GC Content Of DNA Research Articles

Efficient and low-complexity variable-to-variable length coding for DNA storage

BackgroundEfficient DNA-based storage systems offer substantial capacity and longevity at reduced costs, addressing anticipated data growth. However, encoding data into DNA sequences is limited by two key constraints: 1) a maximum of h consecutive identical bases (homopolymer constraint h), and 2) a GC ratio between [0.5-cGC,0.5+cGC]\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ [0.5 - c_{{GC}}, 0.5 + c_{{GC}} ] $$\\end{document} (GC content constraint cGC\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$c_{GC}$$\\end{document}). Sequencing or synthesis errors tend to increase when these constraints are violated.ResultsIn this research, we address a pure source coding problem in the context of DNA storage, considering both homopolymer and GC content constraints. We introduce a novel coding technique that adheres to these constraints while maintaining linear complexity for increased block lengths and achieving near-optimal rates. We demonstrate the effectiveness of the proposed method through experiments on both randomly generated data and existing files. For example, when h=4\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$h = 4$$\\end{document} and cGC=0.05\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$c_{GC} = 0.05$$\\end{document}, the rate reached 1.988, close to the theoretical limit of 1.990. The associated code can be accessed at GitHub.ConclusionWe propose a variable-to-variable-length encoding method that does not rely on concatenating short predefined sequences, which achieves near-optimal rates.

Description and Whole-Genome Sequencing of Mariniflexile litorale sp. nov., Isolated from the Shallow Sediments of the Sea of Japan.

A Gram-negative, aerobic, rod-shaped, non-motile, yellow-pigmented bacterium, KMM 9835T, was isolated from the sediment sample obtained from the Amur Bay of the Sea of Japan seashore, Russia. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences positioned the novel strain KMM 9835T in the genus Mariniflexile as a separate line sharing the highest 16S rRNA gene sequence similarities of 96.6% and 96.2% with Mariniflexile soesokkakense RSSK-9T and Mariniflexile fucanivorans SW5T, respectively, and similarity values of <96% to other recognized Mariniflexile species. The average nucleotide identity and digital DNA-DNA hybridization values between strain KMM 9835T and M. soesokkakense KCTC 32427T, Mariniflexile gromovii KCTC 12570T, M. fucanivorans DSM 18792T, and M. maritimum M5A1MT were 83.0%, 82.5%, 83.4%, and 78.3% and 30.7%, 29.6%, 29.5%, and 24.4%, respectively. The genomic DNA GC content of strain KMM 9835T was 32.5 mol%. The dominant menaquinone was MK-6, and the major fatty acids were iso-C15:0, iso-C15:1ω10c, and C15:0. The polar lipids of strain KMM 9835T consisted of phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, and six unidentified lipids. A pan-genome analysis showed that the KMM 9835T genome encoded 753 singletons. The annotated singletons were more often related to transport protein systems (SusC), transcriptional regulators (AraC, LytTR, LacI), and enzymes (glycosylases). The KMM 9835T genome was highly enriched in CAZyme-encoding genes, the proportion of which reached 7.3%. Moreover, the KMM 9835T genome was characterized by a high abundance of CAZyme gene families (GH43, GH28, PL1, PL10, CE8, and CE12), indicating its potential to catabolize pectin. This may represent part of an adaptation strategy facilitating microbial consumption of plant polymeric substrates in aquatic environments near shorelines and freshwater sources. Based on the combination of phylogenetic and phenotypic characterization, the marine sediment strain KMM 9835T (=KCTC 92792T) represents a novel species of the genus Mariniflexile, for which the name Mariniflexile litorale sp. nov. is proposed.

"Turbo-Charged" DNA Motors with Optimized Sequence Enable Single-Molecule Nucleic Acid Sensing.

