Experimental design in intraspecific organelle DNA sequence studies II: Haplotype detection by Chemical Cleavage of Mismatch (CCM) using SYBR Green II staining

STONEBERG HOLT, Sierra Dawn, Lucie HOROVÁ a Petr BUREŠ. Experimental design in intraspecific organelle DNA sequence studies II: Haplotype detection by Chemical Cleavage of Mismatch (CCM) using SYBR Green II staining. Taxon. Vienna: International Assoc. for Plant Taxonomy, 2007, roč. 56, č. 2, s. 509-515. ISSN 0040-0262.

Základní údaje

• Originální název: Experimental design in intraspecific organelle DNA sequence studies II: Haplotype detection by Chemical Cleavage of Mismatch (CCM) using SYBR Green II staining
• Název česky: Experimental design in intraspecific organelle DNA sequence studies II: Haplotype detection by Chemical Cleavage of Mismatch (CCM) using SYBR Green II staining
• Autoři: STONEBERG HOLT, Sierra Dawn (840 Spojené státy), Lucie HOROVÁ (203 Česká republika) a Petr BUREŠ (203 Česká republika, garant).
• Vydání: Taxon, Vienna, International Assoc. for Plant Taxonomy, 2007, 0040-0262.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Obor: 10600 1.6 Biological sciences
• Stát vydavatele: Rakousko
• Utajení: není předmětem státního či obchodního tajemství
• Impakt faktor: Impact factor: 2.524
• Kód RIV: RIV/00216224:14310/07:00022322
• Organizační jednotka: Přírodovědecká fakulta
• UT WoS: 000244825300015
• Klíčová slova anglicky: chemical cleavage of mismatch (CCM); cpDNA; heteroduplex analysis (HA); intraspecific sequence studies; phylogeography; SYBR Green II staining
• Štítky: cpDNA, heteroduplex analysis (HA), intraspecific sequence studies, phylogeography, SYBR Green II staining
• Příznaky: Mezinárodní význam, Recenzováno

Anotace

Studies of organelle DNA sequence at low taxonomic levels present a researcher with specific experimental design challenges. Such studies require sampling numerous individuals, many of which share identical haplotypes. The process is often limited by the time and money required for DNA sequencing. A number of screening techniques have been devised to combat this limitation, but many have not found wide-spread use in botany. An ideal screening technique would be fast, easy, safe, inexpensive, detect 100% of mutations, be suitable for DNA fragments of about 1 kb, and not require complex equipment. This paper compares the heteroduplex analysis (HA) and chemical cleavage of mismatch (CCM) methods for detecting known point mutations and a deletion in a 1 kb region of non-coding cpDNA from the Poa pratensis agg. A new CCM visualization method, staining with SYBR Green II, was tested. CCM is a powerful tool for discovering different haplotypes in DNA sequence studies at low taxonomic levels. It is quicker and less expensive than sequencing each sample. Compared to HA, CCM is much more sensitive and delivers results in a shorter time, although it is more expensive and considerably more labor intensive. Staining with SYBR Green II allows CCM to be effectively implemented in laboratories with limited access to automated sequencing equipment.

Anotace česky

Studies of organelle DNA sequence at low taxonomic levels present a researcher with specific experimental design challenges. Such studies require sampling numerous individuals, many of which share identical haplotypes. The process is often limited by the time and money required for DNA sequencing. A number of screening techniques have been devised to combat this limitation, but many have not found wide-spread use in botany. An ideal screening technique would be fast, easy, safe, inexpensive, detect 100% of mutations, be suitable for DNA fragments of about 1 kb, and not require complex equipment. This paper compares the heteroduplex analysis (HA) and chemical cleavage of mismatch (CCM) methods for detecting known point mutations and a deletion in a 1 kb region of non-coding cpDNA from the Poa pratensis agg. A new CCM visualization method, staining with SYBR Green II, was tested. CCM is a powerful tool for discovering different haplotypes in DNA sequence studies at low taxonomic levels. It is quicker and less expensive than sequencing each sample. Compared to HA, CCM is much more sensitive and delivers results in a shorter time, although it is more expensive and considerably more labor intensive. Staining with SYBR Green II allows CCM to be effectively implemented in laboratories with limited access to automated sequencing equipment.

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