اسامه ناظم كاظم العيساوي

Endogenous viral elements of the Caulimoviridae family have been registered in different plant families as integrants. As one of the Asteraceae family, Taraxacum has been studied here to find endogenous pararetroviruses (EPRVs), including its three different agamospecies genomes. Three different agamospecies genomes of Taraxacum O978, A978, and S3, have been sequenced using nextgeneration sequencing, and then analyzed by bioinformatics techniques to search endogenous pararetroviral sequences within each examined genome. In the three genomic sequences, two caulimovirus-like sequences were found, one belonging to the Caulimovirus genus and is named as Caulimovirus-TOf, while the second was from the Florendovirus genus and was named ToffiV. The length of Caulimovirus-TOf was 6976 bp with three open reading frames encoding protein domains of cauli-D, peptidase-A3, RT-LTR, RVT, and RNaseH. Cauliflower mosaic virus and Caulimovirus-TOf shared peptidase, RT, and RH domains in 62% pairwise identity based on phylogeny analyses. The Florendovirus sequence has been reversely extracted with a length of 8131 bp and three open reading frames that encode movement protein, RT-LTR, RVT, and RNaseH. The O978 genome showed a high rate of EPRVs than the other two, indicating a very accessible genome and possible DNA marker based on widely fluctuating ratios of both integrants.

Eggplant has recently suffered a serious threat from a virus infection that causes mosaic and fruit deformation in eggplant fields in Iraq. The infection ratio has registered between 1-80% in examined eggplant fields. The Illumina platform has been applied to sequencing genomic DNA and total RNAseq of symptomatic samples in addition to healthy genomic DNA. The analysis of an entire RNA data revealed Eggplant mild leaf mottle virus (EMLMV) as a causal agent of the symptoms. The sequence of EMLMV was composed of 9280 nt encodes ten protein domains and the transcripts per million (TPM) was 9. Two endogenous pararetroviruses registered, Caulimovirus - SMe and SmelV belong to Caulimovirus and Florendovirus genera with lengths of 8233 and 6198 nt respectively, and both were found interestingly in the RNA transcripts. Phylogeny has revealed EMLMV and endogenous elements’ relations to related viruses.

Lettuce (Lactuca sativa L.) is widely planted and considered a valuable crop in Iraq. Next generation technology (NGS) and bioinformatics analysis were used to detect endogenous Para retroviruses in the genome of lettuce. In this study, two virus elements were identified, belong to two genera, Caulimovirus and Florendovirus, which were named Caulimovirus-LSa, and LsatiV respectively. The full length of Caulimovirus-LSa, and LsatiV were 7827, 7205 bp respectively. The Caulimovirus-LSa encodes seven coding domains; movement protein (MP), Cauli-AT, Cauli-DNA-bind, Peptidase-A3, RT-LTR, RNase-H and RT-RH. The LsatiV has five domains of RNaseH (RH), RT-RH, reverse transcriptase (RT and RVT) and movement protein (MP). Interestingly the sequence of LsatiV was inverted from 3' to 5', unlike Caulimovirus-LSa. Transcripts per million values (TPM) were 4.3 and 4.45 for Caulimovirus-LSa, and LsatiV respectively, which considered low in expression. However, the resemblance of almost 60% between Peptidase, RT and RH domains of Dahlia mosaic virus (DMV) and Caulimovirus-LSa probably indicate co-infection alongside pathogenic virus or viroid agents that might be caused symptoms in lettuce. The phylogenetic tree confirms the close relationships of both viruses to endogenous viruses from Taraxacum officinale that belong interestingly to the same family Astraceae.

The genus Aubrieta Adan. (Brassicaceae) is widely distributed and diverges across different elevations. We aimed to study aspects of the genome organization and components to understand evolution and differentiation. Endogenous pararetroviruses (EPRVs) were examined in whole-genome of four Aubrieta species using high-throughput DNA sequencing and bioinformatics. Two genera of caulimovirid sequences have been found in the four examined genomes, caulimoviruses, and florendoviruses with four members each named as Caulimovirus-AAn, Caulimovirus-AEu, Caulimovirus-AGr, Caulimovirus-ASc, AanaV, AeurV, AgraV, and AscaV. The full length of Caulimovirus-AAn, Caulimovirus-AEu, Caulimovirus-AGr, and Caulimovirus-ASc were 7579, 6726, 7223, and 6609 bp, while the florendoviruses, AanaV, AeurV, AgraV, and AscaV were 6675, 6888, 6702, and 6638 bp respectively. The integrants encode four coding domains; movement protein (MP), two domains of reverse transcriptase (RT and RVT), and RNaseH (RH), and except Caulimovirus- AEu, all caulimoviruses are inverted from 3' to 5', while the florendoviruses are arranged from 5' to 3'. Variable numbers of genome proportions and copies have been recorded for these integrants reporting A. eurobsens as more accessible genome in the case of florendoviruses, while caulimovirus-like sequence was most abundant in the genome of the A. anamasica. The genome of A. scardica was limited in EPRVs existence comparing to A. anamasica which having a good marker to separate these species. The phylogenetic tree confirms the close relationships of each group of the EPRVs as they are arranged next to their genus members.

Fig mosaic disease is caused by a complex of viruses and virus-like agents including Fig badnavirus-1 (FBV-1) and Fig mosaic virus (FMV), and both viruses have been found together in mixed infections (Jamous et al., 2020; Preising et al., 2021). Studies of FBV-1 in Iran and the USA indicate that the virus reduces the vigour of fig trees (Laney et al., 2012; Alishiri et al., 2016). The Iranian isolates have been segregated based on geographical origin into two groups and four subgroups while the American isolates grouped into three subgroups (Alishiri et al., 2018). The incidence of fig mosaic disease in Iraq has increased recently in commercial production but studies on the viruses are limited (Mohmmed et al., 2019). Symptomatic leaf samples, previously confirmed to be infected with FMV, were collected from fig trees in the Najaf region of Iraq (Figure 1). Infected leaves were cut into 0.25 cm2 squares and immersed in RNALater (× 5 volume) in microfuge tubes and sent to the DNA Link Inc. (Republic of Korea) for further processing. Total RNA was extracted and next generation sequencing (NGS) was used to sequence the transcriptome using the Novaseq6000 platform. The NGS platform generated total RNAseq data consisting of 39,933,818 short reads, 101 bases in length. All the RNA reads were paired and mapped against putative virus genomes using Geneious software (http://www. geneious.com/) (Kearse et al., 2012). In addition to the sequence of FMV, the FBV-1 sequence was mapped using FBV-1 Arkansas 1 (GenBank Accession No. JF411989.1) as a reference genome and 1,193 reads were assembled to produce a 7,140 bp consensus sequence.

Many attempts have been made to reduce or limit the economic damage caused by the fig mosaic virus to the growth of fig trees and their production from the fruits, in this study the disease in fig seedlings was controlled by aqueous extracts of licorice roots and garlic cloves, salicylic acid. experiments in the greenhouse showed that salicylic acid spraying treatments and aqueous extracts of licorice root and garlic plant cloves individually and twice on intact fig seedlings infected with the fig mosaic virus had a significant effect in reducing the severity of the virus and increasing plant growth indicators such as number of leaves, plant height, leaf content of chlorophyll and elements Nitrogen and phosphorous, and the interaction treatment between licorice extract and garlic cloves extract outperformed in achieving the lowest rate of infection severity, which reached 26.45%, compared to the control treatment, which amounted to 90.36%.

Plant virus related research in Cameroon, Ecuador and Iraq