Understanding the molecular evolution and diversity changes of begomoviruses is crucial for predicting future outbreaks of the begomovirus disease in tomato crops. Thus, a molecular diversity study using high-throughput sequencing (HTS) was carried out on samples of infected tomato leaves collected between 2003 and 2016 from Central Brazil. DNA samples were subjected to rolling circle amplification and pooled in three batches, G1 (2003–2005, N = 107), G2 (2009–2011, N = 118), and G3 (2014–2016, N = 129) prior to HTS. Nineteen genome-sized geminivirus sequences were assembled, but only 17 were confirmed by PCR. In the G1 library, five begomoviruses and one capula-like virus were detected, but the number of identified viruses decreased to three begomoviruses in the G2 and G3 libraries. The bipartite begomovirus tomato severe rugose virus (ToSRV) and the monopartite tomato mottle leaf curl virus (ToMoLCV) were found to be the most prevalent begomoviruses in this survey. Our analyses revealed a significant increase in both relative abundance and genetic diversity of ToMoLCV from G1 to G3, and ToSRV from G1 to G2; however, both abundance and diversity decreased from G2 to G3. This suggests that ToMoLCV and ToSRV outcompeted other begomoviruses from G1 to G2 and that ToSRV was being outcompeted by ToMoLCV from G2 to G3. The possible evolutionary history of begomoviruses that were likely transferred from wild native plants and weeds to tomato crops after the introduction of the polyphagous vector Bemisia tabaci MEAM1 and the wide use of cultivars carrying the Ty-1 resistance gene are discussed, as well as the strengths and limitations of the use of HTS in identification and diversity analysis of begomoviruses.

了解begomoviruses的分子进化和多样性变化对于预测未来番茄作物中begomovirus疾病的爆发至关重要。因此，对2003年至2016年间从巴西中部收集的被感染番茄叶片样品进行了使用高通量测序（HTS）的分子多样性研究。对DNA样品进行滚环扩增，并在HTS之前分三批收集：G1（2003–2005，N = 107），G2（2009–2011，N = 118）和G3（2014–2016，N = 129）。 。组装了19个基因组大小的双生病毒序列，但通过PCR仅确认了17个。在G1库中，检测到5种begomovirus病毒和1种Capula-like病毒，但是在G2和G3库中，已鉴定的病毒数量减少到3种begomovirus。在本次调查中，二倍性begomovirus番茄严重皱纹病毒（ToSRV）和一分性番茄斑驳叶卷曲病毒（ToMoLCV）被发现是最流行的begomovirus。我们的分析表明，ToMoLCV从G1到G3以及ToSRV从G1到G2的相对丰度和遗传多样性都显着增加；但是，丰度和多样性都从G2下降到G3。这表明ToMoLCV和ToSRV在G1到G2方面胜过其他bemomovirus，而ToMoLCV从G2到G3则胜过ToSRV。引入多食性载体后，可能从野生天然植物和杂草转移到番茄作物的begomovirus的可能进化史 我们的分析表明，ToMoLCV从G1到G3以及ToSRV从G1到G2的相对丰度和遗传多样性都显着增加；但是，丰度和多样性都从G2下降到G3。这表明ToMoLCV和ToSRV在G1到G2方面胜过其他bemomovirus，而ToMoLCV从G2到G3则胜过ToSRV。引入多食性载体后，可能从野生天然植物和杂草转移到番茄作物的begomovirus的可能进化史 我们的分析表明，ToMoLCV从G1到G3以及ToSRV从G1到G2的相对丰度和遗传多样性都显着增加；但是，丰度和多样性都从G2下降到G3。这表明ToMoLCV和ToSRV在G1到G2方面胜过其他bemomovirus，而ToMoLCV从G2到G3则胜过ToSRV。引入多食性载体后，可能从野生天然植物和杂草转移到番茄作物的begomovirus的可能进化史 这表明ToMoLCV和ToSRV在G1到G2方面胜过其他bemomovirus，而ToMoLCV从G2到G3则胜过ToSRV。引入多食性载体后，可能从野生天然植物和杂草转移到番茄作物的begomovirus的可能进化史 这表明ToMoLCV和ToSRV在G1到G2方面胜过其他bemomovirus，而ToMoLCV从G2到G3则胜过ToSRV。引入多食性载体后，可能从野生天然植物和杂草转移到番茄作物的begomovirus的可能进化史烟粉虱 MEAM1和携带 1型 讨论了抗药性基因，以及使用HTS鉴定和筛选散发性病毒的多样性的优势和局限性。