GC Content Of Genome Research Articles

The complete chloroplast genome of Viburnum dilatatum (Adoxaceae)

Viburnum dilatatum Thunb. is a large deciduous tree of Adoxaceae. In this study, the chloroplast genome sequence of V. dilatatum is 158,392 bp, consisting of a large single-copy (LSC) region with 87,070 bp, a small single-copy (SSC) region with 18,242 bp , and two inverted repeat (IR) regions with 26,540 bp. The GC content in the chloroplast genome of C. julianae is 38.1%. The chloroplast genome of V. dilatatum contains 126 genes, including 83 protein-coding genes, 39 tRNA genes, and 4 rRNA genes. Phylogenetic tree showed that V. dilatatum was clustered with V. utile.

Complete chloroplast genome and phylogenetic analysis of a wild grass, Hordeum roshevitzii Bowden

The complete circular chloroplast (cp) genome of wild Hordeum roshevitzii Bowden was sequenced and reported in this study. The complete chloroplast genome of wild H. roshevitzii was 12,753 bp in length, including a pair of inverted repeat regions (IRA/IRB) of 21,587 bp separated by one small single-copy (SSC) region of 12,753 bp and one large single-copy (LSC) region of 81,138 bp. A total of 133 genes, including 85 protein-coding genes (PCGs), 40 transfer RNA genes, and 8 ribosomal RNA genes were predicted from the cp genomes. The overall GC content of the cp genome was 38.25% and the corresponding values of the IR, SSC, and LSC were 43.89%, 32.19%, and 36.21%. The phylogenetic analysis of H. roshevitzii determined that H. roshevitzii was clustered closely with Hordeum bogdanii.

The complete chloroplast genome of Desmodium uncinatum (Fabaceae)

Desmodium uncinatum is one of the most important legume forage which distributes in tropical and subtropical regions of the world. In our study, we obtained the complete chloroplast genome of D. uncinatum with a length of 148,853 bp, including a large single copy region of 84,019 bp, small single copy region of 18,223 bp, and a pair of inverted repeat regions of 20,672 bp. The GC content in the whole chloroplast genome of D. uncinatum is 35.16%. Among the 133 unique genes in the circular genome, 37 tRNA, 12 rRNA and 84 protein-coding genes were successfully annotated. We constructed the Maximum likelihood (ML) tree with 11 species, and came to the conclusion that D. uncinatum was phylogenetically closely related to the genus of Glycine and Trifolium.

The complete plastid genome of Lilium regale E.H.Wilson

Lilium regale E.H.Wilson is a native lily species in western Sichuan of China and an important resource for lily breeding. In this study, the plastid genome of L. regale was assembled de novo using the next-generation sequencing data. The plastid genome of L. regale was 152,998 bp in length, with a typical quadripartite circle structure consisting of a small single-copy region of 17,529 bp, a large single-copy region of 82,375 bp, and a pair of inverted repeats of 26,547 bp each. A total of 137 different genes were predicted, including 84 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes, and 7 pseudogenes. The overall GC content of the plastid genome was 36.98%. Phylogenetic analysis revealed that L. regale is most closely related to Lilium leucanthum.

A database of sequenced genomes of different Streptomyces albus J1074 strains and uses thereof

Streptomyces albus J1074 has recently emerged as a powerful chassis strain for natural product research and discovery, as well as model to investigate various aspects of actinobacterial biology. A number of genetic tools have been developed to facilitate the use of this strain for the aforementioned purposes. One of the promising approaches is to introduce into J1074 genome mutations that would improve the antibiotic-producing capacity of J1074. Particularly, we reported a collection of spontaneous and genomically engineered J1074 mutants carrying mutation in genes for ribosomal protein S12, RNA polymerase beta subunit etc. We took advantage of this collection to build an in-house database which would host (both current and future) the primary and curated sequencing data for these mutants. The database is available at https://biotools.online/media/. The main benefits of the database lie in the known pedigree of the strains, which allows deep interpretation of the data. For example, there is lively – and unresolved – debate on the origins and consequences of the GC composition in actinobacteria. A better understanding of this issue should improve our knowledge of genome evolution in bacteria and will have a number of biotechnological ramifications. We used our Streptomyces albus J1074 dataset as an experimental model to reveal genome-wide spectrum of mutation, which appears to be biased towards elevated GC content. We also included the high-quality genomes of the other streptomycetes into our databse for comparative purposes. The genomic GC content in streptomycetes varies from 75 % to 66.5 %, with median value being 72 %. The GC content of secondary metabolic genes of S. coelicolor is less variable than that of primary metabolic genes, an indicative of different selection pressure on these gene groups. Along with selective constraints, the peculiarities of Streptomyces DNA mismatch repair might contribute to the skewed GC content of their genomes. Further uses of the database may include the development of a more precise knowledge of the mutation rate as well as population genetic processes within this species and genus.

