Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda

The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas.

Aproximación a la filogenia de Spodoptera (Lepidoptera: Noctuidae) con el uso de un fragmento del gen de la citocromo oxidasa I (COI) / Approach to Spodoptera (Lepidoptera: Noctuidae) phylogeny based on the sequence of the cytocrhome oxydase I (COI) mitochondrial gene

The genus Spodoptera includes 30 species of moths considered important pests worldwide, with a great representation in the Western Hemisphere. In general, Noctuidae species have morphological similarities that have caused some difficulties for assertive species identification by conventional methods. The purpose of this work was to generate an approach to the genus phylogeny from several species of the genus Spodoptera and the species Bombyx mori as an out group, with the use of molecular tools. For this, a total of 102 S. frugiperda larvae were obtained at random in corn, cotton, rice, grass and sorghum, during late 2006 and early 2009, from Colombia. We took ADN samples from the larval posterior part and we analyzed a fragment of 451 base pairs of the mitochondrial gene cytochrome oxydase I (COI), to produce a maximum likelihood (ML) tree by using 62 sequences (29 Colombian haplotypes were used). Our results showed a great genetic differentiation (K2 distances) amongst S. frugiperda haplotypes from Colombia and the United States, condition supported by the estimators obtained for haplotype diversity and polymorphism. The obtained ML tree clustered most of the species with bootstrapping values from 73-99% in the interior branches; with low values also observed in some of the branches. In addition, this tree clustered two species of the Eastern hemisphere (S. littoralis and S. litura) and eight species of the Western hemisphere (S. androgea, S. dolichos, S. eridania, S. exigua, S. frugiperda, S. latifascia, S. ornithogalli and S. pulchella). In Colombia, S. frugiperda, S. ornithogalli and S. albula represent a group of species referred as “the Spodoptera complex” of cotton crops, and our work demonstrated that sequencing a fragment of the COI gene, allows researchers to differentiate the first two species, and thus it can be used as an alternative method to taxonomic keys based on morphology. Finally, the ML tree did not cluster S. frugiperda with S. ornithogalli, suggesting that both species do not share the same recent ancestral even though they coexist in cotton. We suggest sequencing other genes (mitochondrial and nuclear) to increase our understanding of this genus evolution.

En este trabajo se secuenció un fragmento de 451pb del gen mitocondrial de la citocromo oxidasa I (COI) en 62 secuencias del género Spodoptera y una secuencia de Bombix mori (grupo externo). Los resultados mostraron gran diferenciación genética (distancia K2) entre los haplotipos de Spodoptera frugiperda de Colombia y Estados Unidos, según los estimadores de diversidad haplotípica, diversidad y polimorfismo nucleotídicos calculados. Un árbol de ML agrupó las especies con valores de bootstrap entre 73-99% en las ramas internas. No obstante algunas ramas presentaron bajos valores de bootstrap. Este árbol formó un grupo constituido por las especies del hemisferio oriental (S. littoralis y S. litura) y también agrupó las especies localizadas en el hemisferio occidental (S. androgea, S. dolichos, S. eridania, S. exigua, S. frugiperda, S. latifascia, S. ornithogalli y S. pulchella). Esto demuestra que el árbol agrupó las especies con base en su origen geográfico. Contrariamente, el árbol no agrupó a S. frugiperda con S. ornithogalli, demostrando que a pesar de que ambas coexisten en el cultivo de algodón, no comparten un ancestro común reciente. En Colombia, estas especies forman parte del “complejo Spodoptera” del algodón, y nuestros resultados demuestran que la secuenciación de este gen permite diferenciarlas sin necesidad del uso de claves taxonómicas de sus estadios larvales. Este trabajo es una aproximación a la filogenia de este género, por lo cual la inclusión de más genes (mitocondriales y nucleares) son necesarios para futuros trabajos.

Haplotype identification within Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) corn and rice strains from Colombia

The fall army worm Spodoptera frugiperda (Smith) is a migratory important pest of corn, sorghum, rice, grass and bermudagrass in North and South America. This species has diverged into two genetically differentiated but morphologically identical strains, "the rice" and "the corn". They have been analyzed by sequencing the genes cytochrome oxydase I, II and ITS1 from populations from the United States and Brazil. However, no such studies were performed in Colombia. In here, we identified 43 haplotypes by sequencing a fragment of the COI gene from 102 individuals, of which 40 had already been identified as the "corn" and "rice" strains or to their hybrids from Tolima, and the rest were collected from corn, cotton, sorghum, grass and rice fields in other regions of Colombia. The corn strain haplotype H1 was the most frequently found in this country, representing the main target for FAW monitoring programs. AMOVA analysis confirmed the population structure between Colombian and North American S. frugiperda haplotypes (F ST = 0.76812, P < 0.001), but not within the different Colombian regions, suggesting high gene flow within the country. The ML trees obtained for Tolima and for Colombia as a whole did not generate clustering amongst S. frugiperda sequences, neither via host-plant association nor by geographical areas. The minimum spanning network for Colombia corroborated our finding that the haplotype H1 has the highest frequency in the country. Our data suggest that haplotype frequency determination will be useful in the establishment of a monitoring system for this species.

Host plant association and genetic differentiation of corn and rice strains of Spodoptera frugiperda Smith (Lepidoptera: Noctuidae) in Colombia

Spodoptera frugiperda (Smith) is a polifagous insect of major economic impact in the western hemisphere and exhibits two strains (i.e., corn and rice) that are morphologically identical but differ in ecology, genetics and physiology. In this work we identified these strains and their respective hybrids by using a PCR-RFLP of the COI gene and PCR of the tandem region FR. Moreover, we performed a population structure analysis by using 253 larvae from Tolima, a region where S. frugiperda is a pest on corn, rice, sorghum and cotton. Corn strain was found on 42 percent in corn, 34 percent in cotton, 19 percent in sorghum and 0.04 percent in rice and rice strain on 35 percent in corn, 0.06 percent in cotton, 0.06 percent in sorghum and 53 percent in rice, demonstrating that corn strain specificity is superior to rice strain. Hybrids between these strains were more abundant in corn. The distributions on their host plants reflect a population genetic differentiation in S. frugiperda with values of PhiPT (COI) = 0.31, P < 0.0001, PhiPT (FR) = 0.17, P < 0.0001 for all crops and PhiPT (COI) = 0.42, P < 0.01, PhiPT (FR) = 0.13, P < 0.01 for the sixteen sampled farms. The dendrograms showed two clusters representing both strains. The results obtained in this study suggest that the management of this insect must differ on each host plant, given the specialization that both strains present, particularly in corn and rice.

Use of RAPD in assessing the genetic variability in Spodoptera litura.

A polymerase chain reaction based assay to distinguish six different ecotypes of the Spodoptera litura, a sporadic insect pest and a predominant defoliator of various crops was carried out. A total of 40 random primers were screened to reveal the existence of polymorphism between the populations. Among them eight showed scorable banding patterns and three primers (OPA-01, OPA-05, OPM-01) exhibited distinguishable banding patterns. However, Chengalpattu and Chennai populations revealed their closed relatedness and Coimbatore population stood distantly from others.