Genome and transcriptome architecture of allopolyploid okra (Abelmoschus esculentus)

We present the first annotated genome assembly of the allopolyploid okra (Abelmoschus esculentus). Analysis of telomeric repeats and gene rich regions suggested we obtained whole chromosome and chromosomal arm scaffolds. Besides long distal blocks we also detected short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation upon polyploidization of okra. Ribosomal RNA genes are organized in 5S clusters separated from the 18S-5.8S-28S units, clearly indicating an S-type rRNA gene arrangement. The assembly is consistent with cytogenetic and cytometry observations, identifying 65 chromosomes and 1.45Gb of expected genome size in a haploid sibling. Approximately 57% of the genome consists of repetitive sequence. BUSCO scores and A50 plot statistics indicated a nearly complete genome. Kmer distribution analysis suggests that approximately 75% has a diploid nature, and at least 15% of the genome is heterozygous. We did not observe aberrant meiotic configurations, suggesting there is no recombination among the sub-genomes. BUSCO configurations pointed to the presence of at least 3 sub-genomes. These observations are indicative for an allopolyploid nature of the okra genome. Structural annotation using gene models derived from mapped transcriptome data, generated over 130,000 putative genes. The discovered genes appeared to be located predominantly at the distal ends of scaffolds, gradually decreasing in abundance toward more centrally positioned scaffold domains. In contrast, LTR retrotransposons were more abundant in centrally located scaffold domains, while less frequently represented in the distal ends. This gene and LTR-retrotransposon distribution is consistent with the observed heterochromatin organization of pericentromeric heterochromatin and distal euchromatin. The derived amino acid queries of putative genes were subsequently used for phenol biosynthesis pathway annotation in okra. Comparison against manually curated reference KEGG pathways from related Malvaceae species revealed the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra.

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Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.605825 ◽

2021 ◽

Vol 11 ◽

Author(s):

Shiju Xiao ◽

Guangzhong Zhang ◽

Chunyan Jiang ◽

Xin Liu ◽

Xiaoxu Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Target Genes ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Phosphotransferase System ◽

Microbial Composition ◽

Kegg Pathways ◽

Significant Difference ◽

Rrna Gene Sequencing ◽

Endothelial Growth Factor

BackgroundIncreasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.ObjectivesTo comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.MethodsDNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.ResultsCompared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.ConclusionsA clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.

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The Diversity of the Intestinal Flora Disturbed After Feeding Intolerance Recovery in Preterm Twins

Frontiers in Pediatrics ◽

10.3389/fped.2021.648979 ◽

2021 ◽

Vol 9 ◽

Author(s):

Ying Li ◽

Chunhong Jia ◽

Xiaojun Lin ◽

Lili Lin ◽

Lizhen Li ◽

...

Keyword(s):

Acid Metabolism ◽

Intestinal Flora ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Feeding Intolerance ◽

Fecal Samples ◽

Kegg Pathways ◽

Intestinal Bacterial Community ◽

Β Diversity ◽

Significant Difference

Background: Feeding intolerance (FI) is a common condition in premature infants that results in growth retardation and even necrotizing enterocolitis. The gut microbiome is linked to FI occurrence; however, the outcome after FI recovery is unclear.Methods: Fecal samples were collected from 11 pairs of premature twins/triplets for 16S rRNA gene sequencing. Initial fecal samples were collected shortly after admission, and then every other week until 7 weeks or discharge.Results: After FI recovery, there was no significant difference in the β-diversity of the intestinal flora between the FI group and the feeding tolerance (FT) group. By contrast, there was a significant difference in the β-diversity. Proteobacteria was the predominant phylum in the microbiome of the FI group, whereas Firmicutes was the predominant phylum in the microbiome of the FT group. The predominant bacteria with LDA >4 between the two groups at 13–15 days after birth, 19–28 days after birth, and at discharge were different, with the proportions of Bacillus, Clostridium butyricum, and Clostridium being highest in the FT group and Firmicutes, unidentified_Clostridiales, and Proteobacteria being highest in the FI group. Similarly, there were significant differences in the relative abundances of KEGG pathways, such as fatty acid metabolism, DNA repair and recombination proteins, energy metabolism, and amino acid metabolism, between the two groups (P < 0.01).Conclusions: There was a significant difference in diversity of the intestinal flora after feeding intolerance recovery. Feeding intolerance may disturb the succession of the intestinal bacterial community.