Complete chloroplast genome of a wild-type Gardenia jasminoides ellis (rubiaceae) adapted to island climate

Gardenia jasminoides Ellis is a traditional aromatic and medicinal plant in China. Here, the complete chloroplast genome of a wild-type gardenia adapted to island climate was assembled. The assembled genome was 155,247 bp in length, with four typical regions, i.e., a large single-copy (LSC) region (85,414 bp), a small single-copy (SSC) region (18,235 bp) and two inverted repeats (IRs) regions (25,799 bp each). In total, 138 genes were predicted, including 90 protein-coding genes, 40 tRNA genes and eight rRNA genes. The overall GC content of the chloroplast genome was 37.5%. The chloroplast genome would provide more information for the phylogeography and phylogeny study of G. jasminoides.

The plastid genome of a narrowly distributed species Artocarpus petelotii (Moraceae)

The complete chloroplast genome sequence of Artocarpus petelotii was determined, a narrowly distributed species at high altitudes in the family Moraceae. To better determine its phylogenetic location with respect to the other Moraceae species, the complete plastid genome of A. petelotii was sequenced. The whole chloroplast genome is 161,009 bp in length, consisting of a pair of inverted repeat (IR) regions of 25,682 bp, one large single-copy (LSC) region of 89,552 bp, and one small single-copy (SSC) region of 20,093 bp. The overall GC content of the whole chloroplast genome is 35.8%. Further, maximum likelihood phylogenetic analysis was conducted using 26 complete plastomes of the Moraceae, which support close relationships among A. petelotii, A. nanchuanensis and A. heterophyllus.

The complete chloroplast genome sequence of Sainfoin (Onobrychis viciifolia)

Sainfoin (Onobrychis viciifolia) is one of the dominant legume forages distributed in Northern China. In our study, we assembled and annotated the structure of the complete chloroplast genome of sainfoin. The length of the circular genome is 122,102 bp. It contains 115 genes, including 79 protein-coding genes (68.7%), 31 tRNA genes (26.96%) and 5 rRNA genes (4.35%). The GC content of the total chloroplast genome of sainfoin is 34.58%. We construct the phylogenetic relationships between the chloroplast genome of sainfoin and the other 16 species by the Maximum likelihood (ML), and found sainfoin is most closely related to Hedysarum petrovii and Hedysarum taipeicum.

The complete chloroplast genome of a medical herb, Potentilla parvifolia Fisch. (Rosaceae), from Qinghai-Tibet Plateau in China

Potentilla parvifolia Fisch. (Rosaceae) is one of the genuine medicinal materials in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of P. parvifolia using Illumina NovaSeq 6000 platform. The length of its complete cp genome is 152,898 bp, containing four sub-regions; a large single copy region (LSC) of 84,160 bp and a small single copy region (SSC) of 18,128 bp are separated by a pair of inverted repeat regions (IRs) of 25,305bp. The complete cp genome of P. parvifolia contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the cp genome is 37.2%. The phylogenetic analysis, based on 17 cp genomes, suggested that P. parvifolia is closely related to P. fruticosa L. and Fragaria species.

The characteristics of the chloroplast genome of the Michelia chartacea (Magnoliaceae)

In this study, the complete chloroplast genome of Michelia chartacea B. L. Chen & S. C. Yang was 160,138 bp in length. It includes a large single-copy (LSC) region of 88,164 bp, a small single-copy region (SSC) of 18,824 bp, and with a pair of inverted repeats (IRs) of 26,575 bp. The GC content in the chloroplast genome was 39.23%. In total, 130 genes in the chloroplast genome of Michelia chartacea were annotated, including 83 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that M. chartacea was closely related with M. martini and M. maudiae, forming a clade included in Michelia.

