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The complete chloroplast genome of Semiliquidambar cathayensis (Hamamelidaceae).

ABSTRACT: Semiliquidambar cathayensis is a semi-evergreen broad-leaved tree species distributed in southern China. In 1999, it was approved and published as a national secondary protected plant. We obtained the complete chloroplast genome sequence of S. cathayensis by Illumina sequencing data. The complete chloroplast sequence is 160,430 bp, include large single-copy (LSC) region of 88,991 bp, small single-copy (SSC) region of 18,917 bp, and a pair of invert repeats (IR) regions of 26,261 bp. Plastid genome contain 133 genes, 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that S. cathayensis is closely related to Liquidambar formosana.

SUBMITTER: Zhang M

PROVIDER: S-EPMC7748583 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Complete chloroplast genome sequence of Semiliquidambar cathayensis (hamamelidaceae), a rare and endangered species endemic to China.

Project description:Semiliquidambar cathayensis (Hamamelidaceae) is a rare and endangered species endemic to China. Here, we first report and characterize the complete chloroplast genome sequence of S. cathayensis based on Illumina paired-end sequencing data. The complete plastid genome was 160,406 bp in length, which contained two inverted repeats (IRs) of 26,282 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 88,920 bp and 18,922 bp, respectively. The cpDNA contains 132 genes, comprising 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and one processed pseudogene. The overall GC content of the plastome is 37.9%. The phylogenetic analysis of 20 selected chloroplast genomes demonstrated that S. cathayensis was close to the species Liquidambar formosana.

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The complete chloroplast genome sequence of Distylium macrophyllum (Hamamelidaceae).

Project description:Distylium macrophyllum H.T.Chang is a critically endangered tree species endemic to southern China. In this study, we assembled and characterized the plastome of D. macrophyllum using Illumina paired-end data. The circular genome is 159,089 bp in size, consisting of two copies of inverted repeat (IR) regions of 26,235 bp, one large single-copy (LSC) region of 87,822 bp, and one small single-copy (SSC) region of 18,797 bp. It encodes a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 13 cp genome sequences indicated that D. macrophyllum was sister to the clade of D. tsiangii and Parrotia subaequalis.

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The complete chloroplast genome of Loropetalum chinense var. rubrum yieh (Hamamelidaceae).

Project description:Loropetalum chinense var. rubrum Yieh (L. chinense) is an evergreen shrub or small tree of Hamamelidaceae. In this study, the chloroplast genome sequence of L. chinense is 159,451 bp in length, consisting of a large single-copy region with 88,166 bp (LSC), a small single-copy region with 18,773 bp (SSC), and two inverted repeat regions with 26,256 bp (IRs). The GC content in the chloroplast genome of L. chinense is 38.0%. The chloroplast genome of L. chinense contained 125 genes, including 84 protein-coding genes, 37 tRNA genes, and 4 rRNA genes. The phylogenetic tree showed that L. chinense was closely related to L. subcordatum.

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The complete chloroplast genome sequences of two Chaenomeles species (Chaenomeles cathayensis and Chaenomeles thibetica).

Project description:The complete chloroplast genome sequence of Chaenomeles cathayensis and Chaenomeles thibetica was characterized from Illumina pair-end sequencing. The length of C. cathayensis and C. thibetica chloroplast genome of was 159,875 bp and 159,907 bp, respectively. The C. cathayensis chloroplast genome contained a large single-copy region (LSC) of 87,813bp, a small single-copy region (SSC) of 19,304 bp, and two inverted repeat (IR) regions of 26,379 bp, which is a quadripartite structure. Similarity, The C. thibetica chloroplast genome also contained a quadripartite structure, including a LSC region (87,851 bp), a SSC region (19,298 bp), and two IR regions (26,379 bp). The overall GC content of C. cathayensis and C. thibetica are both 36.57%. The C. cathayensis and C. thibetica chloroplast genome contains 130 complete genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The C. thibetica chloroplast genome contains 130 complete genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The neighbour-joining phylogenetic analysis showed that C. cathayensis and C. thibetica clustered together, indicated that C. cathayensis and C. thibetica have closed evolutionary relationship compared with other Chaenomeles species.

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Keteleeria cyclolepis complete chloroplast genome

Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads

| PRJNA723268 | ENA

Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae).

Project description:BackgroundMost Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes.ResultsThe Distylium chloroplast genome size was 159,041-159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes.ConclusionsThe plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately.

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Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.

Project description:Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.

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Characterization and phylogenetic analysis of the complete chloroplast genome sequence of Disanthus cercidifolius subsp. longipes (Hamamelidaceae), a rare and endangered wild plant species in China.

Project description:Disanthus cercidifolius subsp. longipes is a rare and endangered plant species. In our study, the complete chloroplast genome was assembled by using high-throughput DNA sequencing data. The whole CP genome is 158,076 bp in length, comprising of a large single-copy region of 87,148 bp, a small single-copy region of 18,300 bp, and two inverted repeat regions of 26,314 bp each. There are 136 genes in the genome, including 86 protein-coding genes, 40 transfer RNA genes, eight ribosomal RNA genes, and two pseudogenes (ndhK and ycf1). Phylogenetic results demonstrated that D. cercidifolius subsp. longipes grouped with other Hamamelidaceae species, with a support rate of 100%.

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