Comparative Genome Analysis of ‘Candidatus Phytoplasma luffae’ Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution

AbstractPhytoplasmas are insect-transmitted plant pathogens that cause substantial losses in agriculture. In addition to economic impact, phytoplasmas induce distinct disease symptoms in infected plants, thus attracting attention for research on molecular plant-microbe interactions and plant developmental processes. Due to the difficulty of establishing an axenic culture of these bacteria, culture-independent genome characterization is a crucial tool for phytoplasma research. However, phytoplasma genomes have strong nucleotide composition biases and are repetitive, which make it challenging to produce complete assemblies. In this study, we utilized Illumina and Oxford Nanopore sequencing technologies to obtain the complete genome sequence of ‘Candidatus Phytoplasma luffae’ strain NCHU2019 that is associated with witches’ broom disease of loofah (Luffa aegyptiaca) in Taiwan. The fully assembled circular chromosome is 769 kb in size and is the first representative genome sequence of group 16SrVIII phytoplasmas. Comparative analysis with other phytoplasmas revealed that NCHU2019 has an exceptionally repetitive genome, possessing a pair of 75 kb repeats and at least 13 potential mobile units (PMUs) that account for ∼25% of its chromosome. This level of genome repetitiveness is exceptional for bacteria, particularly among obligate pathogens with reduced genomes. Our genus-level analysis of PMUs demonstrated that these phytoplasma-specific mobile genetic elements can be classified into three major types that differ in gene organization and phylogenetic distribution. Notably, PMU abundance explains nearly 80% of the variance in phytoplasma genome sizes, a finding that provides a quantitative estimate for the importance of PMUs in phytoplasma genome variability. Finally, our investigation found that in addition to horizontal gene transfer, PMUs also contribute to intra-genomic duplications of effector genes, which may provide redundancy for neofunctionalization or subfunctionalization. Taken together, this work improves the taxon sampling for phytoplasma genome research and provides novel information regarding the roles of mobile genetic elements in phytoplasma evolution.

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Complete Genome Sequence of Streptococcus pneumoniae Strain Rx1, a Hex Mismatch Repair-Deficient Standard Transformation Recipient

Microbiology Resource Announcements ◽

10.1128/mra.00799-21 ◽

2021 ◽

Vol 10 (41) ◽

Author(s):

Anna Maria Cuppone ◽

Lorenzo Colombini ◽

Valeria Fox ◽

David Pinzauti ◽

Francesco Santoro ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Mismatch Repair ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Gc Content ◽

Open Reading Frames ◽

Circular Chromosome ◽

Content Type ◽

Sequencing Technologies

The complete genome sequence of Streptococcus pneumoniae strain Rx1, a Hex mismatch repair-deficient standard transformation recipient, was obtained by combining Nanopore and Illumina sequencing technologies. The genome consists of a 2.03-Mb circular chromosome, with 2,054 open reading frames and a GC content of 39.72%.

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An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome

BMC Genomics ◽

10.1186/1471-2164-7-282 ◽

2006 ◽

Vol 7 (1) ◽

Cited By ~ 11

Author(s):

Pierre M Durand ◽

Andries J Oelofse ◽

Theresa L Coetzer

Keyword(s):

Plasmodium Species ◽

Mobile Genetic Elements ◽

Nucleotide Composition ◽

Falciparum Genome ◽

Genetic Elements ◽

Potential Impact

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Complete Genome Sequence ofStreptococcus anginosusJ4211, a Clinical Isolate

Genome Announcements ◽

10.1128/genomea.01440-15 ◽

2015 ◽

Vol 3 (6) ◽

Cited By ~ 4

Author(s):

Maliha Rahman ◽

Scott V. Nguyen ◽

Kimberly A. McCullor ◽

Catherine J. King ◽

James H. Jorgensen ◽

...

Keyword(s):

Clinical Isolate ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Mobile Genetic Elements ◽

Human Pathogen ◽

Genetic Elements ◽

Streptococcus Anginosus ◽

Opportunistic Human Pathogen ◽

The Brain

Streptococcus anginosusis an opportunistic human pathogen that causes abscesses of the brain, liver, and other organs. Here, we announce the complete genome sequence of a clinically isolated strain ofS. anginosusJ4211. The genome sequence contains two prophages and multiple mobile genetic elements.

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Genome sequencing and analysis of the first complete genome ofLactobacillus kunkeeistrain MP2, anApis melliferagut isolate

PeerJ ◽

10.7717/peerj.1950 ◽

2016 ◽

Vol 4 ◽

pp. e1950 ◽

Cited By ~ 9

Author(s):

Freddy Asenjo ◽

Alejandro Olmos ◽

Patricia Henríquez-Piskulich ◽

Victor Polanco ◽

Patricia Aldea ◽

...

Keyword(s):

Honey Bee ◽

Genome Sequencing ◽

Honey Bees ◽

Complete Genome ◽

Mobile Genetic Elements ◽

Ecological Niches ◽

Circular Chromosome ◽

Unique Region ◽

Genetic Elements ◽

Unique Genes

Background.The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease ofFirmicutespopulations, such as theLactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain ofLactobacillus kunkeei(L. kunkeeistrain MP2) from the gut of Chilean honey bees.L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, theL. kunkeeigenetic background and perform a comparative genome analysis with otherLactobacillusspecies.Methods.L. kunkeeiMP2 was originally isolated from the guts of ChileanA. melliferaindividuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology.De novoassembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons betweenL. kunkeeiMP2 with otherL. kunkeei, andLactobacillusstrains were done using Roary.Results.The complete genome ofL. kunkeeiMP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16L. kunkeeistrains, identified 113 unique genes, most of them related to phage insertions. A large and unique region ofL. kunkeeiMP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with otherLactobacillusspecies, identified several unique genes ofL. kunkeeiMP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs).Discussion.The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability inL. kunkeei. Its versatility and ability to survive in different ecological niches (bee guts, flowers, fruits among others) could be given by its genetic capacity to change and adapt to different environments.L. kunkeeicould be a new source ofLactobacilluswith beneficial properties. Indeed,L. kunkeeiMP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.

