Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics

The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.

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Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

BioMed Research International ◽

10.1155/2020/9014873 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13 ◽

Cited By ~ 3

Author(s):

Lu Wang ◽

Na He ◽

Yao Li ◽

Yanming Fang ◽

Feilong Zhang

Keyword(s):

Phylogenetic Analyses ◽

Single Copy ◽

Evolutionary Patterns ◽

Closely Related Species ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Chloroplast Genome Sequence ◽

Cp Genome ◽

Rna Genes ◽

Toxicodendron Vernicifluum

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

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Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Forests ◽

10.3390/f12070861 ◽

2021 ◽

Vol 12 (7) ◽

pp. 861

Author(s):

Huijuan Zhou ◽

Xiaoxiao Gao ◽

Keith Woeste ◽

Peng Zhao ◽

Shuoxin Zhang

Keyword(s):

Comparative Analysis ◽

Phylogenetic Analyses ◽

Single Copy ◽

Nucleotide Substitutions ◽

Protein Coding ◽

Variable Regions ◽

Chloroplast Genomes ◽

Cp Genome ◽

Species Hybrids ◽

Rna Genes

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

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Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae)

PLoS ONE ◽

10.1371/journal.pone.0248556 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248556

Author(s):

Bin Zhu ◽

Fang Qian ◽

Yunfeng Hou ◽

Weicheng Yang ◽

Mengxian Cai ◽

...

Keyword(s):

Phylogenetic Analysis ◽

De Novo ◽

Repetitive Sequences ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Eruca Sativa ◽

Protein Coding ◽

Protein Coding Genes ◽

Cp Genome

Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.

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Analyzing and characterization of the chloroplast genome of Salix suchowensis

10.7287/peerj.preprints.2388 ◽

2016 ◽

Author(s):

Congrui Sun ◽

Jie Li ◽

Xiaogang Dai ◽

Yingnan Chen

Keyword(s):

Tandem Repeats ◽

Gene Annotation ◽

Repetitive Sequences ◽

Single Copy ◽

Phylogenetic Position ◽

Shrub Willow ◽

Protein Coding ◽

Protein Coding Genes ◽

Cp Genome ◽

Rna Genes

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a typical quadripartite structure containing two single copy regions, a large single copy region (LSC 84,385 bp), and a small single copy region (SSC 16,209 bp) separated by inverted repeat regions (IRs 27,457 bp). Gene annotation revealed that the cp genome of S. suchowensis encoded 119 unique genes, including 4 ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes and 3 pseudogenes. Analyzing the repetitive sequences detected 15 tandem repeats, 16 forward repeats and 5 palindromic repeats. In addition, a total of 188 perfect microsatellites were detected, which were characterized as A/T predominance in nucleotide compositions. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with that of other rosids plants. We also built phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae, with 66 orthologous protein-coding genes presented in the cp genomes of 32 species. By sequencing 30 amplicons based on the pseudomolecule, experimental verification achieved accuracy up to 99.84% for the cp genome assembly of S. suchowensis. In conclusion, this study built a high quality pseudomolecule for the cp genome of S. suchowensis, which is a useful resource for facilitating the development of this shrub willow into a more productive bioenergy crop.

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Characterization of the complete chloroplast genome sequence of Vitis vinifera ‘Guifeimeigui’

Scientific Journal of Genetics and Gene Therapy ◽

10.17352/sjggt.000019 ◽

2021 ◽

pp. 001-003

Author(s):

Liu Li ◽

Yang Yang ◽

Li Xiujie ◽

Li Bo

Keyword(s):

Vitis Vinifera ◽

Gc Content ◽

Single Copy ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Chloroplast Genome Sequence ◽

Cp Genome ◽

Eurasian Species ◽

Rna Genes

Vitis vinifera ‘Guifeimeigui’ is a diploid table grape, a Eurasian species. This research first reported the complete chloroplast (cp) genome of Vitis vinifera ‘Guifeimeigui’. The size of the complete cp genome is 160,928 bp and its GC content is 37.38%, including a pair of inverted repeats (26,353 bp each) separated by large (89,150 bp) and small (19,072 bp) single-copy regions. It encodes 85 genes, including 40 protein coding genes, 37 transfer RNA genes (tRNA), and 8 ribosomal RNA genes (rRNA). The Maximum Likelihood (ML) phylogenetic tree demonstrated that Vitis vinifera ‘Guifeimeigui’ is close to Vitis vinifera.

