Mitochondrial characteristics of the powdery mildew genus Erysiphe revealed an extraordinary evolution in protein-coding genes

Ji, Xiaobei; Tian, Ye; Liu, Wenbo; Lin, Chunhua; He, Fei; Yang, Jun; Miao, Weiguo; Li, Zhigang

doi:10.1016/j.ijbiomac.2023.123153

Cited by 6 publications

(4 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Gaps within the scaffolds were filled using LR_Gapcloser 25 . We then manually checked whether long reads aligned the bridging cross the gaps, or whether overlapping contig ends (>20 kb length and 99.9% sequence identity) existed.The mitochondrial genome was assembled independently by Mitochondrial Long-read Iterative Assembly (MLIA) pipeline 9 . The final polishing of the complete genome was performed again using Pilon v1.23 24 .…”

Section: Methodsmentioning

confidence: 99%

“…The Hi-C sequencing data were used to anchor and refined remained contigs. The mitochondrial (2024) 11:380 | https://doi.org/10.1038/s41597-024-03209-z www.nature.com/scientificdata www.nature.com/scientificdata/ genome was assembled independently by Mitochondrial Long-read Iterative Assembly (MLIA) pipeline 9 . The final polishing of the complete genome was performed.…”

Section: Background and Summarymentioning

confidence: 99%

See 1 more Smart Citation

First telomere-to-telomere gapless assembly of the rice blast fungus Pyricularia oryzae

Li,

Yang,

et al. 2024

Sci Data

Self Cite

View full text Add to dashboard Cite

Rice blast caused by Pyricularia oryzae (syn., Magnaporthe oryzae) was one of the most destructive diseases of rice throughout the world. Genome assembly was fundamental to genetic variation identification and critically impacted the understanding of its ability to overcome host resistance. Here, we report a gapless genome assembly of rice blast fungus P. oryzae strain P131 using PacBio, Illumina and high throughput chromatin conformation capture (Hi-C) sequencing data. This assembly contained seven complete chromosomes (43,237,743 bp) and a circular mitochondrial genome (34,866 bp). Approximately 14.31% of this assembly carried repeat sequences, significantly greater than its previous assembled version. This assembly had a 99.9% complement in BUSCO evaluation. A total of 14,982 genes protein-coding genes were predicted. In summary, we assembled the first telomere-to-telomere gapless genome of P. oryzae, which would be a valuable genome resource for future research on the genome evolution and host adaptation.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Background and Summarymentioning

confidence: 99%

First telomere-to-telomere gapless assembly of the rice blast fungus Pyricularia oryzae

Li,

Yang,

et al. 2024

Sci Data

Self Cite

View full text Add to dashboard Cite

show abstract

“…Mitogenome-related investigations across different species revealed a considerable diversity, allowing for a sturdy foundation for taxonomic clarity [ 3 ]. The high copy numbers and evolutionary rates of fungal mtDNFA make it an exceptional tool for evolutionary biology, taxonomy, and molecular phylogenetics [ 4 , 5 , 6 , 7 , 8 , 9 ]. Mitochondrial genomes possess distinct characteristics, such as a condensed size, constrained recombination rates, autonomous evolutionary path, and the abundance of analogous genes, which equip them with remarkable analytical capabilities when examining the subjects of population genetics and evolutionary biology [ 10 , 11 , 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative Mitogenomics Analysis Revealed Evolutionary Divergence among Neopestalotiopsis Species Complex (Fungi: Xylariales)

Huang,

Wang,

Huo

et al. 2024

IJMS

Self Cite

View full text Add to dashboard Cite

The genus Neopestalotiopsis consists of obligate parasites that cause ring spot, scab, and leaf blight diseases in higher plant species. We assembled the three complete mitogenomes for the guava fruit ring spot pathogen, Neopestalotiopsis cubana. The mitogenomes are circular, with sizes of 38,666 bp, 33,846 bp, and 32,593 bp. The comparative analyses with Pestalotiopsis fici showed that N. cubana differs greatly from it in the length of the mitogenomes and the number of introns. Moreover, they showed significant differences in the gene content and tRNAs. The two genera showed little difference in gene skewness and codon preference for core protein-coding genes (PCGs). We compared gene sequencing in the mitogenomes of the order Xylariales and found large-scale gene rearrangement events, such as gene translocations and the duplication of tRNAs. N. cubana shows a unique evolutionary position in the phylum Ascomycota constructed in phylogenetic analyses. We also found a more concentrated distribution of evolutionary pressures on the PCGs of Neopestalotiopsis in the phylum Ascomycota and that they are under little selective pressure compared to other species and are subjected to purifying selection. This study explores the evolutionary dynamics of the mitogenomes of Neopestalotiopsis and provides important support for genetic and taxonomic studies.

show abstract

“…They perform crucial functions in important biological processes, such as cellular senescence and apoptosis [2]. The mitochondrial genome is an effective tool for accurately identifying species across different biological taxa in molecular systematics and evolutionary biology, due to its small size and matrilineal mode of inheritance [3,4]. Currently, mitogenomes are widely used in molecular systematics and evolutionary biology [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae

Xu,

Zhu,

Tian

et al. 2024

Genes

View full text Add to dashboard Cite

Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea.

show abstract

Mitochondrial characteristics of the powdery mildew genus Erysiphe revealed an extraordinary evolution in protein-coding genes

Cited by 6 publications

References 53 publications

First telomere-to-telomere gapless assembly of the rice blast fungus Pyricularia oryzae

First telomere-to-telomere gapless assembly of the rice blast fungus Pyricularia oryzae

Comparative Mitogenomics Analysis Revealed Evolutionary Divergence among Neopestalotiopsis Species Complex (Fungi: Xylariales)

The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae

Contact Info

Product

Resources

About