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Genome Sequence of Brevibacillus brevis HK544, an Antimicrobial Bacterium Isolated from Soil in Daejeon, South Korea

Microbiology Resource Announcements ◽

10.1128/mra.00417-21 ◽

2021 ◽

Vol 10 (31) ◽

Author(s):

Bomin Kim ◽

Yeong Seok Kim ◽

Jae Woo Han ◽

Gyung Ja Choi ◽

Hun Kim

Keyword(s):

Antimicrobial Activity ◽

Phytophthora Infestans ◽

Genome Sequence ◽

Plant Pathogens ◽

Erwinia Amylovora ◽

Draft Genome ◽

Gc Content ◽

Circular Chromosome ◽

Content Type ◽

Brevibacillus Brevis

The Brevibacillus brevis HK544 strain, which was isolated from soil, exhibited antimicrobial activity against plant pathogens such as Botrytis cinerea , Phytophthora infestans , and Erwinia amylovora . Here, we report the draft genome sequence of the B. brevis HK544 strain, which consists of one circular chromosome of 6,486,246 bp with a GC content of 47.3%.

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Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies

Microbiology Resource Announcements ◽

10.1128/mra.01309-19 ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

Amine M. Boukerb ◽

Julien Schaeffer ◽

Joëlle Serghine ◽

Gregory Carrier ◽

Françoise S. Le Guyader ◽

...

Keyword(s):

Genome Sequence ◽

Illumina Sequencing ◽

Complete Genome Sequence ◽

Complete Genome ◽

Sequence Data ◽

Hybrid Approach ◽

Circular Chromosome ◽

Sequencing Technologies ◽

Oxford Nanopore

As determined by a hybrid approach combining Oxford Nanopore MinION and Illumina MiniSeq sequence data, Campylobacter armoricus strain CA639 harbored a circular chromosome of 1,688,169 bp with a G+C content of 28.47% and two plasmids named pCA639-1 and pCA639-2, with lengths of 51,123 and 28,139 bp, and G+C contents of 26.5% and 28.45%, respectively.

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Genome Sequence of Listeria monocytogenes Plasmid pLM-C-273 Carrying Genes Related to Stress Resistance

Genome Announcements ◽

10.1128/genomea.01125-16 ◽

2016 ◽

Vol 4 (5) ◽

Cited By ~ 2

Author(s):

Lindsay Liang ◽

Saravanamuttu Gnaneshan ◽

Rafael A. Garduño ◽

Gustavo V. Mallo

Keyword(s):

Antibiotic Resistance ◽

Listeria Monocytogenes ◽

Genome Sequence ◽

Resistance Genes ◽

Stress Resistance ◽

Clinical Sample ◽

Mobile Genetic Elements ◽

Metal Resistance ◽

Genetic Elements

Mobile genetic elements in bacteria, such as plasmids, act as important vectors for the transfer of antibiotic resistance, virulence, and metal resistance genes. Here, we report the genome sequence of a new plasmid pLM-C-273, identified in a Listeria monocytogenes strain isolated from a clinical sample in Ontario, Canada.

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Florfenicol Resistance in Enterobacteriaceae and Whole-Genome Sequence Analysis of Florfenicol-Resistant Leclercia adecarboxylata Strain R25

International Journal of Genomics ◽

10.1155/2019/9828504 ◽

2019 ◽

Vol 2019 ◽

pp. 1-10

Author(s):

Yuanyuan Ying ◽

Fei Wu ◽

Chongyang Wu ◽

Yi Jiang ◽

Min Yin ◽

...

Keyword(s):

Sequence Analysis ◽

Resistance Gene ◽

Genome Sequence ◽

Resistance Genes ◽

Mobile Genetic Elements ◽

Whole Genome Sequence ◽

Dilution Method ◽

Whole Genome ◽

Genome Sequence Analysis ◽

Genetic Elements

Due to inappropriate use, florfenicol resistance is becoming increasingly serious among animal respiratory tract and gut bacteria. To detect the florfenicol resistance mechanism among Enterobacteriaceae bacteria, 292 isolates from animal feces were examined. The agar dilution method was conducted to determine the minimum inhibitory concentration (MIC) for florfenicol, and polymerase chain reaction (PCR) was performed to detect florfenicol resistance genes. To further explore the molecular mechanism of florfenicol resistance, the whole-genome Leclercia adecarboxylata R25 was sequenced. Of the strains tested, 61.6% (180/292) were resistant to florfenicol, 64.4% (188/292) were positive for floR, and 1.0% (3/292) for cfr. The whole-genome sequence analysis of L. adecarboxylata R25 revealed that the floR gene is carried by a transposon and located on a plasmid (pLA-64). Seven other resistance genes are also encoded on pLA-64, all of which were found to be related to mobile genetic elements. The sequences sharing the greatest similarities to pLA-64 are the plasmids p02085-tetA of Citrobacter freundii and p234 and p388, both from Enterobacter cloacae. The resistance gene-related mobile genetic elements also share homologous sequences from different species or genera of bacteria. These findings indicate that floR mainly contributes to the high rate of florfenicol resistance among Enterobacteriaceae. The resistance gene-related mobile genetic elements encoded by pLA-64 may be transferred among bacteria of different species or genera, resulting in resistance dissemination.

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