Sequencing of Tuta absoluta genome to develop SNP genotyping assays for species identification

Abstract

Tuta absoluta is one of the most devastating pests of fresh market and processing tomatoes. Native to South America, its detection was confined to that continent until 2006 when it was identified in Spain. It has now spread to almost every continent, threatening countries whose economies rely heavily on tomatoes. This insect causes damage to all developmental stages of its host plant, leading to crop losses as high as 80 to 100%. Although T. absoluta has yet to be found in the U.S. and China, which makes up a large portion of the tomato production in the world, computer models project a high likelihood of invasion. To halt the continued spread of T. absoluta and limit economic loss associated with tomato supply chain, it is necessary to develop accurate and efficient methods to identify T. absoluta and strengthen surveillance programs. Current identification of T. absoluta relies on examination of morphology and assessment of host plant damage, which are difficult to differentiate from that of native tomato pests. To address this need, we sequenced the genomes of T. absoluta and two closely related Gelechiidae, Keiferia lycopersicella, and Phthorimaea operculella, and developed a bioinformatic pipeline to design a panel of 21 SNP markers for species identification. The accuracy of the SNP panel was validated in a multiplex format using the iPLEX chemistry of Agena MassARRAY system. Finally, the new T. absoluta genomic resources we generated can be leveraged to study T. absoluta biology and develop species-specific management strategies. Key Message  Surveillance and identification of Tuta absoluta are challenging because it is morphologically similar to closely related species, e.g. Keiferia lycopersicella and Phthorimaea operculella.  We generated new genomic sequences for these three species and identified single nucleotide polymorphisms (SNPs) to facilitate species identification.  We validated a multiplex genotyping panel of 21 SNPs using the iPLEX MassARRAY platform and confirmed its accuracy for species identification.  We generated new molecular tools and genome resources to aid Tuta absoluta management. leaves, where the larvae will emerge from eggs and begin mining host tissues. Larvae can also enter the stems through the buds, and feed within the tomato fruit, leaving them unmarketable. Its distribution was largely confined to South America until it was first detected in Spain in 2006 (Desneux et al. 2010; Guillemaud et al. 2015). Since then T. absoluta has spread rapidly and is now

EYES ABSENT and TIMELESS integrate photoperiodic and temperature cues to regulate seasonal physiology inDrosophila

“…A pool of ten individuals per fly strain was used to extract genomic DNA as described in (10). The tim region containing the polymorphic site was amplified and sequenced using the following forward and reverse primers tim (F): 5’-GTGGTTGCGTAATGCCCTGGAAGA-3’ and tim (R): 5’-TCACCTCCTGCAAAGTGGCC-3’.…”

Tuta absoluta(Meyrick) (Lepidoptera: Gelechiidae): An Invasive Insect Pest Threatening the World Tomato Production

“…Pupa is obtect with greenish coloration at first, turning to chestnut brown and dark brown near adult emergence [8] (Figure 2). Tabuloc et al [10] studies the genome of T. absoluta to generate and design a panel of 21 SNP markers for the species identification instead of depending only on morphological identification and symptoms of damage on the host plants.…”

Predation and reproduction of the generalist predator Nabis pseudoferus preying on Tuta absoluta

“…The South American tomato pinworm, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), is a major invasive pest of tomato (Biondi et al, 2018), and also attacks other solanaceous crops and weeds (Cherif et al, 2019; Sylla et al, 2019). Since 2006, this pest has been increasingly reported in most of Europe, Africa, and Asia (Campos et al, 2017; Mansour et al, 2018; Santana et al, 2019; Han et al, 2019a,b), and it is currently threatening two major tomato producer countries, USA and China (Tabuloc et al, 2019; Verheggen & Fontus, 2019; Han et al, 2019b). In Iran, this pest was initially detected in November 2010 and then quickly invaded all provinces within just 13 months (Javadi Emamzadeh & Cheraghian, 2013; Han et al, 2019a).…”