The dynamics of genome size and GC contents evolution in genus Nicotiana

Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved one’s (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.

Draft Genome Sequences of Saccharopolyspora sp. Strains and Streptomyces sp. Strains, Isolated from Social Wasps (Vespidae; Polistinae: Epiponini)

Strains of the genera Saccharopolyspora and Streptomyces were isolated from Protopolybia sp. and Metapolybia sp. social wasps in Costa Rica. Draft genome sequences were obtained for six isolates, ranging from 6.4 Mb to 9.1 Mb long and having GC contents of 71 to 73%.

Sixteen Genome Sequences of Denitrifying Bacteria Assembled from Enriched Cultures of Anaerobic Pig Manure Digestate

We report 16 genomes assembled from the metagenome of pig manure digestate enriched with the addition of N 2 O. These denitrifying bacterial genomes all contain the nosZ gene, encoding N 2 O reductase. Their sizes range from 1,902,599 bp to 6,264,563 bp, with completeness of 75.03% to 98.89%, GC contents of 32.86% to 69.66%, and contamination of 0% to 8.4%.

A Positive Correlation between Bacterial GC Content and Growth Temperature

Background: Because GC pairs are 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. Results: With a dataset much larger than previous studies (681 bacteria and 155 archaea), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature 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 optimal growth temperature with whole-genome GC content 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 optimal growth temperature 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. Conclusions: This study explains the previous contradictory observations and ends a long debate. Bacteria growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we should be open to other intricate explanations, including nonadaptive ones.

Messenger RNAs Mobile in Salix Matsudana Grafts Were in Association With Plant Rooting

Messenger RNAs exchanged between scions and rootstocks of grafted plants seriously affect their traits performance. The study goals were to identify the long-distance mRNA transmission events in grafted willows using a transcriptome analysis and to reveal the possible effects on rooting traits. The results showed that the Salix matsudana variety 9901 has better rooting ability than YJ, which reasonably improved the rooting performance of the heterologous grafts 9901 (scion) / YJ (rootstock). A transcriptome analysis showed that 2,948 differentially expressed genes (DEGs) were present in the rootstock of 9901/YJ grafted plants in comparison with YJ/YJ. Among them, 692 were identified as mRNAs moved from 9901 scion based on a SNP analysis of two parents. They were mostly 1,001–1,500 bp, had 40–45% GC contents, or had expression abundance values less than 10. However, mRNAs over 4,001 bp, having 50–55% GC contents, or having expression abundance values of 10–20 were preferentially transferred. Eight mRNAs subjected to long-distance trafficking were involved in the plant hormone pathways and may significantly promote the root growth of grafted plants. Thus, heterologous grafts of Salix matsudana could efficiently influence plant rooting since of the mRNAs transport from scion to rootstock. Thus, the grafting parents and grafting patterns would be much concerned in the breeding process to gain the expected results in future.

Comparative Analysis of Mitochondrial Genome Features among Four Clonostachys Species and Insight into Their Systematic Positions in the Order Hypocreales

The mycoparasite fungi of Clonostachys have contributed to the biological control of plant fungal disease and nematodes. The Clonostachys fungi strains were isolated from Ophiocordyceps highlandensis, Ophiocordycepsnigrolla and soil, which identified as Clonostachyscompactiuscula, Clonostachysrogersoniana, Clonostachyssolani and Clonostachys sp. To explore the evolutionary relationship between the mentioned species, the mitochondrial genomes of four Clonostachys species were sequenced and assembled. The four mitogenomes consisted of complete circular DNA molecules, with the total sizes ranging from 27,410 bp to 42,075 bp. The GC contents, GC skews and AT skews of the mitogenomes varied considerably. Mitogenomic synteny analysis indicated that these mitogenomes underwent gene rearrangements. Among the 15 protein-coding genes within the mitogenomes, the nad4L gene exhibited the least genetic distance, demonstrating a high degree of conservation. The selection pressure analysis of these 15 PCGs were all below 1, indicating that PCGs were subject to purifying selection. Based on protein-coding gene calculation of the significantly supported topologies, the four Clonostachys species were divided into a group in the phylogenetic tree. The results supplemented the database of mitogenomes in Hypocreales order, which might be a useful research tool to conduct a phylogenetic analysis of Clonostachys. Additionally, the suitable molecular marker was significant to study phylogenetic relationships in the Bionectriaceae family.

Draft Genome Sequences of Five Staphylococcus saprophyticus Strains Isolated from African Fermented Nono in Nigeria

ABSTRACT Five Staphylococcus saprophyticus strains were isolated from the fermented milk product nono in Nigeria and were sequenced using an Illumina MiSeq platform. The genome sizes ranged from 2.53 to 2.60 Mbp, while the GC contents ranged from 32.99 to 33.07 mol%. The genomes possessed 2,505 to 2,687 protein-coding sequences.

Complete Genome Sequences of 10 Lactococcal Skunavirus Phages Isolated from Cheddar Cheese Whey Samples in Canada

ABSTRACT We report the complete genome sequences of 10 virulent phages of the Skunavirus genus (Siphoviridae) that infect Lactococcus lactis strains used for cheddar cheese production in Canada. Their linear genomes range from 28,969 bp to 31,042 bp with GC contents of 34.1 to 35.1% and 55 to 60 predicted open reading frames (ORFs).

Comparative Chloroplast Genome Analysis and Evolutionary Relationships in Some Species of Asclepiadeae, Apocynaceae

Background: Comparative study of the complete chloroplast genomes of some species in the Subtribe Asclepiadeae was conducted to evaluate the variations and similarities between the species and to resolve the phylogenetic relationship within the subtribe. P. tomentosa has been used for medicinal uses in Saudi Arabia, Middle East, Africa and Brazil. It is used often in cosmetics and tanning industries, although it’s very well utilized as a traditional medicine in many civilizations.Methods: The genomes were compared using Mvista Bioinformatics tools to evaluate the inverted repeats (IR), large single copy (LSC) and small single copy (SSC) regions and also the border junctions were visualized with IR scope to express the expansion and contraction of the circular genome structure. While SSR markers were determined using the Reputer program, the genome map was done using OGDRAW (OrganellarGenomeDRAW).Result: Observed variations of the Mvista alignments is mainly at the coding regions of the sequences, while IR borders were varied at the SSC region of A. nivea genome; with ycf1 and rps19 due to evolutionary events. The genome sizes of C. procera are 166,010 bp, P. tomentosa 164,213bp, A. nivea 161,592 bp and C. wilfordii 161,180 bp. GC contents of A. nivea, C. wilfordii and P. tomentosa are 38% respectively; while C. procera is the least with 37%.; total SSR markers as well as the circular genome map were presented in this study.

Draft Genome Sequences of Lactobacillus delbrueckii subsp. bulgaricus Strains CBC-LB69 and CBC-LB8, Isolated from Homemade Dairy Foods in Bulgaria

ABSTRACT Here, we report the draft genome sequences of Lactobacillus delbrueckii subsp. bulgaricus strains CBC-LB69 and CBC-LB8. The strains were isolated from naturally processed, homemade dairy foods in Bulgaria. The two genome assemblies each resulted in 39 contigs with total lengths of 1,752,493 and 1,759,908 bp and GC contents of 49.80% and 49.90%, respectively.