GC Content Of Genome Research Articles

Enigmatic Entities of the Acellular World: Viruses, Viroids, and Virusoids

Genetic material confined within the lipid based cellular boundaries was earlier considered synonymous with life. However, with the discovery of viruses in late 19th century, the existence of acellular biological entities was established. Viruses, viroids, and virusoids are unique entities which have different relationships with different life forms ranging from mutualistic to parasitic ones. These entities provide evidence in support of the idea of ‘RNA world’ in the origin of life on Earth. In the present time, viruses are relatively well studied but the same cannot be said for viroids and virusoids. There has been a growing focus on the impact of these entities, in terms of human welfare as well as their impact on susceptible varieties of plants. As a result, studying their origin, evolution and pathogenicity has become a subject of the uttermost importance. In this review, we have discussed different facets of viruses, viroids and virusoids like their historical background, classification and mode of entry and replication in the host. We have also summarized various possible theories on their origin and evolution and have provided our take on it. This work indicates the possibility that different viruses originated distinctly by utilizing different strategies and evolved further. Clues like small size and high GC content in genomes indicate that viroids must be an important component of the pre-cellular world and it is possible that they might have originated before viruses. Furthermore, as viroids and virusoids show certain conserved properties, it suggests a probable link between them.

Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla).

Macadamia is a true dicotyledonous plant that thrives in a mild, humid, low wind environment. It is cultivated and traded internationally due to its high-quality nuts thus, has significant development prospects and scientific research value. However, information on the genetic resources of Macadamia spp. remains scanty. The mitochondria (mt) genomes of three economically important Macadamia species, Macadamia integrifolia, M. ternifolia and M. tetraphylla, were assembled through the Illumina sequencing platform. The results showed that each species has 71 genes, including 42 protein-coding genes, 26 tRNAs, and 3 rRNAs. Repeated sequence analysis, RNA editing site prediction, and analysis of genes migrating from chloroplast (cp) to mt were performed in the mt genomes of the three Macadamia species. Phylogenetic analysis based on the mt genome of the three Macadamia species and 35 other species was conducted to reveal the evolution and taxonomic status of Macadamia. Furthermore, the characteristics of the plant mt genome, including genome size and GC content, were studied through comparison with 36 other plant species. The final non-synonymous (Ka) and synonymous (Ks) substitution analysis showed that most of the protein-coding genes in the mt genome underwent negative selections, indicating their importance in the mt genome. The findings of this study provide a better understanding of the Macadamia genome and will inform future research on the genus.

Alternating nuclear DNA content in chrysophytes provides evidence of their isomorphic haploid-diploid life cycle

Across eukaryotic organisms there is a great diversity of life cycles. This particularly applies to unicellular eukaryotes (protists), where the life cycles are still largely unexplored, although this knowledge is key to understanding their biology.To detect the often inconspicuous transitions among life cycle stages, we focused at shifts in ploidy levels within strains of unicellular chrysophyte alga. Representatives of three genera (Chrysosphaerella, Ochromonas, and Synura) were analysed for nuclear DNA contents using a propidium iodide flow cytometry. Selected strains exhibiting ploidy level variation were also surveyed for DNA base composition (GC content) and cell size. Additionally, we tracked ploidy level changes in seven strains under long-term cultivation.An alternation of two ploidy levels was revealed in the life cycle of chrysophytes with both life cycle stages capable of mitotic growth and long-term survival in cultivation. With the exception of a small increase in cell size with higher ploidy, both life cycle stages shared the same phenotype and also had highly similar genomic GC content. Further, we detected three ploidy levels in two Synura species (S. glabra, S. heteropora), where the highest ploidy (putatively 4x) most likely resulted from a polyploidization event.Consequently, chrysophytes have a haploid-diploid life cycle with isomorphic life cycle stages. As far as we know, this is the first report of such life cycle strategy in unicellular algae. Life cycle stages and life stage transitions seem to be synchronized among all cells coexisting within a culture, possibly due to chemical signals. Particular life stages may be more successful under certain environmental conditions, for our studied strains the diploid stage prevailed in cultivation.

An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses.

Viruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed. This study curated an atlas of human viruses from public databases and literature, and built the Human Virus Database (HVD). The HVD contains 1131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue tropism of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue tropism of DNA viruses was predicted using a random-forest algorithm with a middle performance. Overall, the study not only provides a valuable resource for further studies of human viruses but also deepens our understanding toward the diversity and tissue tropism of human viruses. The HVD is available at http://computationalbiology.cn/humanVirusBase/#/. Supplementary data are available at Bioinformatics online.

