Mitochondrial DNA polymorphisms in Phytophthora infestans: New haplotypes are identified and re-defined by PCR

Yang, Zhihui; Qi, Ming-Xing; Qin, Yuxuan; Zhu, Jiehua; Xiumei, Gui; Bu, Tao; Xu, Xiao; Zhang, Fuguang

doi:10.1016/j.mimet.2013.08.001

Cited by 6 publications

(10 citation statements)

References 16 publications

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“…infestans isolates in orf32 to cox1 , cox1 to atp9 (same as P4 locus of [37]), atp9 to nad9 and cob to atp1 ; our locus 3 ( cox1 to nad9 ) spanned two of these regions and the SNPs they had reported were also observed in the isolates we examined. Yang et al [41] observed differing numbers of the 36 bp repeat between orf79 and cox2 and proposed changing haplotype naming to include an "R" with a subscript denoting the number of times the repeat was present (1 to 3 times). This convention was not followed in our current naming system as it does not take into account SNPs and indels in other loci that were examined.…”

Section: Discussionmentioning

confidence: 99%

“…Griffith and Shaw [37] simplified this analysis by developing a PCR -RFLP based technique for the specific regions of the mitochondrial genomes associated with haplotype classification (labelled as P1 through P4). While these remain the primary criteria for haplotype classification, additional analysis using a combination of Southern analysis, PCR-RFLP or DNA sequence analysis has been done [7], [38], [39], [40], [41], [42]. The identification of additional polymorphisms among mitochondrial haplotypes from these studies indicates that the current haplotype classification scheme should be further expanded to improve the number of markers available for population studies.…”

Section: Introductionmentioning

confidence: 99%

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Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs

et al. 2019

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In many parts of the world the damaging potato late blight pathogen, Phytophthora infestans, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 P. infestans isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of P. infestans.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs

et al. 2019

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“…Mitochondrial barcoding genes have been shown to be a valuable addition to the taxonomic resources of the oomycetes45. Especially in Phytophthora , mitochondrial variation, exhibiting both inter- and intraspecific variation46, has previously been used to trace the spread of the different mitochondrial haplotypes4748, and as a marker for examining the population structure of historical samples of P. infestans 252627.…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans

Makkonen

Vesterbacka

Martin

et al. 2016

Sci Rep

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The genus Aphanomyces (Saprolegniales, Oomycetes) includes species with a variety of ecologies from saprotrophs to plant and animal parasites. Two important species in this genus are A. astaci, the cause of crayfish plague and its close relative, A. invadans, which causes the epizootic ulcerative syndrome on fish. In this study, we have assembled and annotated the mitochondrial (mt) genomes of A. astaci and A. invadans from the whole genome shotgun sequence reads (PRJNA187372; PRJNA258292, respectively). The assembly was generated from A. astaci Pc-genotype strain APO3 and A. invadans strain NJM9701. The sizes of the mtDNAs were 49,489 bp and 49,061 bp for A. astaci and A. invadans, respectively. The species shared similar genetic content and organization encoding 35 proteins, two ribosomal RNAs, three putative open reading frames and 33 transfer RNAs of 19 amino acids for peptide synthesis. Both species also had a large inverted repeat region (LIR) of approximately 12 kb, the LIR contained large and small ribosomal RNAs and eight protein coding genes. These annotated mt genomes serve as a valuable genetic backbone for further development of diagnostic methods and phylogenetic and migration studies of the animal parasitic species of Aphanomyces.

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“…A total of 200–300 mg of mycelia were harvested for DNA extraction using Easy Pure Plant Genomic DNA Kit (Transgen, Beijing). The genomic DNA was amplified with the two sets of primers specified to the mitochondria of P. infestans (Yang et al, 2013 ). One set of the primers (i.e., Insertion-F and Insertion-R) amplifies the HVRi region of the mtDNA while another set (i.e., VNTR-F and VNTR-R) amplifies the HVRii region.…”

Section: Methodsmentioning

confidence: 99%

“…The mtDNA of P. infestans is ~40 kb in size with 53 predicted protein-coding genes (Avila-Adame et al, 2006 ; Patil et al, 2017 ), much smaller compared to its nuclear counterpart. In addition to the common features of uniparental inheritance (probably maternal inheritance), rapid mutation, and non-recombination (Avila-Adame et al, 2006 ), P. infestans mtDNA is easy to work with and has shown spatial heterogeneity of genetic polymorphism (Yang et al, 2013 ), making it a useful material to study the thermal adaptation of species.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial Genome Contributes to the Thermal Adaptation of the Oomycete Phytophthora infestans

et al. 2022

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As a vital element of climate change, elevated temperatures resulting from global warming present new challenges to natural and agricultural sustainability, such as ecological disease management. Mitochondria regulate the energy production of cells in responding to environmental fluctuation, but studying their contribution to the thermal adaptation of species is limited. This knowledge is needed to predict future disease epidemiology for ecology conservation and food security. Spatial distributions of the mitochondrial genome (mtDNA) in 405 Phytophthora infestans isolates originating from 15 locations were characterized. The contribution of MtDNA to thermal adaptation was evaluated by comparative analysis of mtDNA frequency and intrinsic growth rate, relative population differentiation in nuclear and mtDNA, and associations of mtDNA distribution with local geography climate conditions. Significant variation in frequency, intrinsic growth rate, and spatial distribution was detected in mtDNA. Population differentiation in mtDNA was significantly higher than that in the nuclear genome, and spatial distribution of mtDNA was strongly associated with local climatic conditions and geographic parameters, particularly air temperature, suggesting natural selection caused by a local temperature is the main driver of the adaptation. Dominant mtDNA grew faster than the less frequent mtDNA. Our results provide useful insights into the evolution of pathogens under global warming. Given its important role in biological functions and adaptation to local air temperature, mtDNA intervention has become an increasing necessity for future disease management. To secure ecological integrity and food production under global warming, a synergistic study on the interactive effect of changing temperature on various components of biological and ecological functions of mitochondria in an evolutionary frame is urgently needed.

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Mitochondrial DNA polymorphisms in Phytophthora infestans: New haplotypes are identified and re-defined by PCR

Cited by 6 publications

References 16 publications

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs

Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans

Mitochondrial Genome Contributes to the Thermal Adaptation of the Oomycete Phytophthora infestans

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