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Evolutionary relationships of completely sequenced Clostridia species and close relatives

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.000638 ◽

2015 ◽

Vol 65 (Pt_11) ◽

pp. 4276-4283 ◽

Cited By ~ 12

Author(s):

Takashi Kunisawa

Keyword(s):

Maximum Likelihood ◽

Phylogenetic Trees ◽

Gene Arrangement ◽

Evolutionary Relationships ◽

Rrna Gene ◽

Sequence Information ◽

Bayesian Tree ◽

Maximum Likelihood Methods ◽

Genome Sequence Information ◽

Close Relatives

The class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.

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Analysis of Panax ginseng miRNAs and Their Target Prediction Based on High-Throughput Sequencing

Planta Medica ◽

10.1055/a-0989-7302 ◽

2019 ◽

Vol 85 (14/15) ◽

pp. 1168-1176

Author(s):

Yingfang Wang ◽

Mengyuan Peng ◽

Yanlin Chen ◽

Wenjuan Wang ◽

Zhihua He ◽

...

Keyword(s):

Panax Ginseng ◽

High Throughput Sequencing ◽

Gene Prediction ◽

Target Prediction ◽

Valuable Insight ◽

Illumina Hiseq ◽

Immune System Diseases ◽

Kegg Pathways ◽

Pathway Annotation ◽

Human Genes

Abstract Panax ginseng has been widely and effectively used as medicine for thousands of years. However, only limited studies have been conducted to date on ginseng miRNAs. In the present study, we collected 3 ginseng samples from the Changbai Mountain in China. Small RNA libraries were constructed and sequenced on the Illumina HiSeq platform. Sequencing analyses identified 3798 miRNAs, including 298 known miRNAs and 3500 potentially novel miRNAs. The miR166, miR159, and miR396 families were among the most highly expressed miRNAs in all libraries. The results of miRNA expression analyses were validated by qRT-PCR. Target gene prediction through computational and pathway annotation analyses revealed that the primary pathways were related to plant development, including metabolic processes and single-organism processes. It has been reported that plant miRNAs might be one of the hidden bioactive ingredients in medicinal plants. Based on the combined use of RNAhybrid, Miranda, and TargetScan software, a total of 50,992 potential human genes were predicted as the putative targets of 2868 miRNAs. Interestingly, the enriched KEGG pathways were associated with some human diseases, especially cancer, immune system diseases, and neurological disorders, and this could support the clinical use of ginseng. However, the human targets of ginseng miRNAs should be confirmed by further experimental validation. Our results provided valuable insight into ginseng miRNAs and the putative roles of these miRNAs.

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Biogeography of terrestrial cyanobacteria from Antarctic ice-free areas

Annals of Glaciology ◽

10.3189/172756411795931930 ◽

2010 ◽

Vol 51 (56) ◽

pp. 171-177 ◽

Cited By ~ 37

Author(s):

Z. Namsaraev ◽

M.-J. Mano ◽

R. Fernandez ◽

Annick Wilmotte

Keyword(s):