The complete chloroplast genome of Celtis julianae (Ulmaceae)

Celtis julianae C.K. Schneid. is a large deciduous tree of Ulmaceae. In this study, the chloroplast genome sequence of C. julianae was 159,064 bp in length, consisting of a large single-copy (LSC) region with 86,139 bp, a small single-copy (SSC) region with 19,137 bp, and two inverted repeat regions (IRs) with 26,894 bp. The GC content in the chloroplast genome of C. julianae was 36.3%. The chloroplast genome of C. julianae contained 127 genes, including 86 protein-coding genes, 37 tRNA genes, and four rRNA genes. Phylogenetic tree showed that C. julianae was clustered with C. tetrandra.

The complete chloroplast genome sequence of cultivated peach (Prunus persica var. nectarina cv. ‘Rui Guang 18’)

Peach (Prunus persica) is one of the most important economic fruit crops in the current society. In this study, we reported the complete chloroplast genome sequence of peach cultivar ‘Rui Guang 18’ (Prunus persica var. nectarina cv. ‘Rui Guang 18’) using whole genome sequencing data. The complete chloroplast genome size was 157,494 bp as a circle, which contained a large single-copy (LSC) region of 85,848 bp, a small single-copy (SSC) region of 18,983 bp, and a pair of inverted repeats (IRs) region of 52,663 bp. The total GC content of the chloroplast genome is 36.8%. The chloroplast genome contains 116 genes, including 76 protein coding genes (PCG), 6 ribosome RNA (rRNA) genes, and 35 transfer RNA (tRNA) genes. The complete chloroplast genome will be a potential genetic resource for peach breeding.

The complete plastid genome of Phoenix canariensis Chabaud (Arecaceae) and phylogenetic analysis

Phoenix canariensis Chabaud is a vital ornamental and widely planted in the urban landscape of China. In this study, we reported the complete chloroplast genome (cpDNA) of P. canariensis, which is 158,477 bp in length, including a large single copy region (LSC) of 86,189 bp, a small single copy region (SSC) of 17,704 bp, and a pair of inverted repeats (IR) regions of 27,292 bp inserted between LSC and SSC. 132 genes are encoded, including 86 protein-encoding genes, 8 ribosomal RNA genes, and 38 transfer RNA genes. The overall GC content of the chloroplast genome is 37.22%, wherein the corresponding values in the LSC, SSC, and IR regions are 35.3%, 30.79%, and 42.35%, respectively. Phylogenetic analysis showed that P. canariensis is sister to P. dactylifera with strong bootstrap support.

The complete chloroplast genome of Prunus japonica thunb.(Rosaceae), an ornamental and medicinal plant

Prunus japonica is an ornamental and medicinal plant that is widely cultivated. The complete chloroplast genome of P. japonica was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 158,080 bp in length, containing two short inverted repeat (IRa and IRb) regions of 26,385 bp, which was separated by a large single copy (LSC) region of 86,270 bp and a small single copy (SSC) region of 19,040 bp. The GC content of the whole chloroplast genome was 36.8%. The chloroplast DNA of P. japonica comprised 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. Phylogenetic analysis indicated that all species of Prunus formed a monophyletic group, P. japonica was closely related to P. hulimis.

Complete mitochondrial genome of a Korean endemic freshwater mussel Nodularia breviconcha (Bivalvia: Unionidae)

Mitochondrial genome sequences were first determined and analyzed for a Korean endemic freshwater mussel Nodularia breviconcha (synonym Nodularia douglasiae sinuolatus; Unionidae, Unionida, Bivalvia). The complete mitochondrial genome was 15,741 bp in length, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The overall GC content of mitochondrial genome for N. breviconcha was 34.3%. Phylogenetic analysis of 18 species within the family Unionidae suggested that Nodularia douglasiae is the most closely related to N. breviconcha. Our study will provide baseline, but important information for future research on ecological and genetic/genomic characteristics of this species.

The Complete Chloroplast Genome of a Variety of <i>Lagenaria siceraria var. microcarpa</i> (Naud.) Hara

Small gourd ( Lagenaria siceraria  var .  microcarpa  (Naud.) Hara), a cultivar of  Lagenaria  family, is an important medicinal and ornamental plants. However, there are few studies on its chloroplast (cp) genome. In this study, we characterized its complete chloroplast (cp) genome with high throughput sequencing. The circular cp genome is determined to be 157, 121 bp in length, with a long sing-copy and a small sing-copy separated by a pair of inverted repeat regions. A total of 132 genes were annotated, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudo gene. The overall GC content of cp genome was 37.09%. The maximum likelihood tree suggested that small gourd was closely related to  Lagenaria siceraria.  These results provided an understanding of small gourd cp genome and might be useful for future genetic studies.