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Complete chloroplast genome of Oryza sativa L. (B810s) and its phylogenetic analysis

Bangladesh Journal of Botany ◽

10.3329/bjb.v50i5.56442 ◽

2021 ◽

pp. 895-901

Author(s):

Kebao Song ◽

Congtian Wang ◽

Zhongbo Li ◽

Peng Ning

Keyword(s):

Amino Acids ◽

Phylogenetic Analysis ◽

Oryza Sativa ◽

Gene Annotation ◽

Oryza Sativa L ◽

Amino Acid Sequences ◽

Coding Region ◽

Protein Coding ◽

Cp Genome ◽

Rna Genes

The complete chloroplast (cp) genome of Oryza sativa L.(B810S) was 134546 bp in length in the study, which contains 149 genes including 99 coding protein genes, 41 transfer RNA genes, 8 ribosomal RNA genes and 1 non-coding region by gene annotation. A total of 20879 amino acids were encoded by this cp genome, TTT (Phe) and TTG (Leu) codon were the most frequent amino acids, whereas the ACC (Thr), GCC (Ala), CTC (Leu), and AAC (Asn) codon were the least frequent ones. The content of the four bases on the cp genome were 30.6% for A, 30.4% for T, 19.4% for C and 19.6% for G, respectively. Obviously, the A+T (61.0%) content is more higher than G+C (39.0%). The gene order and content are the same as those of previously reported cp genome of Rice. Phylogenetic analysis was implemented based on concatenated amino acid sequences of 99 protein-coding genes using Neighbor-Joining method (NJ) method. Therefore, the complete B810S cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny. Bangladesh J. Bot. 50(3): 895-901, 2021 (September) Special

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Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation

Scientific Reports ◽

10.1038/s41598-021-81784-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mingzheng Duan ◽

Haiying Bao ◽

Tolgor Bau

Keyword(s):

Life History ◽

De Novo ◽

Phylogenetic Analyses ◽

Gene Families ◽

Single Copy ◽

Mushroom Species ◽

Protein Coding ◽

Homologous Genes ◽

Metabolic Genes ◽

History Of

AbstractIn this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.

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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus

Molecules ◽

10.3390/molecules23102426 ◽

2018 ◽

Vol 23 (10) ◽

pp. 2426 ◽

Cited By ~ 9

Author(s):

Xiaofeng Shen ◽

Shuai Guo ◽

Yu Yin ◽

Jingjing Zhang ◽

Xianmei Yin ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Chinese Herb ◽

Single Copy ◽

Future Research ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Chloroplast Genome Sequence ◽

Rna Genes ◽

Small Single Copy

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.

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Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis

Scientific Reports ◽

10.1038/s41598-021-91071-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Huu Quan Nguyen ◽

Thi Ngoc Lan Nguyen ◽

Thi Nhung Doan ◽

Thi Thu Nga Nguyen ◽

Mai Huong Phạm ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Reconstruction ◽

Single Copy ◽

Potential Health ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Long Read ◽

Phylogenetic Resolution ◽

Rna Genes

AbstractAdrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla.

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The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species

Scientific Reports ◽

10.1038/s41598-019-50620-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Ueric José Borges de Souza ◽

Rhewter Nunes ◽

Cíntia Pelegrineti Targueta ◽

José Alexandre Felizola Diniz-Filho ◽

Mariana Pires de Campos Telles

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Reconstruction ◽

Single Copy ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Coding Regions ◽

Phylogenetic Studies ◽

Rna Genes ◽

Small Single Copy

Abstract Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminosae. The chloroplast genome was reconstructed using de novo and referenced-based assembly of paired-end reads generated by shotgun sequencing of total genomic DNA. The size of the S. adstringens chloroplast genome was 162,169 bp. This genome included a large single-copy (LSC) region of 91,045 bp, a small single-copy (SSC) region of 19,014 bp and a pair of inverted repeats (IRa and IRb) of 26,055 bp each. The S. adstringens chloroplast genome contains a total of 111 functional genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. A total of 137 SSRs and 42 repeat structures were identified in S. adstringens chloroplast genome, with the highest proportion in the LSC region. A comparison of the S. adstringens chloroplast genome with those from other mimosoid species indicated that gene content and synteny are highly conserved in the clade. The phylogenetic reconstruction using 73 conserved coding-protein genes from 19 Leguminosae species was supported to be paraphyletic. Furthermore, the noncoding and coding regions with high nucleotide diversity may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels in this group.

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