Rrna Gene ◽

Distribution Analysis ◽

Operational Taxonomic Units ◽

Terrestrial Cyanobacteria ◽

Victoria Land ◽

Low Degree ◽

Range Transport ◽

Antarctic Continent ◽

The Antarctic ◽

Further Development

AbstractCyanobacteria inhabit the Antarctic continent and have even been observed in the most southerly ice-free areas of Antarctica (86–87° S). The highest molecular diversity of cyanobacterial communities was found in the areas located between 70° S and 80° S. Further south and further north from this zone, the diversity abruptly decreased. Seventy-nine per cent (33 of 42 operational taxonomic units) of Antarctic terrestrial cyanobacteria have a cosmopolitan distribution. Analysis of the sampling efforts shows that only three regions (southern Victoria Land, the Sør Rondane Mountains and Alexander Island) have been particularly well studied, while other areas did not receive enough attention. Although cyanobacteria possess a capacity for long-range transport, regional populations in Antarctic ice-free areas seem to exist. The cyanobacterial communities of the three most intensively studied regions, separated from each other by a distance of 3000–3400 km, had a low degree of similarity with each other. Further development of microbial biogeography demands a standardized approach. For this purpose, as a minimal standard, we suggest using the sequence of cyanobacterial 16S rRNA gene between Escherichia coli positions 405 and 780.

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Evolution of rRNA gene clusters and telomeric repeats during explosive genome repatterning in Taterillus X (Rodentia, Gerbillinae)

Cytogenetic and Genome Research ◽

10.1159/000076296 ◽

2003 ◽

Vol 103 (1-2) ◽

pp. 94-103 ◽

Cited By ~ 25

Author(s):

G. Dobigny ◽

C. Ozouf-Costaz ◽

C. Bonillo ◽

V. Volobouev

Keyword(s):

Gene Clusters ◽

Rrna Gene ◽

Telomeric Repeats

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Bacterial Diversity and Community in Regional Water Microbiota between Different Towns in World’s Longevity Township Jiaoling, China

Diversity ◽

10.3390/d13080361 ◽

2021 ◽

Vol 13 (8) ◽

pp. 361

Author(s):

Lei Wu ◽

Xinqiang Xie ◽

Jumei Zhang ◽

Yu Ding ◽

Qingping Wu

Keyword(s):

16S Rrna ◽

High Throughput Sequencing ◽

The Other ◽

Rrna Gene ◽

Metabolic Characteristics ◽

Kegg Pathways ◽

Healthy Longevity ◽

And Function ◽

Regional Water

Healthy longevity is associated with many factors, however, the potential correlation between longevity and microbiota remains elusive. To address this, we explored environmental microbiota from one of the world’s longevity townships in China. We used 16S rRNA gene high-throughput sequencing to analyze the composition and function of water microbiota. The composition and diversity of water microbiota significantly differed between the towns. Lactobacillus, Streptococcus, Bacteroides, Faecalibacterium, and Stenotrophomonas were only dominant in Xinpu, a town with an exceptionally high centenarian population. Several biomarkers were identified, including Flavobacterium, Acinetobacter, Paracoccus, Lactobacillales, Psychrobacter, Bacteroides, Ruminococcaceae, and Faecalibacterium, and these shown to be responsible for the significant differences between towns. The main species contributing to the differences between towns were Cyanobacteria, Cupriavidus and Ralstonia. Based on KEGG pathways showed that the predicted metabolic characteristics of the water microbiota in Xinpu towns were significantly different to those of the other towns. The results revealed significant differences in the composition and diversity of water microbiota in the longevity township. These findings provide a foundation for further research on the role of water microbiota in healthy longevity.

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Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China

PeerJ ◽

10.7717/peerj.9500 ◽

2020 ◽

Vol 8 ◽

pp. e9500

Author(s):

Xiaojuan Chen ◽

Da He ◽

Lianfeng Zhou ◽

Yankun Cao ◽

Zhanjing Li

Keyword(s):

Algal Blooms ◽

Sequence Similarity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Microbial Composition ◽

Jinsha River ◽

Kegg Pathways ◽

Significant Difference ◽

The Impact ◽

Hydropower Stations

Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.