Analysis of Codon Usage Bias in the <i>Platycarya</i> Chloroplast Genome

To detect the codon usage characteristics of chloroplast genomes in  Platycarya  genus, the CodonW 、 CUSP and SPSSAU software were employed to analyze the codon usage patterns of the chloroplast genomes protein-coding sequence in  Platycarya longipes  and  Platycarya strobilacea   in this research. Results show that the GC content of chloroplast genomes was 37.75% and 37.80%, the average GC content in the 3rd position was 27.16% and 27.25%. the range of effective codon number from 35.19 to 56.98, and there were more than 2/3 genes when ENC value greater than 45, which indicated a weak preference. According to the results of neutrality plot analysis, ENC-plot analysis and PR2-plot analysis, codon bias in most  Platycarya  chloroplast genes were affected by natural selection, while a few were affected by mutations or other factors. And based on the ENC value, five groups of high-expressed and low-expressed genes were identified, 16 codons were ended with A/U among the 18 optimal codons. The research has implications on codon optimization, enhancing the expression efficiency of exogenous gene and phylogenetic analysis.

Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers.

Akebia trifoliata (Lardizabalaceae) is an important medicinal plant with multiple pharmacological effects. However, the lack of genomic information had limited the further excavation and utilization of this plant. An initial survey of the genome A. trifoliata was performed by next-generation sequencing, and then the genome size was inferred by flow cytometry. The whole genome survey of A. trifoliata generated 61.90Gb of sequence data with approximately 95.51 × coverage. The genome size, heterozygosity and GC content obtained by k-mer analysis were almost 648.07Mb, 0.72% and 36.11%, respectively. The genome size calculated by flow cytometry was 685.77Mb, which was consistent with the results of genome survey. A total of 851,957 simple sequence repeats (SSR) were identified in the A. trifoliata genome. Twenty-eight phenotypic traits and thirty pairs of SSR primers were selected for the analysis of the genetic diversity of 43 accessions of cultivated A. trifoliata. The results showed that 216 bands were generated by 30 pairs of SSR primers, of which 189 (87.5%) were polymorphic. In addition, the phenotypes and SSR markers were used for cluster analysis of 43 cultivated accessions. The results of the two clustering methods were partially consistent. The genome survey of A. trifoliata demonstrated that the genome size of this plant was about 648.07Mb. In the present study, the size and characteristics of the genome of A. trifoliata were reported for the first time, which greatly enriched the genomic resources of A. trifoliata for the further research and utilization.

ChIAMM: A Mixture Model for Statistical Analysis of Long-Range Chromatin Interactions From ChIA-PET Experiments.

Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is an important experimental method for detecting specific protein-mediated chromatin loops genome-wide at high resolution. Here, we proposed a new statistical approach with a mixture model, chromatin interaction analysis using mixture model (ChIAMM), to detect significant chromatin interactions from ChIA-PET data. The statistical model is cast into a Bayesian framework to consider more systematic biases: the genomic distance, local enrichment, mappability, and GC content. Using different ChIA-PET datasets, we evaluated the performance of ChIAMM and compared it with the existing methods, including ChIA-PET Tool, ChiaSig, Mango, ChIA-PET2, and ChIAPoP. The result showed that the new approach performed better than most top existing methods in detecting significant chromatin interactions in ChIA-PET experiments.

Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism.

Detecting and quantifying low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants remains difficult; this is a major roadblock for the investigation of plant nucleotide (NT) metabolism. Here, we present a method that overcomes this limitation, allowing the detection of all deoxy- and ribonucleotides as well as the corresponding nucleosides from the same plant sample. The method is characterized by high sensitivity and robustness enabling the reproducible detection and absolute quantification of these metabolites even if they are of low abundance. Employing the new method, we analyzed Arabidopsis thaliana null mutants of CYTIDINE DEAMINASE, GUANOSINE DEAMINASE, and NUCLEOSIDE HYDROLASE 1, demonstrating that the deoxyribonucleotide (dNT) metabolism is intricately interwoven with the catabolism of ribonucleosides (rNs). In addition, we discovered a function of rN catabolic enzymes in the degradation of deoxyribonucleosides in vivo. We also determined the concentrations of dNTs in several mono- and dicotyledonous plants, a bryophyte, and three algae, revealing a correlation of GC to AT dNT ratios with genomic GC contents. This suggests a link between the genome and the metabolome previously discussed but not experimentally addressed. Together, these findings demonstrate the potential of this new method to provide insight into plant NT metabolism.