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The complete chloroplast genome sequence of Paris polyphylla var. alba H.Li & R.J.Mitchell and its phylogenetic analysis.

ABSTRACT: Paris polyphylla var. alba is a medicinal plant commonly used in the southwest of China. This study characterized the complete chloroplast (cp) genome sequence of P. polyphylla var. alba to investigate its phylogenetic relationship in Melanthiaceae. The cp genome of P. polyphylla var. alba is 165,079 base pairs (bp) in length with 36.96% G + C content. The cp genome is divided into (a) large single copy (LSC) (84,393 bp), (b) small single copy (SSC) (16,066 bp), and (c) two inverted regions (32,310 bp). The cp genome contains 135 genes, including 89 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that P. polyphylla var. alba is closest to P. polyphylla var. emeiensis, and Paris had a close relationship with Trillium in Melanthiaceae.

SUBMITTER: Jiang Y

PROVIDER: S-EPMC8330706 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The first complete chloroplast genome sequence of Paris polyphylla var. emeiensis, a rare and endangered species.

Project description:Paris polyphylla var. emeiensis H. X. Yin, H. Zhang & D. Xue is a member of the genus Paris endemic to southwest of China. The complete chloroplast (cp) genome of P. polyphylla var. emeiensis was 164,854 bp in length with 36.96% overall GC content, including a large single-copy (LSC) region of 84,438 bp and a small single-copy (SSC) region of 12,892 bp, which were separated by a pair of inverted repeats (IRs) of 33,762 bp. There were 135 genes in total, including 89 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated P. polyphylla var. emeiensis was closely related to P. fargesii and P. cronquistii.

| S-EPMC7510578 | biostudies-literature

The complete chloroplast genome sequence of the medicinal plant Paris polyphylla (Melanthiaceae).

Project description:Paris polyphylla is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of P. polyphylla to investigate its phylogenetic relationship in the genus Paris. The chloroplast genome of P. polyphylla was 163,533 bp in length with 37.1% overall GC content, including a large single copy (LSC) region of 84,272 bp, a small single copy (SSC) region of 12,899 bp and a pair of inverted repeats (IRs) of 33,181 bp. The cp genome contained 114 genes, including 79 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated P. polyphylla was closely related to P. marmorata.

| S-EPMC7707746 | biostudies-literature

The complete chloroplast genome of Paris polyphylla var. chinensis, an endemic medicinal herb in China.

Project description:Paris polyphylla var. chinensis is a species of flowering herb of the family Liliaceae and widely distributed in 12 provinces in China. It has been used in Chinese traditional medicine for centuries. The chloroplast (cp) genome of P. polyphylla var. chinensis, sequenced based on next-generation platform (NEOSAT), is 164,429?bp in size. The cp genome encodes 133 genes, including eight rRNA genes, 87 protein-coding genes (PCGs), and 38 tRNA genes. Phylogenetic relationship analysis based on complete cp genome sequences exhibited that P. polyphylla var. chinensis was most related to Daiswa forrestii.

| S-EPMC7707722 | biostudies-literature

Paris polyphylla var. alba

Project description:Paris polyphylla var. alba Raw sequence reads

| PRJNA728587 | ENA

Identification, molecular characterization and phylogenetic analysis of a novel nucleorhabdovirus infecting Paris polyphylla var. yunnanensis.

Project description:A novel betanucleorhabdovirus infecting Paris polyphylla var. yunnanensis, tentatively named Paris yunnanensis rhabdovirus 1 (PyRV1), was recently identified in Yunnan Province, China. The infected plants showed vein clearing and leaf crinkle at early stage of infection, followed by leaf yellowing and necrosis. Enveloped bacilliform particles were observed using electron microscopy. The virus was mechanically transmissible to Nicotiana bethamiana and N. glutinosa. The complete genome of PyRV1 consists of 13,509 nucleotides, the organization of which was typical of rhabdoviruses, containing six open reading frames encoding proteins N-P-P3-M-G-L on the anti-sense strand, separated by conserved intergenic regions and flanked by complementary 3'-leader and 5'-trailer sequences. The genome of PyRV1 shared highest nucleotide sequence identity (55.1%) with Sonchus yellow net virus (SYNV), and the N, P, P3, M, G, and L proteins showed 56.9%, 37.2%, 38.4%, 41.8%, 56.7%, and 49.4% amino acid sequence identities with respective proteins of SYNV, suggesting RyRV1 belongs to a new species of the genus Betanucleorhabdovirus.

| S-EPMC10282024 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Paris delavayi (Melanthiaceae).