Mitochondrial genome structure, phylogenetic analyses and substitution rate estimation of the Oedogoniales

The order Oedogoniales comprises three genera, Oedogonium, Oedocladium and Bulbochaete, which were classified based on traditional morphological criteria, and includes more than 600 described species. This group is economically important in astaxanthin production and the energy sector. However, only one mitochondrial genome (mitogenome) has been reported so far. This study determined the mitochondrial genomes of seven Oedogoniales species, including six Oedogonium species and Oedocladium prescottii. Comparative analyses between the newly determined mitogenomes and the previously reported Bulbochaete rectangularis var. hiloensis mitogenome showed that all eight mitogenomes comprised 12 protein-coding genes (PCGs) and two rRNAs; however, the mitogenomes differed in their genome sizes, GC content, tRNAs, non-coding regions and introns. Synteny analysis of the eight mitogenomes revealed a high degree of syntenic conservation in general, with some rearrangements and inversions. The average nucleotide identity (ANI) analysis of the eight mitogenomes indicated Oedogonium dentireticulatum showed high similarity with Oedogonium sp3 (ANI of 96.32%). Most of the PCGs of the eight mitogenomes presented the conventional start codon ATG and stop codon TAR (TAA/TAG/TGA), and the synonymous codon preferences were conserved. Phylogenetic results indicated that Oedogonium was polyphyletic, and species of Oedocladium clustered with Oedogonium, while the position of B. rectangularis var. hiloensis was uncertain for the incongruent phylogenetic results. Statistical analyses of substitution rates demonstrated no significant differences among the three genera, and the dN/dS ratios based on branch model showed that cob, cox1 and nad4 of Oedocladium prescottii and B. rectangularis var. hiloensis were putative fast-evolving genes. These findings suggested that the traditional taxonomy of Oedogoniales did not define natural groups, and that species of Oedocladium and Bulbochaete may have undergone rapid evolution.

The complete chloroplast genome of Medicago arabica (Fabaceae)

Medicago arabica (Linnaeus, 1762) Huds. is an important annual legume forage that grows in a wide range of climates, from subtropical to temperate. This study aimed to sequence the chloroplast genome of M. arabica and compare it with other legumes. In this study, we sequenced the entire chloroplast genome of M. arabica, which has 125,056 base pairs. The total GC content of the chloroplast genome of M. arabica was 34.4%. From the 110 unique genes of the circular genome, 30 tRNA genes, four rRNA genes, and 76 protein-coding genes were successfully annotated. A maximum likelihood (ML) tree was constructed using the model species and 17 species of the Medicago genus. M. arabica was shown to be phylogenetically closely related to M. polymorpha. The nucleotide diversity of the chloroplast genome may provide valuable molecular markers to study chloroplast, genetic breeding, and plant molecular evolution. These findings provide a solid foundation for future research on the molecular biology of the chloroplast.

Characterization and phylogenetic analysis of the complete chloroplast genome sequence of xerophyta retinervis (velloziaceae)

Xerophyta retinervis has great ornamental value and numerous traditional uses. This study reported its first complete chloroplast genome sequence, which was 155,109 bp in length, including a pair of inverted repeat regions (IRs) (27,093 bp), a small single-copy (SSC) region (17,385 bp), and a large single-copy (LSC) region (83,538bp). The chloroplast genome encoded 133 genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The total GC content of the chloroplast genome was 37.55%. The phylogenetic tree showed that X. retinervis was closely related to X. spekei.

The complete chloroplast genome of Indosasa hispida ‘Rainbow’ (Poaceae, Bambuseae): an ornamental bamboo species in horticulture

Indosasa hispida ‘Rainbow’ is a new horticultural plant variety for anthocyanin production, which has great ornamental value and huge market potential. The chloroplast genome is 139,690 bp in length, containing a large single-copy region (LSC) of 83,268 bp, a small single-copy region (SSC) of 12,830 bp, and a pair of 21,796 bp inverted repeats region (IR). The GC content of chloroplast genome is 38.9%. There are 130 genes in the cp genome, including 83 protein-coding genes, 8 ribosomal RNA genes, and 39 transfer RNA genes. In addition, phylogenetic analysis firmly supported that I. hispida 'Rainbow' constituted that a sister species with Pleioblastus maculatus.

