complete plastid genome of the subfamily Dialioideae. The total length of this genome is 159,358 bp with a large single copy (LSC) region (88,507 bp), a small single copy (SSC) region (18,689 bp), and two inverted repeat regions (IRs, 26,081 bp). We recovered 128 functional genes, including 83 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis strongly supported a sister relationship between Z. insignis and the clade consisting of Caesalpinioideae and Papilionoideae.

| S-EPMC7706690 | biostudies-literature

The complete plastid genome of Delonix regia (Hook.) Raf. (Leguminosae).

Project description:Delonix regia, a plant species of the legume family native to Madagascar, has been widely cultivated in the tropical and subtropical regions as an ornamental tree due to its remarkable showy orange-red flowers over summer. Here we report for the first time the complete plastid genome of this species, which has a typical circular structure with a total length of 162,756 bp and contains two inverted repeat regions (IRs, 25,544 bp), a large single copy region (LSC, 92,490 bp), and a small single copy region (SSC, 19,178 bp). The phylogenetic analysis based on the complete plastome sequences of this species and those of the related species from GenBank strongly suggested that D. regia is nested in the subfamily Caesalpinioideae and is sister to a clade consisting of Erythrophlium fordii and the old-sense Mimosoideae.

| S-EPMC7748758 | biostudies-literature

The complete plastid genome of Hong Kong Orchid Tree, Bauhinia × blakeana Dunn (Leguminosae).

Project description:Bauhinia × blakeana Dunn, or the Hong Kong Orchid Tree, is a popular ornamental plant in the tropical and subtropical regions. In this study, we report and characterise the complete plastid genome of B. × blakeana in an effort to provide genomic resources for genetic utilization. The complete plastome is 156,100 bp in length and contains the typical quadripartite structure, including two inverted repeat (IR) regions of 25,847 bp, a large single-copy (LSC) region of 86,484 bp and a small single-copy (SSC) region of 17,922 bp. 126 genes are annotated, including 81 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. The phylogenetic analysis based on the plastomes from B. × blakeana and 11 previously reported species of Cercidoideae suggested a sister-relationship between B. × blakeana and B. acuminata L. with strong bootstrap support.

| S-EPMC7707366 | biostudies-literature

Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida.

Project description:In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.

| S-EPMC4591262 | biostudies-literature

The complete plastid genome sequence of Begonia guangxiensis.

Project description:Begonia guangxiensis was assessed as endangered according to Red List of Chinese Plants. In this study, we described the complete plastid genome of B. guangxiensis. The plastid genome sequence of B. guangxiensis is 157,648 bp in size, having a large single-copy region (LSC) of 86,514 bp, a small single-copy region (SSC) of 18,076 bp, and two inverted repeat (IR) regions of 26,529 bp. The complete plastid genome of B. guangxiensis encoding 112 unique genes including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. The overall GC content of the plastid genome is 35.9%. Phylogenetic analysis confirmed that B. guangxiensis is closely related to B. varipeltata.

| S-EPMC7707394 | biostudies-literature

The complete chloroplast genome sequence of the Pueraria lobata (Willd.) Ohwi (Leguminosae).

Project description:Pueraria lobata (Willd.) Ohwi is an essential traditional oriental medicine with therapeutic effects. In this study, we assembled the complete chloroplast genome of P. lobata. The total genome size was 153,442 bp in length, containing a large single-copy (LSC) region of 84,162 bp, a small single-copy (SSC) of 17,998 bp, and a pair of inverted repeats (IRs) of 25,641 bp, and possessing 35.41% GC content. In addition, the whole chloroplast genome encodes a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree analysis of 48 species in the family Papilionoideae of Leguminosae indicated that P. lobata was belong to Papilionoideae and closely related to the genus, Pachyrhizus, Vigna and Phaseolus.

| S-EPMC7671689 | biostudies-literature

The Bryopsis hypnoides plastid genome: multimeric forms and complete nucleotide sequence.