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The symbiotic mites of some Appalachian Xystodesmidae (Diplopoda:Polydesmida) and the complete mitochondrial genome sequence of the mite Stylochyrus rarior (Berlese) (Acari:Mesostigmata:Ologamasidae)

Invertebrate Systematics ◽

10.1071/is09036 ◽

2009 ◽

Vol 23 (5) ◽

pp. 445 ◽

Cited By ~ 11

Author(s):

Lynn Swafford ◽

Jason E. Bond

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Mite Species ◽

Gene Arrangement ◽

Trna Genes ◽

Rrna Gene ◽

Protein Coding ◽

Coding Regions ◽

The Family ◽

Coding Control

Millipedes of the family Xystodesmidae (Polydesmida) are often host to several symbiotic mite species, but very little work has been done to identify these acarines or to understand their relationship to the millipedes. In an attempt to better understand these associations, mites found on xystodesmid millipedes, a group for which a species phylogeny has been proposed, were collected in the Appalachian Mountains of Kentucky, Virginia, Tennessee and North Carolina. Mites in the genera Stylochyrus Canestrini & Canestrini, 1882 (Mesostigmata: Ologamasidae) and Schwiebea Oudemans, 1916 (Sarcoptiformes: Acaridae) were prevalent among millipedes in the genera Apheloria Chamberlin, 1921, Appalachioria Marek & Bond, 2006, Boraria Chamberlin, 1943, Brachoria Chamberlin, 1939, Dixioria Chamberlin, 1947, Nannaria Chamberlin, 1918, Pleuroloma Rafinesque, 1820, Prionogonus Shelley, 1982, Rudiloria Causey, 1955 and Sigmoria Chamberlin, 1939. Of the mite taxa collected, the species Stylochyrus rarior (Berlese, 1916) was found on the greatest number of sampled millipede taxa. To enhance future coevolutionary studies of xystodesmid millipedes and their mite symbionts, the complete mitochondrial genome of S. rarior associated with the millipede genus Apheloria (Polydesmida: Xystodesmidae) was sequenced. The genome is 14 899 nucleotides in length, has all the typical genes of an arthropod mitochondrion, differs in gene arrangement from that of the ancestral arthropod, and has a gene order that is unique among mites and ticks. The major difference in S. rarior is the placement of the protein-coding gene nad1, which is positioned between the rRNA gene 12S and the protein-coding gene nad2 (tRNA genes and non-coding regions excluded). There are also two non-coding control regions within this mitochondrial genome.

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Characterization and structure of the mitochondrial small rRNA gene of the entomopathogenic fungus Beauveria bassiana

Genome ◽

10.1139/g98-040 ◽

1998 ◽

Vol 41 (3) ◽

pp. 471-476 ◽

Cited By ~ 4

Author(s):

D D Hegedus ◽

T A Pfeifer ◽

D S Mulyk ◽

G G Khachatourians

Keyword(s):

Phylogenetic Analysis ◽

Filamentous Fungi ◽

Beauveria Bassiana ◽

Ribosomal Rna ◽

Entomopathogenic Fungus ◽

Rna Secondary Structure ◽

Structural Model ◽

Gene Arrangement ◽

Rrna Gene ◽

Fungus Beauveria Bassiana

The entire mitochondrial (mt) small ribosomal RNA (srRNA) gene from the entomopathogenic fungus Beauveria bassiana was sequenced. Alignment of the sequence to those of other filamentous fungi revealed gross length differences in their respective products. Construction of a secondary structural model showed that these differences were restricted to known variable srRNA subdomains. Several features were identified that were common only to the hyphomycetous fungi examined. Phylogenetic analysis indicated that the anamorph B. bassiana was more closely related to the pyrenomycete than to the plectomycete ascomycetous fungi. Based on our previous comparison of mt gene arrangement in filamentous fungi, this was unexpected. The possibility that the smaller mt genomes reflect the ancestral arrangement of genes is discussed.Key words: Beauveria bassiana, mitochondria, small ribosomal RNA, secondary structure, phylogeny.

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