Characterization of nematode mitochondrial genomes.

Abstract

This chapter presents procedures on polymerase chain reaction (PCR) amplification, protocols for PCR, cloning and sequencing, and mitochondrial genome annotation and gene identification for the characterization of nematodes.

Report of the Texas peanut root-knot nematode, Meloidogyne haplanaria (Tylenchida: Meloidogynidae) from American pitcher plants (Sarracenia sp.) in California

“…DNA extraction and PCR protocols were as described by Janssen et al (2016) and Subbotin (2021a). The following primer sets were used in this study: D2A (5′-ACA AGT ACC GTG AGG GAA AGT TG-3′) and D3B (5′-TCG GAA GGA ACC AGC TAC TA-3′) amplifying the D2-D3 expansion segments of 28S rRNA gene, TW81 (5′-GTT TCC GTA GGT GAA CCT GC-3′) and AB28 (5′-ATA TGC TTA AGT TCA GCG GGT-3′) amplifying the ITS rRNA gene, NAD5F2 (5′ -TAT TTT TTG TTT GAG ATA TAT TAG-3′) and NAD5R1 (5′ -CGT GAA TCT TGA TTT TCC ATT TTT-3′) amplifying the partial mitochondrial nad5 gene, TRANAH (5′ -TGA ATT TTT TAT TGT GAT TAA-3′) and MRH106 (5′-AAT TTC TAA AGA CTT TTC TTA GT-3′) amplifying the partial mitochondrial l-rRNA gene, J3 (5′-TTT TTT GGG CAT CCT GAG GTT TAT-3′) and J4.5 (5′ -TAA AGA AAG AAC ATA ATG AAA ATG-3′) amplifying the partial mitochondrial COI gene (Humphreys-Pereira et al, 2021;Subbotin, 2021a). The new sequences for each gene were aligned using ClustalX 1.83 with their corresponding published gene sequences of M. haplanaria and other root-knot nematode species (Alvarez-Ortega et al, 2019;Georgi and Abbott, 1998;Joseph et al, 2016;Khanal et al, 2016;Powers et al, 2005;Ye et al, 2019 and others).…”