Project description:BACKGROUND: Bryopsis hypnoides Lamouroux is a siphonous green alga, and its extruded protoplasm can aggregate spontaneously in seawater and develop into mature individuals. The chloroplast of B. hypnoides is the biggest organelle in the cell and shows strong autonomy. To better understand this organelle, we sequenced and analyzed the chloroplast genome of this green alga. PRINCIPAL FINDINGS: A total of 111 functional genes, including 69 potential protein-coding genes, 5 ribosomal RNA genes, and 37 tRNA genes were identified. The genome size (153,429 bp), arrangement, and inverted-repeat (IR)-lacking structure of the B. hypnoides chloroplast DNA (cpDNA) closely resembles that of Chlorella vulgaris. Furthermore, our cytogenomic investigations using pulsed-field gel electrophoresis (PFGE) and southern blotting methods showed that the B. hypnoides cpDNA had multimeric forms, including monomer, dimer, trimer, tetramer, and even higher multimers, which is similar to the higher order organization observed previously for higher plant cpDNA. The relative amounts of the four multimeric cpDNA forms were estimated to be about 1, 1/2, 1/4, and 1/8 based on molecular hybridization analysis. Phylogenetic analyses based on a concatenated alignment of chloroplast protein sequences suggested that B. hypnoides is sister to all Chlorophyceae and this placement received moderate support. CONCLUSION: All of the results suggest that the autonomy of the chloroplasts of B. hypnoides has little to do with the size and gene content of the cpDNA, and the IR-lacking structure of the chloroplasts indirectly demonstrated that the multimeric molecules might result from the random cleavage and fusion of replication intermediates instead of recombinational events.

| S-EPMC3038852 | biostudies-literature

The complete plastid genome sequence of Ilex micrococca Maxim.

Project description:Ilex micrococca Maxim. is a widely distributed species of Aquifoliaceae in Eastern Asia. In this study, the complete chloroplast (cp) genome sequence of I. micrococca was assembled and characterized by high-throughput sequencing data. The entire cp genome was 157,782 bp in length, containing a large single-copy region (LSC) of 87,200 bp, and a small single-copy region (SSC) of 18,434 bp, which were separated by a pair of 26,074 bp inverted repeat (IR) regions. The cp genome contained 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Eighteen genes occur in double copies. The overall GC content is 37.6%. The phylogenetic tree reconstructed by 13 chloroplast genomes reveals that I. micrococca is most related with Ilex wilsonii. The complete cp genome provides valuable information for further phylogenetic and cp genetic engineering studies of this important Ilex species I. micrococca.

| S-EPMC7755317 | biostudies-literature

The complete plastid genome sequence of garlic Allium sativum L.

Project description:The complete plastid genome sequence of garlic Allium sativum was determined using Illumina sequencing. The plastid DNA is 153,172?bp in length and includes a large single copy region (LSC) of 82,035?bp and a small single copy region (SSC) of 18,015?bp, which are separated by a pair of 26,561?bp inverted repeat regions (IRs). In total, 134 genes are identified, containing 82 protein-coding genes, 38 tRNA genes, eight rRNA genes and six pseudogenes. Most of genes occur as a single copy, while 19 genes are duplicated in IRs. Among 15 intron-containing genes, clpP and ycf3 contain two introns and the rest have one intron.

| S-EPMC7800674 | biostudies-literature

Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes.

Project description:Ardisia is a basal asterid genus well known for its medicinal values and has the potential for development of novel phytopharmaceuticals. In this genus of nearly 500 species, many ornamental species are commonly grown worldwide and some have become invasive species that caused ecological problems. As there is no completed plastid genome (plastome) sequence in related taxa, we sequenced and characterized the plastome of Ardisia polysticta to find plastid markers of potential utility for phylogenetic analyses at low taxonomic levels. The complete A. polysticta plastome is 156,506 bp in length and has gene content and organization typical of most asterids and other angiosperms. We identified seven intergenic regions as potentially informative markers with resolution for interspecific relationships. Additionally, we characterized the diversity of asterid plastomes with respect to GC content, plastome organization, gene content, and repetitive sequences through comparative analyses. The results demonstrated that the genome organizations near the boundaries between inverted repeats (IRs) and single-copy regions (SCs) are polymorphic. The boundary organization found in Ardisia appears to be the most common type among asterids, while six other types are also found in various asterid lineages. In general, the repetitive sequences in genic regions tend to be more conserved, whereas those in noncoding regions are usually lineage-specific. Finally, we inferred the whole-plastome phylogeny with the available asterid sequences. With the improvement in taxon sampling of asterid orders and families, our result highlights the uncertainty of the position of Gentianales within euasterids I.

| S-EPMC3640096 | biostudies-literature