Family-specific vs. Universal PCR primers for the study of mitochondrial DNA in plants
Апстракт
Mitochondrial genomes (mtDNAs or mitogenomes) of seed plants are characterized by a notoriously unstable organization on account of which available so-called universal or consensus primers may fail to fulfil their foreseen function-amplification of various mtDNA regions in a broad range of plant taxa. Thus, the primers developed for groups assumed to have similar organization of their mitogenomes, such as families, may facilitate a broader usage of more variable non-coding portions of these genomes in group members. Using in silico PCR method and six available complete mitogenomes of Fabaceae, it has been demonstrated that only three out of 36 published universal primer and three Medicago sativa-specific primer pairs that amplify various mtDNA regions are suitable for six representatives of the Fabaceae family upon minor modifications, and develop 21 Fabaceae-specific primer pairs for amplification of all 14 cis-splicing introns in genes of NADH subunits (nad genes) which represent the... most commonly used noncoding mtDNA regions in various studies in plants. Using the same method and six available complete mitogenomes of representatives of related families Cucurbitaceae, Euphorbiaceae and Rosaceae and a model plant, Arabidopsis thaliana, it has further been demonstrated that applicability of newly developed primer pairs for amplification of nad introns in more or less related taxa was dependent not only on species evolutionary distances but also on their genome sizes. A reported set of 24 primer pairs is a valuable resource which may facilitate a broader usage of mtDNA variability in future studies at both intra- and inter-specific levels in Fabaceae, which is the third largest family of flowering plants rarely studied at the mtDNA level, and in other more or less related taxa.
Кључне речи:
PCR primers / NADH dehydrogenase / mitochondrion / introns / in silico PCR method / FabaceaeИзвор:
Genetika-Belgrade, 2016, 48, 2, 777-798Издавач:
- Društvo genetičara Srbije, Beograd
Финансирање / пројекти:
- Молекуларни механизми одговора биљака на абиотички стрес-улога транскрипционих фактора и малих РНК и анализа генетичког диверзитета биљних култура од интереса за пољопривреду и биотехнологију (RS-MESTD-Basic Research (BR or ON)-173005)
- Republic of Serbia [680-00-132/2012-09/15]
- Republic of France [680-00-132/2012-09/15]
DOI: 10.2298/GENSR1602777A
ISSN: 0534-0012
WoS: 000389658100029
Scopus: 2-s2.0-84994545728
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - JOUR AU - Aleksić, Jelena M. PY - 2016 UR - https://imagine.imgge.bg.ac.rs/handle/123456789/959 AB - Mitochondrial genomes (mtDNAs or mitogenomes) of seed plants are characterized by a notoriously unstable organization on account of which available so-called universal or consensus primers may fail to fulfil their foreseen function-amplification of various mtDNA regions in a broad range of plant taxa. Thus, the primers developed for groups assumed to have similar organization of their mitogenomes, such as families, may facilitate a broader usage of more variable non-coding portions of these genomes in group members. Using in silico PCR method and six available complete mitogenomes of Fabaceae, it has been demonstrated that only three out of 36 published universal primer and three Medicago sativa-specific primer pairs that amplify various mtDNA regions are suitable for six representatives of the Fabaceae family upon minor modifications, and develop 21 Fabaceae-specific primer pairs for amplification of all 14 cis-splicing introns in genes of NADH subunits (nad genes) which represent the most commonly used noncoding mtDNA regions in various studies in plants. Using the same method and six available complete mitogenomes of representatives of related families Cucurbitaceae, Euphorbiaceae and Rosaceae and a model plant, Arabidopsis thaliana, it has further been demonstrated that applicability of newly developed primer pairs for amplification of nad introns in more or less related taxa was dependent not only on species evolutionary distances but also on their genome sizes. A reported set of 24 primer pairs is a valuable resource which may facilitate a broader usage of mtDNA variability in future studies at both intra- and inter-specific levels in Fabaceae, which is the third largest family of flowering plants rarely studied at the mtDNA level, and in other more or less related taxa. PB - Društvo genetičara Srbije, Beograd T2 - Genetika-Belgrade T1 - Family-specific vs. Universal PCR primers for the study of mitochondrial DNA in plants EP - 798 IS - 2 SP - 777 VL - 48 DO - 10.2298/GENSR1602777A ER -
@article{ author = "Aleksić, Jelena M.", year = "2016", abstract = "Mitochondrial genomes (mtDNAs or mitogenomes) of seed plants are characterized by a notoriously unstable organization on account of which available so-called universal or consensus primers may fail to fulfil their foreseen function-amplification of various mtDNA regions in a broad range of plant taxa. Thus, the primers developed for groups assumed to have similar organization of their mitogenomes, such as families, may facilitate a broader usage of more variable non-coding portions of these genomes in group members. Using in silico PCR method and six available complete mitogenomes of Fabaceae, it has been demonstrated that only three out of 36 published universal primer and three Medicago sativa-specific primer pairs that amplify various mtDNA regions are suitable for six representatives of the Fabaceae family upon minor modifications, and develop 21 Fabaceae-specific primer pairs for amplification of all 14 cis-splicing introns in genes of NADH subunits (nad genes) which represent the most commonly used noncoding mtDNA regions in various studies in plants. Using the same method and six available complete mitogenomes of representatives of related families Cucurbitaceae, Euphorbiaceae and Rosaceae and a model plant, Arabidopsis thaliana, it has further been demonstrated that applicability of newly developed primer pairs for amplification of nad introns in more or less related taxa was dependent not only on species evolutionary distances but also on their genome sizes. A reported set of 24 primer pairs is a valuable resource which may facilitate a broader usage of mtDNA variability in future studies at both intra- and inter-specific levels in Fabaceae, which is the third largest family of flowering plants rarely studied at the mtDNA level, and in other more or less related taxa.", publisher = "Društvo genetičara Srbije, Beograd", journal = "Genetika-Belgrade", title = "Family-specific vs. Universal PCR primers for the study of mitochondrial DNA in plants", pages = "798-777", number = "2", volume = "48", doi = "10.2298/GENSR1602777A" }
Aleksić, J. M.. (2016). Family-specific vs. Universal PCR primers for the study of mitochondrial DNA in plants. in Genetika-Belgrade Društvo genetičara Srbije, Beograd., 48(2), 777-798. https://doi.org/10.2298/GENSR1602777A
Aleksić JM. Family-specific vs. Universal PCR primers for the study of mitochondrial DNA in plants. in Genetika-Belgrade. 2016;48(2):777-798. doi:10.2298/GENSR1602777A .
Aleksić, Jelena M., "Family-specific vs. Universal PCR primers for the study of mitochondrial DNA in plants" in Genetika-Belgrade, 48, no. 2 (2016):777-798, https://doi.org/10.2298/GENSR1602777A . .