DNA motors that consume chemical energy to generate processive mechanical motion mimic natural motor proteins and have garnered interest due to their potential applications in dynamic nanotechnology, biosensing, and drug delivery. Such motors translocate by a catalytic cycle of binding, cleavage, and rebinding between DNA "legs" on the motor body and RNA "footholds" on a track. Herein, we address the well-documented trade-off between motor speed and processivity and investigate how these parameters are controlled by the affinity between DNA legs and their complementary footholds. Specifically, we explore the role of DNA leg length and GC content in tuning motor performance by dictating the rate of leg-foothold dissociation. Our investigations reveal that motors with 0 % GC content exhibit increased instantaneous velocities of up to 150 nm/sec, three-fold greater than previously reported DNA motors and comparable to the speeds of biological motor proteins. We also demonstrate that the faster speed and weaker forces generated by 0 % GC motors can be leveraged for enhanced capabilities in sensing. We observe single-molecule sensitivity when programming the motors to stall in response to the binding of nucleic acid targets. These findings offer insights for the design of high-performance DNA motors with promising real-world biosensing applications.

“Turbo‐Charged” DNA Motors with Optimized Sequence Enable Single‐Molecule Nucleic Acid Sensing

AbstractDNA motors that consume chemical energy to generate processive mechanical motion mimic natural motor proteins and have garnered interest due to their potential applications in dynamic nanotechnology, biosensing, and drug delivery. Such motors translocate by a catalytic cycle of binding, cleavage, and rebinding between DNA “legs” on the motor body and RNA “footholds” on a track. Herein, we address the well‐documented trade‐off between motor speed and processivity and investigate how these parameters are controlled by the affinity between DNA legs and their complementary footholds. Specifically, we explore the role of DNA leg length and GC content in tuning motor performance by dictating the rate of leg‐foothold dissociation. Our investigations reveal that motors with 0 % GC content exhibit increased instantaneous velocities of up to 150 nm/sec, three‐fold greater than previously reported DNA motors and comparable to the speeds of biological motor proteins. We also demonstrate that the faster speed and weaker forces generated by 0 % GC motors can be leveraged for enhanced capabilities in sensing. We observe single‐molecule sensitivity when programming the motors to stall in response to the binding of nucleic acid targets. These findings offer insights for the design of high‐performance DNA motors with promising real‐world biosensing applications.

Draft genome sequence of multi-drug resistant Klebsiella quasipneumoniae subsp. similipneumoniae isolated from a teaching hospital wastewater in South West, Nigeria.

This broadcast is about the whole genome sequence of Klebsiella quasipneumoniae subsp. similipneumoniae (ST 1422) isolated from a teaching hospital wastewater in South West, Nigeria, in May 2022. This data set compiles information on the DNA size (5,332,183 bp) and GC content (57.91%) in its genome.

Rhodoalgimonas zhirmunskyi gen. nov., sp. nov., a Marine Alphaproteobacterium Isolated from the Pacific Red Alga Ahnfeltia tobuchiensis: Phenotypic Characterization and Pan-Genome Analysis.

A novel Gram-staining negative, strictly aerobic, rod-shaped, and non-motile bacterium, designated strain 10Alg 79T, was isolated from the red alga Ahnfeltia tobuchiensis. A phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Roseobacteraceae, class Alphaproteobacteria, phylum Pseudomonadota, where the nearest neighbor was Shimia sediminis ZQ172T (97.33% of identity). However, a phylogenomic study clearly showed that strain 10Alg 79T forms a distinct evolutionary lineage at the genus level within the family Roseobacteraceae combining with strains Aquicoccus porphyridii L1 8-17T, Marimonas arenosa KCTC 52189T, and Lentibacter algarum DSM 24677T. The ANI, AAI, and dDDH values between them were 75.63-78.15%, 67.41-73.08%, and 18.8-19.8%, respectively. The genome comprises 3,754,741 bp with a DNA GC content of 62.1 mol%. The prevalent fatty acids of strain 10Alg 79T were C18:1 ω7c and C16:0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. A pan-genome analysis showed that the unique part of the 10Alg 79T genome consists of 13 genus-specific clusters and 413 singletons. The annotated singletons were more often related to transport protein systems, transcriptional regulators, and enzymes. A functional annotation of the draft genome sequence revealed that this bacterium could be a source of a new phosphorylase, which may be used for phosphoglycoside synthesis. A combination of the genotypic and phenotypic data showed that the bacterial isolate represents a novel species and a novel genus, for which the name Rhodoalgimonas zhirmunskyi gen. nov., sp. nov. is proposed. The type strain is 10Alg 79T (=KCTC 72611T = KMM 6723T).

