Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes DOI Creative Commons
Hsin-Ying Chang, Hsi-Ching Yen, Hsiu‐An Chu

и другие.

Botanical studies, Год журнала: 2024, Номер 65(1)

Опубликована: Ноя. 28, 2024

Abstract Background Cyanobacteria are diverse phototrophic microbes with ecological importance and potential for biotechnology applications. One species of thermophilic cyanobacteria, Thermosynechococcus taiwanensis , has been studied biomass pyrolysis, estrogen degradation, the production bioethanol, monosaccharide, phycocyanin. To better understand diversity evolution this species, we sampled across different regions in Taiwan strain isolation genomic analysis. Results A total 27 novel strains were isolated from nine 12 hot springs subjected to whole genome sequencing. Including previously, our analyses encompassed 32 11 springs. Genome sizes among these ranged 2.64 2.70 Mb, an average 2.66 Mb. Annotation revealed between 2465 2576 protein-coding genes per genome, averaging 2537 genes. Core-genome phylogeny, gene flow estimates, overall content divergence consistently supported within-species into two major populations. While by distance partially explained within-population divergence, factors driving populations remain unclear. Nevertheless, likely a closed pan-genome comprising approximately 3030 genes, sampling providing sufficient coverage its diversity. investigate adaptations, identified significantly lower nucleotide diversity, indicating loci that may have undergone selective sweeps within each population. We 149 289 B, respectively. Only 16 common both populations, suggesting primarily targeted Key related functions such as photosynthesis, motility, ion transport highlighted. Conclusions This work provides population genomics perspective on spring cyanobacterial Taiwan. Beyond advancing understanding microbial evolution, collected sequences generated provide valuable materials future development utilization biological resources.

Язык: Английский

Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias DOI Creative Commons

Qiao-Hui Mou,

Zhe Hu, Jing Zhang

и другие.

Acta Biochimica Polonica, Год журнала: 2025, Номер 71

Опубликована: Янв. 8, 2025

Members of the families Thermosynechococcaceae and Thermostichaceae are well-known unicellular thermophilic cyanobacteria a non-thermophilic genus Pseudocalidococcus was newly classified into former. Analysis codon usage bias (CUB) cyanobacterial species inhabiting different thermal non-thermal niches will benefit understanding their genetic evolutionary characteristics. Herein, CUB context patterns protein-coding genes were systematically analyzed compared between members two families. Overall, nucleotide composition indices found to differ thermophiles non-thermophiles. The showed higher G/C content in base tended end with Correlation analysis indicated significant associations indices. results effective number codons, parity-rule 2, neutral correspondence analyses that mutational pressure natural selection primarily account for these species, but primary driving forces exhibit variation among genera. Moreover, optimal codons identified based on relative synonymous values genera even within In addition, pattern revealed specificity sequence start stop Intriguingly, clustering appeared be more related thermotolerance than phylogenomic relationships. conclusion, this study facilitates characteristics sources evolution surveyed clades provides insights adaptation environments.

Язык: Английский

Процитировано

0
High‐quality genome of a novel Thermosynechococcaceae species from Namibia and characterization of its protein expression patterns at elevated temperatures DOI Creative Commons
Nathanael David Arnold,

Michael Paper,

Tobias A. Fuchs

и другие.

MicrobiologyOpen, Год журнала: 2024, Номер 13(5)

Опубликована: Окт. 1, 2024

Abstract Thermophilic cyanobacteria thrive in extreme environments, making their thermoresistant enzymes valuable for industrial applications. Common habitats include hot springs, which act as evolutionary accelerators speciation due to geographical isolation. The family Thermosynechococcaceae comprises thermophilic known ability high‐temperature environments. These bacteria are notable photosynthetic capabilities, significantly contributing primary production habitats. Members of exhibit unique adaptations that allow them perform photosynthesis efficiently at elevated temperatures, subjects interest studies on microbial ecology, evolution, and potential biotechnological In this study, the genome a cyanobacterium, isolated from spring near Okahandja Namibia, was sequenced using PacBio Sequel IIe long‐read platform. Cultivations were performed temperatures 40, 50, 55°C, followed by proteome analyses based annotated genome. Phylogenetic investigations, informed 16S rRNA gene aligned nucleotide identity (ANI), suggest novel cyanobacterium is member Thermosynechococcaceae. Furthermore, new species assigned separate branch, potentially representing genus. Whole‐genome alignments supported finding, revealing few conserved regions multiple genetic rearrangement events. Additionally, 129 proteins identified differentially expressed temperature‐dependent manner. results study broaden our understanding cyanobacterial adaptation providing high‐quality sp. several promising candidate expression characterization studies.

