Gene decay in archaea

The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.

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Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes

PeerJ ◽

10.7717/peerj.10343 ◽

2020 ◽

Vol 8 ◽

pp. e10343

Author(s):

Pattsarun Cheawchanlertfa ◽

Sawannee Sutheeworapong ◽

Piroon Jenjaroenpun ◽

Thidathip Wongsurawat ◽

Intawat Nookaew ◽

...

Keyword(s):

Related Species ◽

Anaerobic Bacterium ◽

Comparative Genomic ◽

Whole Genome ◽

Circular Chromosome ◽

Closely Related Species ◽

Degrading Enzymes ◽

Cassava Pulp ◽

Pectinolytic Enzymes ◽

Genes Encoding

Background Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. Methods A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. Results Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).

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SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

International Journal of Molecular Sciences ◽

10.3390/ijms21249421 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9421

Author(s):

Lidia Skuza ◽

Ewa Filip ◽

Izabela Szućko ◽

Jan Bocianowski

Keyword(s):

Mitochondrial Dna ◽

Molecular Markers ◽

Related Species ◽

Economic Importance ◽

Closely Related Species ◽

Coding Sequences ◽

Coding Regions ◽

Genomic Regions ◽

Tribe Triticeae

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

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Analysis of Draft Genome Sequences of Two New Pantoea Strains Associated with Wheat Leaf Necrotic Tissues Caused by Xanthomonas translucens Reveals Distinct Species

Microbiology Resource Announcements ◽

10.1128/mra.00638-20 ◽

2020 ◽

Vol 9 (30) ◽

Author(s):

Alexandre Malette ◽

Renlin Xu ◽

Suzanne Gerdis ◽

Sylvia I. Chi ◽

Greg C. Daniels ◽

...

Keyword(s):

Draft Genome ◽

Distinct Species ◽

Whole Genome ◽

Genome Sequences ◽

Coding Sequences ◽

Content Type ◽

Wheat Leaf ◽

Xanthomonas Translucens ◽

Wheat Leaves

ABSTRACT We report whole-genome sequences of two new Pantoea strains (DOAB1048 and DOAB1050) isolated from necrotic wheat leaves caused by Xanthomonas translucens. The draft genome sequences of DOAB1048 and DOAB1050 consist of 52 and 57 scaffolds and have sizes of 4,795,525 bp and 4,962,883 bp with 4,418 and 4,517 coding sequences, respectively.

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Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480

Journal of Molecular Microbiology and Biotechnology ◽

10.1159/000471924 ◽

2017 ◽

Vol 27 (3) ◽

pp. 147-158 ◽

Cited By ~ 3

Author(s):

Liliana Godoy ◽

Evelyn Silva-Moreno ◽

Wladimir Mardones ◽

Darwin Guzman ◽

Francisco A. Cubillos ◽

...

Keyword(s):

Ethanol Production ◽

Survival Strategies ◽

Whole Genome ◽

Biotechnological Applications ◽

Genome Sequences ◽

Wine Production ◽

Brettanomyces Bruxellensis ◽

Biotechnological Potential ◽

Spoilage Yeast ◽

Genome Comparisons

Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to Brettanomyces bruxellensis contamination is currently a problem. This yeast causes a “horse sweat” flavor in wine, which is an undesired organoleptic attribute. To date, 6 B. bruxellensis annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited. In this article, we reassembled and reannotated the genome of B. bruxellensis LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of B. bruxellensis LAMAP2480 was analyzed in the context of spoilage yeast and potential as a biotechnological tool. In addition, we carried out an exploratory transcriptomic analysis of this strain grown in synthetic wine. Several genes related to stress tolerance, micronutrient acquisition, ethanol production, and lignocellulose assimilation were found. In conclusion, the analysis of the genome of B. bruxellensis LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast B. bruxellensis.