Increased mutation and gene conversion within human segmental duplications

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions3,4. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have ‘relocated’ on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences5,6.

Microbacterium elymi sp. nov., Isolated from the Rhizospheric Soil of Elymus tsukushiensis, a Plant Native to the Dokdo Islands, Republic of Korea.

Microbacterium elymi KUDC0405T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405T was a rod-shaped bacterium with size dimensions of 0.3-0.4 × 0.7-0.8 μm. Based on 16S rRNA gene sequences, KUDC0405T was most closely related to Microbacterium bovistercoris NEAU-LLET (97.8%) and Microbacterium pseudoresistens CC-5209T (97.6%). The dDDH (digital DNA-DNA hybridization) values between KUDC0405T and M. bovistercoris NEAU-LLET and M. pseudoresistens CC-5209T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405T, M. bovistercoris NEAU-LLET, and M. pseudoresistens CC-5209T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405T and its closest related type strains. The genome contained 3,596 CDCs, three rRNAs, 46 tRNAs, and three non-coding RNAs (ncRNAs). The genomic DNA GC content was 70.4%. The polar lipids included diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and unknown phospholipid, and the major fatty acids were anteiso-C17:0 and iso-C16:0. Strain KUDC0405T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405T should be considered a novel species within the genus Microbacterium, for which we propose the name M. elymi sp. nov., and the type strain as KUDC0405T (=KCTC 49411T, =CGMCC1.18472T).

Geoalkalibacter halelectricus SAP-1 sp. nov. possessing extracellular electron transfer and mineral-reducing capabilities from a haloalkaline environment.

The extracellular electron transfer (EET)-capable electroactive microorganisms (EAMs) play crucial roles in mineral cycling and interspecies electron transfer in different environments and are used as biocatalysts in microbial electrochemical technologies. Studying EAMs from extreme environments is desired to advance the electromicrobiology discipline, understanding their unique metabolic traits with implications to extreme microbiology, and develop specific bioelectrochemical applications. Here, we present a novel haloalkaliphilic bacterium named Geoalkalibacter halelectricus SAP-1, isolated from a microbial electroactive biofilm enriched from the haloalkaline lake sediments. It is a rod-shaped Gram-negative heterotrophic anaerobe that uses various carbon and energy sources and respires on soluble and insoluble terminal electron acceptors. Besides 16S-rRNA and whole-genome sequence-based phylogeny, the GGDC values of 21.7%, ANI of 78.5%, and 2.77% genomic DNA GC content difference with the closest validly named species Geoalkalibacter ferrihydriticus (DSM 17813T ) confirmed its novelty. When grown with the solid-state electrode as the only electron acceptor, it produced 460 ± 23 μA/cm2 bioelectrocatalytic current, thereby confirming its electroactivity. Further electrochemical analysis revealed the presence of membrane redox components with a high formal potential, putatively involved in the direct mode of EET. These are distinct from EET components reported for any known electroactive microorganisms, including well-studied Geobacter spp., Shewanella spp., and Desulfuromonas acetexigens. The capabilities of G. halelectricus SAP-1 to respire on soluble and insoluble electron acceptors including fumarate, SO4 2- , Fe3+ , and Mn4+ suggests its role in cycling these elements in haloalkaline environments.

Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity.

A white-pigmented, non-motile, gram-negative, and rod-shaped bacterium, designated CYS-02T, was isolated from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 20-28ºC and hydrolyzed Tween 40. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CYS-02T formed a lineage within the family Comamonadaceae and clustered as members of the genus Variovorax. The closest members were Variovorax guangxiensis DSM 27352T (98.6% sequence similarity), Variovorax paradoxus NBRC 15149T (98.5%), and Variovorax gossypii JM-310T (98.3%). The principal respiratory quinone was Q-8 and the major polar lipids contain phosphatidylethanolamine (PE), phosphatidylethanolamine (PG), and diphosphatidylglycerol (DPG). The predominant cellular fatty acids were C16:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The DNA GC content was 67.7 mol%. The ANI and dDDH values between strain CYS-02T and the closest members in the genus Variovorax were ≤ 79.0 and 22.4%, respectively, and the AAI and POCP values between CYS-02T and the other related species in the family Comamonadaceae were > 70% and > 50%, respectively. The genome of strain CYS-02T showed a putative terpene biosynthetic cluster responsible for antioxidant activity which was supported by DPPH radical scavenging activity test. Based on genomic, phenotypic and chemotaxonomic analyses, strain CYS-02T was classified into a novel species in the genus Variovorax, for which the name Variovorax terrae sp. nov., has been proposed. The type strain is CYS-02T (= KACC 22656T = NBRC 115645 [corrected] T).

Genetic and Chemical Diversity of Edible Mushroom Pleurotus Species.

The genus Pleurotus is one of the most widely cultivated and edible mushrooms with various cultivators. Three molecular characteristics were used to evaluate the genetic diversity of 132 tested samples. Phylogenetic analysis showed five clades for tested samples of the genus Pleurotus by the combined ITS and LSU sequences with strong bootstraps and Bayesian posterior probability supports. A total of 94 polymorphic fragments ranging from 10 to 100 bp were observed by using an intersimple sequence repeat (ISSR) marker. The DNA fragment pattern showed that P. ostreatus cultivator (strain P9) was clearly distinguished from wild strain based on their clear banding profiles produced. DNA GC content of the genus Pleurotus varied from 55.6 mol% to 43.3 mol%. Their chemical composition was also determined, including sugar, amino acid, polar lipid, mycolic acid, quinone, and fatty acid, which presented some high homogeneity. Most of the tested samples contained mycolic acid; glucose and arabinose as the main sugars; aspartic acid, arginine, lysine, tyrosine, and alanine as the main amino acids; and C16:0, C18:0, C18:2cis-9,12, anteiso-C14:0, and summed feature 8 as the main fatty acids. In addition, their polar lipid profiles were investigated for the first time, which significantly varied among Pleurotus species. The genus Pleurotus contained menaquinone-6 as the sole respiratory quinone, which showed a significant difference with that of its closely related genera. These results of this study demonstrated that the combined method above could efficiently differentiate each Pleurotus species and thus be considered an efficient tool for surveying the genetic diversity of the genus Pleurotus.

The complete chloroplast genome of Prunus tangutica (Batal.) Korsh

The complete cp genome of Prunus tangutica is 158,131 bp in length, exhibits a typical quadripartite structural organization, consisting of a large single copy (LSC) region of 86,266 bp, two inverted repeats (IR) regions of 26,389 bp, and a small single copy (SSC) region of 19,087 bp. The cp genome contains 131 complete genes, including 86 protein-coding genes (86 PCGs), 8 ribosomal RNA genes (8 rRNAs), and 37 tRNA genes (37 tRNAs). Most genes occur in a single copy, while 19 genes occur in double, including 4 rRNAs (4.5S, 5S, 16S, and 23S rRNA), 7 tRNAs (trnA-UGC, trnI-GAU, trnL-CAA, trnI-CAU, trnN-GUU, trnR-ACG, and trnV-GAC), and 5 PCGs (rps7, ndhB, ycf2, rpl2 and rpl23). The overall GC content of cp DNA is 36.7%, the corresponding values of the LSC, SSC, and IR regions are 34.6%, 30.1%, and 42.6%, respectively. Further, the phylogenetic analysis suggested that the P. tangutica was closely related to Prunus tenella. The results of P. tangutica will lay a foundation for further research.