Project description:Paris delavayi Franchet is a perennial herb of the family Melanthiaceae. In this study, the complete chloroplast (cp) genome sequence of P. delavayi was characterized. The cp genome is 164,195 bp in length and contains a pair of inverted repeats (33,415 bp) separated by a large (84,400 bp) and small (12,965 bp) single-copy regions. A total of 112 unique genes were predicted, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis suggested that P. delavayi is sister to P. mairei but with low support.

| S-EPMC7510667 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Paris stigmatosa (Melanthiaceae).

Project description:Paris stigmatosa is a new described species of Melanthiaceae. In this study, the complete chloroplast (cp) genome sequence of P. stigmatosa was first reported and characterized. The cp genome is 165,623 bp in length and contains a pair of inverted repeats (IRs, 34,165 bp) separated by a large (84,327 bp) and small (12,966 bp) single-copy regions. A total of 113 genes were predicted, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis suggested that P. stigmatosa is sister of the clade formed by P. marmorata and P. luquanensis.

| S-EPMC8519551 | biostudies-literature

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae).

Project description:The genus Paris in the broad concept is an economically important group in the monocotyledonous family Melanthiaceae (tribe Parideae). The phylogeny of Paris was controversial in previous morphology-based classification and molecular phylogeny. Here, the complete cp genomes of eleven Paris taxa were sequenced, to better understand the evolutionary relationships among these plants and the mutation patterns in their chloroplast (cp) genomes. Comparative analyses indicated that the overall cp genome structure among the Paris taxa is quite similar. The triplication of trnI-CAU was found only in the cp genomes of P. quadrifolia and P. verticillata. Phylogenetic analyses based on the complete cp genomes did not resolve Paris as a monophyletic group, instead providing evidence supporting division of the twelve taxa into two segregate genera: Paris sensu strict and Daiswa. The sister relationship between Daiswa and Trillium was well supported. We recovered two fully supported lineages with divergent distribution in Daiswa; however, none of the previously recognized sections in Daiswa was resolved as monophyletic using plastome data, suggesting that the infrageneric relationships and biogeography of Daiswa species require further investigation. Ten highly divergent DNA regions, suitable for species identification, were detected among the 12 cp genomes. This study is the first successful attempt to provide well-supported evolutionary relationships in Paris based on phylogenomic analyses. The findings highlight the potential of the whole cp genomes for improving resolution in phylogeny as well as species identification in phylogenetically and taxonomically difficult plant genera.

| S-EPMC5126724 | biostudies-literature

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus.

Project description:We sequenced and analyzed the complete chloroplast genome of Aster tataricus (family Asteraceae), a Chinese herb used medicinally to relieve coughs and reduce sputum. The A. tataricus chloroplast genome was 152,992 bp in size, and harbored a pair of inverted repeat regions (IRa and IRb, each 24,850 bp) divided into a large single-copy (LSC, 84,698 bp) and a small single-copy (SSC, 18,250 bp) region. Our annotation revealed that the A. tataricus chloroplast genome contained 115 genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. In addition, 70 simple sequence repeats (SSRs) were detected in the A. tataricus chloroplast genome, including mononucleotides (36), dinucleotides (1), trinucleotides (23), tetranucleotides (1), pentanucleotides (8), and hexanucleotides (1). Comparative chloroplast genome analysis of three Aster species indicated that a higher similarity was preserved in the IR regions than in the LSC and SSC regions, and that the differences in the degree of preservation were slighter between A. tataricus and A. altaicus than between A. tataricus and A. spathulifolius. Phylogenetic analysis revealed that A. tataricus was more closely related to A. altaicus than to A. spathulifolius. Our findings offer valuable information for future research on Aster species identification and selective breeding.

| S-EPMC6222381 | 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

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