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Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species

Genes ◽

10.3390/genes10020113 ◽

2019 ◽

Vol 10 (2) ◽

pp. 113 ◽

Cited By ~ 2

Author(s):

Pavel Kroupin ◽

Victoria Kuznetsova ◽

Dmitry Romanov ◽

Alina Kocheshkova ◽

Gennady Karlov ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Related Species ◽

Evolutionary Divergence ◽

Whole Genome ◽

Target Genome ◽

Target Species ◽

Closely Related Species ◽

Chromosome Markers

Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.

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Draft Genome Sequences of Basidiomycetous Epiphytic Phylloplane Yeast Type Strains Dioszegia crocea JCM 2961 and Dioszegia aurantiaca JCM 2956

Microbiology Resource Announcements ◽

10.1128/mra.01727-18 ◽

2019 ◽

Vol 8 (26) ◽

Cited By ~ 1

Author(s):

Masako Takashima ◽

Ri-ichiroh Manabe ◽

Moriya Ohkuma

Keyword(s):

Related Species ◽

Draft Genome ◽

Genome Sequences ◽

Closely Related Species ◽

Content Type ◽

Phylloplane Yeasts ◽

Type Strains ◽

Plant Microbiome

We report the draft genome sequences of type strains for Dioszegia crocea and its closely related species Dioszegia aurantiaca, which should improve our understanding of the epiphytic phylloplane yeasts. These data will also have implications for the plant microbiome, since Dioszegia is considered a microbial “hub” taxon.

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Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes

Annals of Botany ◽

10.1093/aob/mcy220 ◽

2018 ◽

Vol 123 (5) ◽

pp. 857-865 ◽

Cited By ~ 5

Author(s):

Jacqueline Heckenhauer ◽

Ovidiu Paun ◽

Mark W Chase ◽

Peter S Ashton ◽

A S Kamariah ◽

...

Keyword(s):

Related Species ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Plastid Genome ◽

Gc Content ◽

Genome Sequences ◽

Closely Related Species ◽

Plastid Genomes ◽

Snp Data ◽

Phylogenomic Analyses

Abstract Background and Aims Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. Methods A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Key Results Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Conclusions Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

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Genome comparisons indicate recent transfer of wRi-like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

10.1101/135475 ◽

2017 ◽

Cited By ~ 4

Author(s):

William R. Conner ◽

Mark L. Blaxter ◽

Gianfranco Anfora ◽

Lino Ometto ◽

Omar Rota-Stabelli ◽

...

Keyword(s):

Relative Frequency ◽

Cytoplasmic Incompatibility ◽

Single Copy ◽

Sister Species ◽

Published Data ◽

Drosophila Suzukii ◽

Closely Related Species ◽

Coding Sequences ◽

Genome Comparisons ◽

Rates Of Molecular Evolution

AbstractWolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full-length copies of 703 of the 734 single-copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014-0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar - by at least a factor of 100 - to be plausible candidates for cladogenic transmission. These three wRi-like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria and Wolbachia.

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Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments

Genome Announcements ◽

10.1128/genomea.00223-18 ◽

2018 ◽

Vol 6 (15) ◽

pp. e00223-18 ◽

Cited By ~ 5

Author(s):

Hyein Jang ◽

Nicole Addy ◽

Laura Ewing ◽

Junia Jean-Gilles Beaubrun ◽

YouYoung Lee ◽

...

Keyword(s):

Draft Genome ◽

Whole Genome ◽

Cronobacter Sakazakii ◽

Plant Origin ◽

Genome Sequences ◽

Food Manufacturing ◽

Coding Sequences ◽

Content Type ◽

Gene Coding ◽

Manufacturing Environments

ABSTRACT Here, we present draft genome sequences of 29 Cronobacter sakazakii isolates obtained from foods of plant origin and dried-food manufacturing facilities. Assemblies and annotations resulted in genome sizes ranging from 4.3 to 4.5 Mb and 3,977 to 4,256 gene-coding sequences with G+C contents of ∼57.0%.

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