scholarly journals Comparative Chloroplast Genomics of Corydalis Species (Papaveraceae): Evolutionary Perspectives on Their Unusual Large Scale Rearrangements

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiaodong Xu ◽  
Dong Wang
Keyword(s):  
Large Scale ◽  
Posterior Part ◽  
Gc Content ◽  
Single Copy ◽  
Intergenic Regions ◽  
Phylogeny And Evolution ◽  
Phylogenomic Analyses ◽  
Small Single Copy ◽  
Evolutionary Perspectives ◽  
Dispersed Repeats

The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed Corydalis to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced Corydalis plastomes that represent all the three subgenera of Corydalis, we detected (1) two independent relocations of the same five genes (trnV-UAC-rbcL) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the atpH gene in Corydalis saxicola or the trnK-UUU gene in both Corydalis davidii and Corydalis hsiaowutaishanensis; (2) relocation of the rps16 gene from the LSC region to the inverted repeat (IR) region in Corydalis adunca; (3) uniform inversion of an 11–14 kb segment (ndhB-trnR-ACG) in the IR region of all the four Corydalis species (the same below); (4) expansions (>10 kb) of IR into the small single-copy (SSC) region and corresponding contractions of SSC region; and (5) extensive pseudogenizations or losses of 13 genes (accD, clpP, and 11 ndh genes). In addition, we also found that the four Corydalis plastomes exhibited elevated GC content in both gene and intergenic regions and high number of dispersed repeats. Phylogenomic analyses generated a well-supported topology that was consistent with the result of previous studies based on a few DNA markers but contradicted with the morphological character-based taxonomy to some extent. This study provided insights into the evolution of plastomes throughout the three Corydalis subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of Corydalis.

Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics

Genome ◽  
2011 ◽  
Vol 54 (8) ◽  
pp. 663-673 ◽  
Author(s):  
Dai-Yong Kuang ◽  
Hong Wu ◽  
Ya-Ling Wang ◽  
Lian-Ming Gao ◽  
Shou-Zhou Zhang ◽  
...  
Keyword(s):  
Population Genetics ◽  
Gc Content ◽  
Single Copy ◽  
Phylogenetic Study ◽  
Complete Chloroplast Genome ◽  
Noncoding Regions ◽  
Its Gene ◽  
Study Population ◽  
Chloroplast Genome Sequence ◽  
Small Single Copy

Here, we report a completely sequenced plastome using Illumina/Solexa sequencing-by-synthesis (SBS) technology. The plastome of Magnolia kwangsiensis Figlar & Noot. is 159 667 bp in length with a typical quadripartite structure: 88 030 bp large single-copy (LSC) and 18 669 bp small single-copy (SSC) regions, separated by two 26 484 bp inverted repeat (IR) regions. The overall predicted gene number is 129, among which 17 genes are duplicated in IR regions. The plastome of M. kwangsiensis is identical in its gene order to previously published plastomes of magnoliids. Furthermore, the C-to-U type RNA editing frequency of 114 seed plants is positively correlated with plastome GC content and plastome length, whereas plastome length is not correlated with GC content. A total of 16 potential putative barcoding or low taxonomic level phylogenetic study markers in Magnoliaceae were detected by comparing the coding and noncoding regions of the plastome of M. kwangsiensis with that of Liriodendron tulipifera L. At least eight markers might be applied not only to Magnoliaceae but also to other taxa. The 86 mononucleotide cpSSRs that distributed in single-copy noncoding regions are highly valuable to study population genetics and conservation genetics of this endangered rare species.

scholarly journals Construction of complete chloroplast genome of the endemic species Paphiopedilum delenatii Guillaumin (1924) of Vietnam

2020 ◽  
Vol 18 (1) ◽  
pp. 87-102
Author(s):  
Nguyen Thanh Diem ◽  
Le Thi Ly ◽  
Nguyen Huu Thuan Anh ◽  
Nguyen Thanh Cong ◽  
Vu Thi Huyen Trang
Keyword(s):  
Chloroplast Genome ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Single Copy ◽  
Complete Chloroplast Genome ◽  
Genome Data ◽  
A Cell ◽  
Chloroplast Genome Sequencing ◽  
Small Single Copy ◽  
Generation Sequencing