Characterization of the complete plastome of Delphinium montanum, a polyploid, endemic and endangered Pyrenean Larkspur

Delphinium montanum DC. 1815, is an endangered larkspur endemic to the Eastern Pyrenees. For biogeographic and conservation purpose, a hybrid assembly approach based on long- and short-read genomic data allowed us to successfully assemble whole plastid genome of Delphinium montanum. The complete plastome is 154,185 bp in length, consisting of a pair of inverted repeats (IRs) of 26,559 bp, a large single-copy (LSC) region and a small single-copy region (SSC) of 84,746 and 16,320 bp, respectively. It was found to contain 136 genes, including 84 protein-coding genes, 44 trRNA genes and 8 rRNA genes. The overall GC content of the plastid genome is 38.3%. Phylogenetic inference supports the polyphyly of the Delphinium genus.

The chloroplast genome of aromatic plants Cinnamomum pauciflorum (Lauraceae)

Cinnamomum pauciflorum is a valuable aromatic tree of the genus Cinnamomum Trew in the family Lauraceae. To better determine its phylogenetic location with other Cinnamomum species, the complete chloroplast (cp) genome of C. pauciflorum was sequenced. The total cp genome size is 152,766 bp, consisting of a pair of inverted repeats (IRa/b) with a length of 20,074 bp separated by a large single-copy region (LSC) and a small single-copy region (SSC) which are 93,693 and 18,925 bp, respectively. The overall GC content of the cp genome is 39.14%. Maximum-likelihood analysis showed that C. pauciflorum has phylogenetic affinities with Cinnamomum osmophloeum, Cinnamomum aromaticum, Cinnamomum mollifolium, and Cinnamomum tenuipile, providing new insight into the evolution of Lauraceae.

Characterization of the complete chloroplast genome of Carex myosuroides Villars, 1779 (Cyperaceae)

Carex myosuroides Villars, 1779 is a typical alpine sedge with both ecological and agricultural value. The work reported here is the first complete chloroplast genome of this species. The chloroplast genome, with a total size of 185,609 bp, consists of two inverted repeats (IRs, 38,374 bp) separated by a large single-copy (LSC, 99,911 bp) region, and a small single-copy (SSC, 8950 bp) region. The overall genome GC content is 34.12%. The genome contains 125 genes, consisting of 82 protein-coding genes, 35 tRNA genes, and eight rRNA genes. Phylogenetic analysis supports the taxonomic treatment of incorporating genus Kobresia to a broader circumscription of Carex. Our work could be helpful to future research on Cyperaceae.

The complete chloroplast genome of Calohypnum plumiforme (Wilson) (hypanceae, bryophyta)

Calohypnum plumiforme is a widely distributed moss in East Asia. In this study, Illumina sequencing data was used to assemble the complete chloroplast genome of C. plumiforme. The length of the circular genome is 124,037 bp. It contains a total of 121 genes, including 81 protein-coding, 36 tRNA, and 4 rRNA genes. The GC content of the chloroplast genome of C. plumiforme is 29.07%. The phylogenetic analysis suggested that C. plumiforme is sister to Calliergonella cuspidata. This study provides important sequence information for species identification and its phylogenetic relationship in the Bryopsida.

Characterization of the complete chloroplast genome of Lonicera tangutica (Caprifoliaceae), an ornamental and medicinal plant in China

In the present study, the complete chloroplast genome of Lonicera tangutica is presented and characterized for the first time. The complete chloroplast genome was 156,121 bp in length, including 23,899 bp inverted repeat (IR) regions, an 89,466 bp large single-copy (LSC) region, and an 18,851 bp small single-copy (SSC) region. A total of 129 genes, including 37 tRNA genes, eight rRNA genes, and 84 protein-coding genes, were annotated, and the overall GC content of the chloroplast genome was 38.35%. Two introns in the ycf3 gene and a single intron in another gene were detected. Maximum-likelihood phylogenetic analysis indicated that L. tangutica has a very close evolutionary relationship with Lonicera praeflorens, Lonicera hispida, Lonicera fragrantissima, and Lonicera stephanocarpa. These results are valuable for studying the evolution and genetic diversity of L. tangutica.

The complete chloroplast genome of a coastal plant, Euphorbia jolkinii (Euphorbiaceae)

The complete chloroplast genome sequence of a coastal plant, Euphorbia jolkinii Boiss. (Euphorbiaceae), was determined. The chloroplast genome was 162,854 bp in length, consisting of a large single copy region (90,726 bp), a small single copy region (18,422 bp), and two inverted repeats (26,853 bp). The chloroplast genome contained 115 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, four unique rRNA genes, and one pseudogene, rps16. GC content of the whole chloroplast genome was 35.6%. The phylogenetic analysis showed a close relationship between E. jolkinii and E. pekinensis Rupr. The sequence data would provide useful information to understand the evolutionary process of E. jolkinii.

