Molecular Characterization of a Begomovirus, α-Satellite, and β-Satellite Associated with Leaf Curl Disease of Parthenium hysterophorus in India

Reconstructing the biological invasion of noxious invasive weed Parthenium hysterophorus and invasion risk assessment in China

Invasive alien plants (IAPs) present a severe threat to native ecosystems and biodiversity. Comprehending the potential distribution patterns of these plant invaders and their responses to climate change is essential. Parthenium hysterophorus, native to the Americas, has become an aggressively invasive species since its introduction to China in the 1930s. This study aims to collect and reconstruct the historical occurrence and invasion of P. hysterophorus. Using the optimal MaxEnt model, the potential geographical distributions of P. hysterophorus were predicted based on screened species occurrences and environmental variables under the current and three future scenarios in the 2030s, 2050s, and 2070s (i.e., SSP1-2.6, SSP2-4.5, and SSP5-8.5), and the invasion risk of P. hysterophorus in Chinese cities, croplands, forests, and grasslands was assessed. The results show that: (1) The species initially invaded highly suitable areas and further spread to regions with non-analogous climate conditions. (2) Under the current climatic conditions, the overall potential distribution of P. hysterophorus is characterized by more in the southeast and less in the northwest. Climate variables, including mean annual temperature (bio1), precipitation in the wettest month (bio13), isothermality (bio3), and temperature seasonality (bio4), are the primary factors influencing its distribution. (3) The potential distribution of P. hysterophorus will expand further under future climate scenarios, particularly toward higher latitudes. (4) Forests and crop lands are the areas with the most serious potential invasion risk of P. hysterophorus. Therefore, we suggest that the government should strengthen the monitoring and management of P. hysterophorus to prevent its spread and protect agro-ecosystems and human habitats. Depending on the potential risk areas, measures such as quarantine, removal, and publicity should be taken to mitigate the threat of P. hysterophorus invasion and to raise awareness of P. hysterophorus invasion prevention.

Patterns of Genetic Diversity among Alphasatellites Infecting Gossypium Species

Alphasatellites are small single-stranded circular DNA molecules associated with geminiviruses and nanoviruses. In this study, a meta-analysis of known alphasatellites isolated from the genus Gossypium (cotton) over the last two decades was performed. The phylogenetic and pairwise sequence identity analysis suggested that cotton-infecting begomoviruses were associated with at least 12 different alphasatellites globally. Three out of twelve alphasatellite were associated with cotton leaf curl geminiviruses but were not isolated from cotton plants. The cotton leaf curl Multan alphasatellite, which was initially isolated from cotton, has now been reported in several plant species, including monocot plants such as sugarcane. Our recombination analysis suggested that four alphasatellites, namely cotton leaf curl Lucknow alphasatellites, cotton leaf curl Multan alphasatellites, Ageratum yellow vein Indian alphasatellites and Ageratum enation alphasatellites, evolved through recombination. Additionally, high genetic variability was detected among the cotton-infecting alphasatellites at the genome level. The nucleotide substitution rate for the replication protein of alphasatellites (alpha-Rep) was estimated to be relatively high (~1.56 × 10−3). However, unlike other begomoviruses and satellites, the first codon position of alpha-Rep rapidly changed compared to the second and third codon positions. This study highlights the biodiversity and recombination of alphasatellites associated with the leaf curl diseases of cotton crops.

Identification and Analysis of Potential Genes Regulated by an Alphasatellite (TYLCCNA) that Contribute to Host Resistance against Tomato Yellow Leaf Curl China Virus and Its Betasatellite (TYLCCNV/TYLCCNB) Infection in Nicotiana benthamiana

Recently, begomovirus/betasatellite disease complexes were found to be associated with alphasatellites, and their presence modulated disease symptoms and/or viral DNA accumulation in infected plants. However, the biological functions of alphasatellites during begomovirus/betasatellite infections remain unclear. Tomato yellow leaf curl China virus (TYLCCNV) associated with a betasatellite (TYLCCNB) is a widespread monopartite begomovirus in China. In the Yunnan province of China, the TYLCCNV/TYLCCNB disease complex is found in association with an alphasatellite (TYLCCNA). In this study, in order to explain the mechanisms underlying TYLCCNV/TYLCCNB infection and reductions in viral DNA accumulation caused by TYLCCNA, we analyzed the transcriptome profiles of Nicotiana benthamiana seedlings challenged by TYLCCNV/TYLCCNB or TYLCCNV/TYLCCNB/TYLCCNA using RNA sequencing. In total, 2272 and 1207 differentially expressed genes (DEGs) were identified to respond to TYLCCNV/TYLCCNB and TYLCCNV/TYLCCNB/TYLCCNA infections, respectively. Compared with the DEGs in the TYLCCNV/TYLCCNB-infected N. benthamiana seedlings, the number of DEGs in plants co-infected with TYLCCNV/TYLCCNB + TYLCCNA was significantly reduced. Additionally, 36 DEGs were identified to be regulated by TYLCCNA, six of which were further analyzed using the virus-induced gene silencing (VIGS) approach. Silencing of these six TYLCCNA responsive DEGs caused more severe disease symptoms and higher viral DNA accumulation levels, suggesting that TYLCCNA responsive DEGs may attenuate TYLCCNV/TYLCCNB infection.

Barcoding of Plant Viruses with Circular Single-Stranded DNA Based on Rolling Circle Amplification

The experience with a diagnostic technology based on rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) analyses, and direct or deep sequencing (Circomics) over the past 15 years is surveyed for the plant infecting geminiviruses, nanoviruses and associated satellite DNAs, which have had increasing impact on agricultural and horticultural losses due to global transportation and recombination-aided diversification. Current state methods for quarantine measures are described to identify individual DNA components with great accuracy and to recognize the crucial role of the molecular viral population structure as an important factor for sustainable plant protection.