Chloroplasts and mitochondria are organelles that have their own genome in a cell. The chloroplast genome provides information on the evolutionary relationship and species identification, valuable markers for transgenic plants, and cloning plants, etc. The application of Next Generation Sequencing has improved the chloroplast genome sequencing. However, the assembly process of chloroplast genome is quite complicated due to the need of different complex bioinformatics tools, high configuration computer and laborous. Here we configured the process of assembling the chloroplast genome of Paphiopedilum delenatii. The assembled chloroplast genome was 160,955 bp in length, including a large and a small single copy region (LSC, SSC) separated by a pair of inverted repeats (IR). Total genes were 130 genes, GC content is 35.6%. Genome data was mapped and registered in GenBank under accession number MK463585. The optimal parameters for genome assembling were recommended. This study not only provided information for conservation of the Vietnam endemic Paphiopedilum delenatii species but also supported the genome assemble researches which could be applied on other subjects.

scholarly journals The Complete Chloroplast Genome of Ardisia Japonica（Thunb.）Blume

2022 ◽  
Author(s):  
Ruyou Deng ◽  
Shujin Ding ◽  
Sujie Wang ◽  
Hanyao Zhang
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Inverted Repeat Region ◽  
Complete Chloroplast Genome ◽  
Content Ratio ◽  
Whole Plant ◽  
Genome Information ◽  
Small Single Copy

Abstract Ardisia japonica（Thunb）Blume is a small shrub or sub-shrub of the genus Taurus in the Taurus family. The whole plant and root of A. japonica are used for medicinal purposes. It is a common Chinese herbal medicine and a common flower. To study its complete chloroplast genome, we collected leaves and obtained chloroplast genome information through next-generation sequencing. The results showed that the length of the genome is 155,996 bp, and the GC content ratio is 37.0%. The large single-copy region (LSC) is 86803 bp, the small single-copy region (SSC) is 18080 bp, and the inverted repeat region (IR) is 25507 bp. The chloroplast genome encodes 130 genes, including 85 protein genes, 8 rRNA genes, and 37tRNA genes. By analyzing the phylogeny of A. japonica, it is found that A. japonica and other Ardisia species are closely related.

scholarly journals A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem

2020 ◽  
Vol 10 (10) ◽  
pp. 3549-3555
Author(s):  
Like Fokkens ◽  
Li Guo ◽  
Susanne Dora ◽  
Bo Wang ◽  
Kai Ye ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Large Scale ◽  
Plant Pathogens ◽  
Single Copy ◽  
Model Systems ◽  
Fungal Genome ◽  
Suitable Model ◽  
Sequencing Data ◽  
High Coverage ◽  
Phylogenomic Analyses

Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step toward the establishment of a highly promising pathosystem.

scholarly journals Phylogenomic Analyses of Hepatica Species and Comparative Analyses Within Tribe Anemoneae (Ranunculaceae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Kyu Tae Park ◽  
SeonJoo Park
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Rrna Genes ◽  
Large Single Copy ◽  
Protein Coding ◽  
Comparative Analyses ◽  
Phylogenomic Analyses ◽  
Small Genus ◽  
Small Single Copy ◽  
Large Single Copy Region

Hepatica is a small genus of Ranunculaceae with medicinal and horticultural value. We characterized nine complete chloroplast (cp) genomes of Hepatica, which ranged from 159,549 to 161,081 bp in length and had a typical quadripartite structure with a large single-copy region (LSC; 80,270–81,249 bp), a small single-copy region (SSC; 17,029–17,838 bp), and two copies of inverted repeat (IR; 31,008–31,100 bp). The cp genomes of Hepatica possess 76 protein-coding genes (PCGs), 29 tRNAs, and four rRNA genes. Comparative analyses revealed a conserved ca. 5-kb IR expansion in Hepatica and other Anemoneae; moreover, multiple inversion events occurred in Hepatica and its relatives. Analyses of selection pressure (dN/dS) showed that most of the PCGs are highly conserved except for rpl20 and rpl22 in Hepatica falconeri, Hepatica americana, and Hepatica acutiloba. Two genes (rps16 and infA) were identified as pseudogenes in Hepatica. In contrast, rpl32 gene was completely lost. The phylogenetic analyses based on 76 PCGs resolved the phylogeny of Hepatica and its related genera. Non-monophyly of Anemone s.l. indicates that Hepatica should be reclassified as an independent genus. In addition, Hepatica nobilis var. japonica is not closely related to H. nobilis.