Characterization of the complete chloroplast genome of Astragalus galactites (Fabaceae)

Astragalus galactites is a medicinal plant. The total plastome length of A. galactites is 126,117 bp. It contains a large single-copy region of 69,805 bp, two inverted repeat regions of 20,638 bp, and a small single-copy region of 15,036 bp. The cp genome contains 110 complete genes, including 75 protein-coding genes (75 PCGs), 4 ribosomal RNA genes (4 rRNAs), and 30 tRNA genes (30 tRNAs). The overall GC content of cp DNA is 33.9%, the corresponding values of the LSC, SSC, and IR regions are 33.0%, 30.4%, and 43.3% respectively. The phylogenetic tree shows that A. galactites has the closest relationship with A. laxmannii.

Actinomyces capricornis sp. nov., isolated from the oral cavity of a Japanese serow.

A novel Gram-positive, facultatively anaerobic, rod-shaped, nonspore forming, nonmotile organism was isolated from a Japanese serow oral cavity. Designated strain MAS-1T , it is most closely related to Actinomyces bowdenii DSM 15435T , with which it shares 98.07% sequence homology in the 16S ribosomal RNA gene. The primarily detected cellular fatty acids in strain MAS-1T were C16:0 and C18:1 w9c. The predominant respiratory quinone was MK-9 (H4 ). The major polar lipids were phosphatidylcholines, phosphatidylinositols, and glycophospholipids. The genomic DNA GC content of the isolate was 71.3 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between MAS-1T and its related species were 23.5%-39.5% and 82.11%-91.01%, respectively, which were below the threshold (70% and 95%, respectively) for species delineation, indicating that strain MAS-1T represents a novel species. Strain MAS-1T can be differentiated from A. bowdenii by their reactions to naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase, and N-acetyl-β-glucosaminidase, as well as differing acid production from glycogen. Based on the results of genotypic, phenotypic, and biochemical analyses, herein it is proposed that the identified bacteria can be classified as a novel species, Actinomyces capricornis sp. nov., strain MAS-1T (=JCM 34236T = DSM 111732T ).

A hybrid CNN-LSTM model for high resolution melting curve classification

High resolution melting (HRM) curve analysis is an efficient, correct, and rapid technique for analyzing real-time polymerase chain reaction (PCR) results. HRM curves are formed based on increasing temperature and decreasing amount of fluorescent dye in real-time PCR process. The shapes of them are unique for each species due to the sequence, length, and GC content of species' DNA. In the literature, the classification of HRM curves is usually conducted through visual inspection and a limited number of data mining methods have been used to classify these curves. However, it becomes challenging as the number of species and their samples and the number of closely related species increase. In this study, a hybrid classification model, which is based on convolutional neural network (CNN) and long short-term memory (LSTM) models, is proposed to classify HRM curves, efficiently. In the proposed CNN-LSTM model, CNN model was used for feature extraction, and LSTM model was used for classification. It takes both the HRM curves and derivative curves as inputs and gives the predicted species of HRM curves as outputs. The performance of the proposed CNN-LSTM model was compared with that of CNN and support vector machines (SVM) approaches. The results show that the proposed CNN-LSTM model outperforms other models. The accuracy, macro-average of F1, specificity, precision, and recall values of the proposed model were 0.96±0.02,0.95±0.02,1±0,0.96±0.02, and 0.96±0.02, respectively.