Язык: Английский

Процитировано

0
Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes DOI Creative Commons
Hsin-Ying Chang, Hsi-Ching Yen, Hsiu‐An Chu

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 22, 2024

Abstract Background Cyanobacteria are diverse phototrophic microbes with ecological importance and potential for biotechnology applications. One species of thermophilic cyanobacteria, Thermosynechococcus taiwanensis , has been studied biomass pyrolysis, estrogen degradation, the production bioethanol, monosaccharide, phycocyanin. To better understand diversity evolution this species, we sampled across different regions in Taiwan strain isolation genomic analysis. Results A total 27 novel strains were isolated from nine 12 hot springs subjected to whole genome sequencing. Including previously, our analyses encompassed 32 11 springs. Genome sizes among these ranged 2.64 2.70 Mb, an average 2.66 Mb. Annotation revealed between 2,465 2,576 protein-coding genes per genome, averaging 2,537 genes. Core-genome phylogeny, gene flow estimates, overall content divergence consistently supported within-species into two major populations. While by distance partially explained within-population divergence, factors driving populations remain unclear. Nevertheless, likely a closed pan-genome comprising approximately 3,030 genes, sampling providing sufficient coverage its diversity. investigate adaptations, identified significantly lower nucleotide diversity, indicating loci that may have undergone selective sweeps within each population. We 149 289 B, respectively. Only 16 common both populations, suggesting primarily targeted Key related functions such as carbon fixation, photosynthesis, motility, ion transport highlighted. Conclusions This work provides population genomics perspective on spring cyanobacterial Taiwan. Beyond advancing understanding microbial evolution, collected sequences generated provide valuable materials future development utilization biological resources.

Язык: Английский

Процитировано

0
Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes DOI Creative Commons
Hsin-Ying Chang, Hsi-Ching Yen, Hsiu‐An Chu

и другие.

Botanical studies, Год журнала: 2024, Номер 65(1)

Опубликована: Ноя. 28, 2024

Abstract Background Cyanobacteria are diverse phototrophic microbes with ecological importance and potential for biotechnology applications. One species of thermophilic cyanobacteria, Thermosynechococcus taiwanensis , has been studied biomass pyrolysis, estrogen degradation, the production bioethanol, monosaccharide, phycocyanin. To better understand diversity evolution this species, we sampled across different regions in Taiwan strain isolation genomic analysis. Results A total 27 novel strains were isolated from nine 12 hot springs subjected to whole genome sequencing. Including previously, our analyses encompassed 32 11 springs. Genome sizes among these ranged 2.64 2.70 Mb, an average 2.66 Mb. Annotation revealed between 2465 2576 protein-coding genes per genome, averaging 2537 genes. Core-genome phylogeny, gene flow estimates, overall content divergence consistently supported within-species into two major populations. While by distance partially explained within-population divergence, factors driving populations remain unclear. Nevertheless, likely a closed pan-genome comprising approximately 3030 genes, sampling providing sufficient coverage its diversity. investigate adaptations, identified significantly lower nucleotide diversity, indicating loci that may have undergone selective sweeps within each population. We 149 289 B, respectively. Only 16 common both populations, suggesting primarily targeted Key related functions such as photosynthesis, motility, ion transport highlighted. Conclusions This work provides population genomics perspective on spring cyanobacterial Taiwan. Beyond advancing understanding microbial evolution, collected sequences generated provide valuable materials future development utilization biological resources.

Язык: Английский

Процитировано

0