scholarly journals The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhongyu Du ◽  
Ke Lu ◽  
Kai Zhang ◽  
Yiming He ◽  
Haitao Wang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Higher Plants ◽  
Genomic Structure ◽  
Divergence Time ◽  
Gc Content ◽  
Single Copy ◽  
Genome Sequences ◽  
Cp Genome ◽  
Small Single Copy ◽  
Large Single Copy Region

Abstract Background Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg. Amygdalus. Results The results showed that subg. Amygdalus species exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137–26,467 bp, a large single-copy region that ranged from 85,757–86,608 bp, and a small single-copy region that ranged from 19,020–19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg. Amygdalus complete cp genomes was highly conserved, and the 12 subg. Amygdalus species had an rps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg. Amygdalus species. All 12 subg. Amygdalus species clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg. Amygdalus species diverged approximately 15.65 Mya. Conclusion Our results provide data on the genomic structure of subg. Amygdalus and elucidates their phylogenetic relationships and divergence time.

scholarly journals A chromosome-scale genome assembly for the Fusarium oxysporum strain Fo5176 to establish a model Arabidopsis-fungal pathosystem

2020 ◽  
Author(s):  
Like Fokkens ◽  
Li Guo ◽  
Susanne Dora ◽  
Bo Wang ◽  
Kai Ye ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Large Scale ◽  
Plant Pathogens ◽  
Single Copy ◽  
Model Systems ◽  
Fungal Genome ◽  
Suitable Model ◽  
Sequencing Data ◽  
High Coverage ◽  
Phylogenomic Analyses

AbstractPlant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step towards the establishment of a highly promising pathosystem.

scholarly journals Phylogenomics and the evolution of hemipteroid insects

2018 ◽  
Vol 115 (50) ◽  
pp. 12775-12780 ◽  
Author(s):  
Kevin P. Johnson ◽  
Christopher H. Dietrich ◽  
Frank Friedrich ◽  
Rolf G. Beutel ◽  
Benjamin Wipfler ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Single Copy ◽  
Molecular Dating ◽  
Protein Coding ◽  
Fossil Calibration ◽  
Large Scale Analysis ◽  
Phylogenetic Framework ◽  
Phylogenomic Analyses

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.

scholarly journals Large-Scale, High-Throughput Validation of Short Hairpin RNA Sequences for RNA Interference

2006 ◽  
Vol 11 (3) ◽  
pp. 236-246 ◽  
Author(s):  
Laurence H. Lamarcq ◽  
Bradley J. Scherer ◽  
Michael L. Phelan ◽  
Nikolai N. Kalnine ◽  
Yen H. Nguyen ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Strong Support ◽  
Gc Content ◽  
Rapid Identification ◽  
Hairpin Rna ◽  
Rna Sequences ◽  
Short Hairpin ◽  
Short Hairpin Rnas ◽  
Interfering Rna

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for positionspecific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNAinterference (RNAi).

scholarly journals The Evolution of Isochores: Evidence From SNP Frequency Distributions

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1805-1810 ◽  
Author(s):  
Martin J Lercher ◽  
Nick G C Smith ◽  
Adam Eyre-Walker ◽  
Laurence D Hurst
Keyword(s):  
Population Genetics ◽  
Large Scale ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Compositional Variation ◽  
Mutation Bias ◽  
Single Nucleotide ◽  
Frequency Distributions ◽  
Noncoding Regions ◽  
Standard Population

AbstractThe large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.

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