Alfalfa leaf curl virus (ALCV), which causes severe disease symptoms in alfalfa (Medicago sativa L.) and is transmitted by the widespread aphid species, Aphis craccivora Koch, has been found throughout the Mediterranean basin as well as in Iran and Argentina. Here we reconstruct the evolutionary history of ALCV and attempt to determine whether the recent discovery and widespread detection of ALCV is attributable either to past diagnostic biases or to the emergence and global spread of the virus over the past few years. One hundred and twenty ALCV complete genome sequences recovered from ten countries were analyzed and four ALCV genotypes (ALCV-A, ALCV-B, ALCV-C, and ALCV-D) were clearly distinguished. We further confirm that ALCV isolates are highly recombinogenic and that recombination has been a major determinant in the origins of the various genotypes. Collectively, the sequence data support the hypothesis that, of all the analyzed locations, ALCV likely emerged and diversified in the Middle East before spreading to the western Mediterranean basin and Argentina.

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DNA sequencing is used by virtually all branches of biological research. Among the first advanced sequencing technologies, scientists were able to elucidate genetic information from any particular biological system using the Sanger sequencing method. Although Sanger sequencing generates high quality sequencing data, its limitations such as scalability, speed and resolution often preclude scientists from obtaining the essential information. To overcome these barriers, next generation sequencing technique (NGS) was introduced at the beginning of the 21 st century. This technique provided a highly efficient, rapid, and low cost DNA sequencing platform beyond the reach of the standard and traditional DNA sequencing technologies that developed in late 1970s. In 2009, NGS technologies began to be applied to several areas of plant virology including virus/viroid genome sequencing, discovery and detection, ecology, epidemiology and replication. It is expected that NGS plays very significant roles in many plant virology researches.