The complete chloroplast genome sequence of medicinal plant: Peganum nigellastrum (Zygophyllaceae)

Peganum nigellastrum is a medicinal plant. The total chloroplast (cp) genome length of P. nigellastrum is 160,066 bp, Containing a large single copy region of 88,275 bp, two inverted repeat regions of 26,486 bp and a small single copy region of 18,855 bp. The chloroplast genome contains 132 complete genes, including 87 protein-coding genes (87 PCGs), 8 ribosomal RNA genes (8 rRNAs), and 37 tRNA genes (37 tRNAs). The overall GC content of cp DNA is 37.5%, the corresponding values of the LSC, SSC, and IR regions are 35.6%, 31.4%, and 42.8%. Phylogenetic tree shows that P. nigellastrum has the closest relationship with P. harmala.

Characterization of the complete chloroplast genome of Dracocephalum heterophyllum (Lamiaceae)

Dracocephalum heterophyllum is a medicinal plant. The complete chloroplast genome sequence is 150,860 bp in length, which contains 133 complete genes, among them, 88 are protein-coding genes (88 PCGs), 8 are ribosomal RNA genes (8 rRNAs), and 37 are tRNA genes (37 tRNAs). The overall GC content of chloroplast DNA is 37.6%, the respective values of the LSC, SSC, and IR regions are 36.0%, 31.6%, and 43.0%. Phylogenetic tree shows that D. heterophyllum is a sister to D. moldavica and D. palmatum.

Sequence determinants, function, and evolution of CpG islands.

In vertebrates, cytosine-guanine (CpG) dinucleotides are predominantly methylated, with ∼80% of all CpG sites containing 5-methylcytosine (5mC), a repressive mark associated with long-term gene silencing. The exceptions to such a globally hypermethylated state are CpG-rich DNA sequences called CpG islands (CGIs), which are mostly hypomethylated relative to the bulk genome. CGIs overlap promoters from the earliest vertebrates to humans, indicating a concerted evolutionary drive compatible with CGI retention. CGIs are characterised by DNA sequence features that include DNA hypomethylation, elevated CpG and GC content and the presence of transcription factor binding sites. These sequence characteristics are congruous with the recruitment of transcription factors and chromatin modifying enzymes, and transcriptional activation in general. CGIs colocalize with sites of transcriptional initiation in hypermethylated vertebrate genomes, however, a growing body of evidence indicates that CGIs might exert their gene regulatory function in other genomic contexts. In this review, we discuss the diverse regulatory features of CGIs, their functional readout, and the evolutionary implications associated with CGI retention in vertebrates and possibly in invertebrates.

The complete chloroplast genome sequence of medicinal plant: Dianthus chinensis (Caryophyllaceae)

Dianthus chinensis is a medicinal plant. Its complete chloroplast genome sequence is 149,570 bp in length, containing 126 complete genes, including 84 protein-coding genes (84 PCGs), 8 ribosomal RNA genes (8 rRNAs), and 34 tRNA genes (34 tRNAs). The overall GC content of cp DNA is 34.1%, the corresponding values of the LSC, SSC, and IR regions are 34.0%, 29.8%, and 42.5%, respectively. Phylogenetic tree shows that D. chinensis is a sister to D. longicalyx.

Characterization of the complete chloroplast genome sequence of medicinal plant: Potentilla bifurca (Rosaceae)

Potentilla bifurca is a medicinal plant, the root extracts have been applied for the treatment of certain viral infections as folk medicinal herbs. The complete chloroplast genome sequence of is 155,841 bp in length, contains 128 complete genes, including 84 protein-coding genes (84 PCGs), 8 ribosomal RNA genes (4 rRNAs), and 37 tRNA genes (37 tRNAs). The overall GC content of cp DNA is 37.1%, the corresponding values of the LSC, SSC, and IR regions are 35.0%, 31.0%, and 42.8%. Phylogenetic tree shows that P. bifurca was identified as the basal clade of Potentilla.