The complete chloroplast genome of Caroxylon passerinum (Chenopodiaceae), an annual desert plant

ABSTACT Caroxylon passerinum is an important constructive species, which is widely distributed in both desert and desert steppe in north-western China. C. passerinum is one of hosts of holoparasitic Cistanche species. In this study, we report the complete chloroplast genome sequence of C. passerinum, which is 150,925 bp in length and comprises a large single-copy region (83,057 bp), a small single-copy region (18,180 bp), and a pair of inverted repeats (24,844 bp). It encodes 132 unique genes, including 89 protein-coding genes (PCGs), 35 tRNAs, and eight rRNAs. The overall GC content of this chloroplast genome is 36.8%. Maximum likelihood (ML) phylogenetic tree strongly supports that C. passerinum is closely related to the hosts of Cistanche deserticola, Haloxylon persicum and Haloxylon ammodendron.

Characterization of the complete chloroplast genome of Brassica oleracea var. italica and phylogenetic relationships in Brassicaceae.

Broccoli (Brassica oleracea var. italica) is an important B. oleracea cultivar, with high economic and agronomic value. However, comparative genome analyses are still needed to clarify variation among cultivars and phylogenetic relationships within the family Brassicaceae. Herein, the complete chloroplast (cp) genome of broccoli was generated by Illumina sequencing platform to provide basic information for genetic studies and to establish phylogenetic relationships within Brassicaceae. The whole genome was 153,364 bp, including two inverted repeat (IR) regions of 26,197 bp each, separated by a small single copy (SSC) region of 17,834 bp and a large single copy (LSC) region of 83,136 bp. The total GC content of the entire chloroplast genome accounts for 36%, while the GC content in each region of SSC,LSC, and IR accounts for 29.1%, 34.15% and 42.35%, respectively. The genome harbored 133 genes, including 88 protein-coding genes, 37 tRNAs, and 8 rRNAs, with 17 duplicates in IRs. The most abundant amino acid was leucine and the least abundant was cysteine. Codon usage analyses revealed a bias for A/T-ending codons. A total of 35 repeat sequences and 92 simple sequence repeats were detected, and the SC-IR boundary regions were variable between the seven cp genomes. A phylogenetic analysis suggested that broccoli is closely related to Brassica oleracea var. italica MH388764.1, Brassica oleracea var. italica MH388765.1, and Brassica oleracea NC_0441167.1. Our results are expected to be useful for further species identification, population genetics analyses, and biological research on broccoli.

Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes

BackgroundAmong the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species.ResultsMangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63–69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24–27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7–10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407 to 6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value.ConclusionsWe sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

Comparative Analysis the Complete Chloroplast Genomes of Nine Musa Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications.

Musa (family Musaceae) is monocotyledonous plants in order Zingiberales, which grows in tropical and subtropical regions. It is one of the most important tropical fruit trees in the world. Herein, we used next-generation sequencing technology to assemble and perform in-depth analysis of the chloroplast genome of nine new Musa plants for the first time, including genome structure, GC content, repeat structure, codon usage, nucleotide diversity and etc. The entire length of the Musa chloroplast genome ranged from 167,975 to 172,653 bp, including 113 distinct genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. In comparative analysis, we found that the contraction and expansion of the inverted repeat (IR) regions resulted in the doubling of the rps19 gene. The several non-coding sites (psbI–atpA, atpH–atpI, rpoB–petN, psbM–psbD, ndhf–rpl32, and ndhG–ndhI) and three genes (ycf1, ycf2, and accD) showed significant variation, indicating that they have the potential of molecular markers. Phylogenetic analysis based on the complete chloroplast genome and coding sequences of 77 protein-coding genes confirmed that Musa can be mainly divided into two groups. These genomic sequences provide molecular foundation for the development and utilization of Musa plants resources. This result may contribute to the understanding of the evolution pattern, phylogenetic relationships as well as classification of Musa plants.

A positive correlation between GC content and growth temperature in prokaryotes

BackgroundGC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate.ResultsWith a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation.ConclusionsThis study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

The complete chloroplast genome of the aromatic tree species Cinnamomum tenuipile Kosterm (Lauraceae)

Cinnamomum tenuipile Kosterm is a precious aromatic tree in Lauraceae. To better determine its phylogenetic location with other Cinnamomum species, the chloroplast genome of C. tenuipile was sequenced. The complete chloroplast genome size is 152,761 bp, consisting of a pair of inverted repeats (IRa/b) with a length of 20,074 bp separated by a large single-copy region (LSC) and a small single-copy region (SSC) which are 93,685 and 18,928 bp, respectively. The overall GC content of the cp genome is 39.16%. The maximum-likelihood phylogenetic tree showed that C. tenuipile is more closely related to C. aromaticum, providing new insight into the evolution of Lauraceae.