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Numerous comparative genome analyses have revealed the wide extent of horizontal gene transfer (HGT) in living organisms, which contributes to their evolution and genetic diversity. Viruses play important roles in HGT. Endogenous viral elements (EVEs) are defined as viral DNA sequences present within the genomes of non-viral organisms. In eukaryotic cells, the majority of EVEs are derived from RNA viruses using reverse transcription. In contrast, endogenous non-retroviral elements (ENREs) are poorly studied. However, the increasing availability of genomic data and the rapid development of bioinformatics tools have enabled the identification of several ENREs in various eukaryotic organisms. To date, a small number of ENREs integrated into plant genomes have been identified. Of the known non-retroviruses, most identified ENREs are derived from double-strand (ds) RNA viruses, followed by single-strand (ss) DNA and ssRNA viruses. At least eight virus families have been identified. Of these, viruses in the family Partitiviridae are dominant, followed by viruses of the families Chrysoviridae and Geminiviridae. The identified ENREs have been primarily identified in eudicots, followed by monocots. In this review, we briefly discuss the current view on non-retroviral sequences integrated into plant genomes that are associated with plant-virus evolution and their possible roles in antiviral resistance.

Sour cherry (Prunus cerasus) in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170). De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing.

Prunus mume, belonging to the Prunus genus, is an Asian tree, and its common names are Chinese plum and Japanese plum. P. mume are cultivated for fruit production as well as ornamental purposes. In this study, we conducted de novo transcriptome assembly for two selected P. mume cultivars referred to as Takada and Wallyoung (commercially important cultivars for fruit production and ornamental trees, respectively) by RNA-sequencing. We obtained 9.14 GB and 9.48 GB sequence data from Takada and Wallyoung (NCBI accession numbers: SRX1187101 and SRX1187169), respectively. De novo transcriptome assembly identified 130,989 and 116,941 transcripts for Takada and Wallyoung, respectively. In addition, we identified 96,681 and 91,429 proteins from Takada and Wallyoung, respectively, by TransDecoder program. We performed BLASTP against the NCBI non-redundant (nr) datasets to annotate identified proteins. This study provides transcriptomes and proteomes for two different P. mume cultivars, which might be useful for comparative transcriptome analyses and assist development of genetic markers.

Peach (Prunus persica) is one of the most popular stone fruits worldwide. Next generation sequencing (NGS) has facilitated genome and transcriptome analyses of several stone fruit trees. In this study, we conducted de novo transcriptome analyses of two peach cultivars grown in Korea. Leaves of two cultivars, referred to as Jangtaek and Mibaek, were harvested and used for library preparation. The two prepared libraries were paired-end sequenced by the HiSeq2000 system. We obtained 8.14 GB and 9.62 GB sequence data from Jangtaek and Mibaek (NCBI accession numbers: SRS1056585 and SRS1056587), respectively. The Trinity program was used to assemble two transcriptomes de novo, resulting in 110,477 (Jangtaek) and 136,196 (Mibaek) transcripts. TransDecoder identified possible coding regions in assembled transcripts. The identified proteins were subjected to BLASTP search against NCBI's non-redundant database for functional annotation. This study provides transcriptome data for two peach cultivars, which might be useful for genetic marker development and comparative transcriptome analyses.

Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree. Apricot is native to Armenia and is currently cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. However, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars referred to as Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing. We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste (NCBI accession numbers: SRX1186946 and SRX1186893), respectively. De novo transcriptome assembly using Trinity identified 147,501 and 152,235 transcripts for Harcot and Ungarische Beste, respectively. Next, we identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste using the TransDecoder program. We performed BLASTP against an NCBI non-redundant (nr) dataset to annotate identified proteins. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq.

Plum is a globally grown stone fruit and can be divided into several species. In particular, the Prunus salicina, which is native to China, is widely grown in many fruit orchards in Korea and Japan, as well as the United States and Australia. The transcriptome data for Prunus salicina has not been reported to our knowledge. In this study, we performed de novo transcriptome assembly for two selected P. salicina cultivars referred to as Akihime and Formosa (commercially important plum cultivars in Korea) using next generation sequencing. We obtained a total of 9.04 GB and 8.68 GB raw data from Akihime and Formosa, respectively. De novo transcriptome assembly using Trinity revealed 155,169 and 160,186 transcripts for Akihime and Formosa. Next, we identified 121,278 and 116,544 proteins from Akihime and Formosa using TransDecoder. We performed BLASTP against the NCBI non-redundant (nr) dataset to annotate proteins. Taken together, this is the first transcriptome data for P. salicina to our knowledge.