Introduction

Alphasatellitidae is a family of replication-associated protein (Rep)-expressing circular, single-stranded DNA molecules (~1–1.4 kb) that have commonly been found in association with some members of the families Geminiviridae (viruses in the genera Begomovirus and Mastrevirus) [14] and Nanoviridae [12]. Similar molecules have also been found associated with coconut foliar decay virus [4] (family Metaxyviridae, genus Cofodevirus) [13]. Alphasatellites are unable to trans-replicate the bona fide genome components of these ‘helper viruses’ or vice versa, but they do rely on them for encapsidation, movement, and vector transmission [1].

Since the establishment of the family Alphasatellitidae in 2018 [1], various new alphasatellites have been identified, and here, we provide a taxonomic update. The update includes: (1) the establishment of a new subfamily, Petromoalphasatellitinae; (2) reassignment of existing family members and assignment of new members to the subfamily Petromoalphasatellitinae; (3) the establishment of three new genera and 14 new species in the subfamily Geminialphasatellitinae; and (4) the establishment of five new species in the subfamily Nanoalphasatellitinae.

Geminialphasatellitinae

A genus demarcation threshold of 70% and a species demarcation threshold of 88% based on genome-wide pairwise identity values were recommended by Briddon et al. [1] (Fig. 1). Accordingly, the members were classified into four genera (Ageyesisatellite, Clecrusatellite, Colecusatellite, and Gosmusatellite) and a total of 41 species. In the last couple of years, various geminialphasatellites have been identified, and using the taxonomic guidelines outlined by Briddon et al. [1], we established three new genera (Draflysatellite, Somasatellite, and Whiflysatellite) to accommodate the two previously unassigned species (Dragonfly associated alphasatellite and Whitefly associated Guatemala alphasatellite 1) and one new species (Sorghum mastrevirus associated alphasatellite). In addition to these, we established 12 new species in the genera Clecrusatellite (n = 7), Colecusatellite (n = 2), and Gosmusatellite (n = 3). The details of the new taxa are provided in Table 1. With all the new geminialphasatellites being identified, we reanalysed the distribution of pairwise identity values for 960 complete sequences with intact Rep open reading frames using SDT v1.2 [7] and determined that the 88% species demarcation threshold is still a valid criterion for their classification (Fig. 1).

Fig. 1
figure 1

Distribution of pairwise identity values of complete sequences with intact Rep ORFs of members of the subfamilies Geminialphasatellitinae (n = 960), Nanoalphasatellitinae (n = 104), and Petromoalphasatellitinae (n = 28), determined using SDT v1.2 [7]

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Table 1 Summary of the genera and species in the subfamilies Geminialphasatellitinae, Nanoalphasatellitinae, and Petromoalphasatellitinae
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Nanoalphasatellitinae

A genus demarcation threshold of 67% and a species demarcation threshold of 80% based on genome-wide pairwise identity values were recommended previously by Briddon et al. [1]. This resulted in the original creation of 19 species, which were assigned to seven genera (Babusatellite, Clostunsatellite, Fabenesatellite, Milvetsatellite, Mivedwarsatellite, Sophoyesatellite, and Subclovsatellite). The major change in this subfamily is the reassignment of the genus Babusatellite to the subfamily Petromoalphasatellitinae. We also established five new species in the genera Mivedwarsatellite (n = 3), Sophoyesatellite (n = 1), and Subclovsatellite (n = 1). To verify that, with the reassignment of Babusatellite to the subfamily Petromoalphasatellitinae, the species demarcation threshold of 80% is still valid, we reanalysed the distribution of pairwise identity values for 104 complete nanoalphasatellite sequences with intact Rep open reading frames using SDT v1.2 [7] and confirmed the species demarcation threshold (Fig. 1).

Petromoalphasatellitinae

In 2018, novel types of single-stranded DNA molecules comprising the genome of coconut foliar decay virus [4] (family Metaxyviridae) were identified. The virus was found to affect only coconut palm (Cocos nucifera) and is restricted to the Vanuatu Archipelago [8, 9]. Nine different alphasatellites are associated with coconut foliar decay virus. Our analysis of these alphasatellites revealed that, based on a species demarcation threshold of 81% sequence identity, they can be classified in several distinct species (Fig. 1). Applying a genus demarcation threshold of 68% sequence identity among members, three new genera, Cocosatellite (Coco for coconut), Coprasatellite (Copra for coconut meat), and Kobbarisatellite (Kobbari is an Indian dish from coconut meat) were established. Five of the seven alphasatellite species were assigned to the genus Cocosatellite, one to the genus Coprasatellite, and one to the genus Kobbarisatellite (Table 1).

In addition to the creation of these three genera, we reassigned the genus Babusatellite to the new subfamily Petromoalphasatellitinae, as these alphasatellites collectively associate with viruses that infect perennial tropical monocotyledonous plants. Moreover, their respective size range is between those of the members of the subfamilies Geminialphasatellitinae and Nanoalphasatellitinae. Finally, phylogenetic analysis clearly supports inclusion of the species of the genus Babusatellite in the same subfamily along with the species of the newly established genera Cocosatellite, Coprasatellite, and Kobbarisatellite (Fig. 2). The distribution of the pairwise identity values for the 28 petromoalphasatellites is shown in Fig. 1.

Fig. 2
figure 2

Maximum-likelihood phylogenetic tree constructed from a MUSCLE [3] sequence alignment of representative alphasatellites using PHYML [5] with the GTR+I+G4 nucleotide substitution model (determined to be the best-fitting model by jModelTest [2]). The tree shows support for the proposed establishment of the new subfamily Petromoalphasatellitinae as well as support for the reassignment of the viruses in the genus Babuvirus. Branches with less than 60% bootstrap support have been collapsed using TreeGraph2 [11]. The tree was visualized in iToL v6 [6].

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Based on the phylogenetic analysis coupled with pairwise comparisons, we moved three species (Banana bunchy top alphasatellite 2, Banana bunchy top alphasatellite 3, and Cardamom bushy dwarf alphasatellite) from the genus Babusatellite to a new genus, Muscarsatellite (Muscar from Musa and Elettaria cardamomum). A summary of the genera and species is provided in Table 1.

For the classification of new petromoalphasatellites, we recommend similar steps to those outlined by Briddon et al. [1]. To resolve conflict in cases where (1) a complete petromoalphasatellite sequence shares ≥81% pairwise identity with sequences of members of two different species or (2) a complete petromoalphasatellite sequence shares ≥81% pairwise identity with sequences of one or more members of a particular species while sharing <81% identity with the sequences of the majority of the members of that particular species:

  1. (1)

    The new petromoalphasatellite should be assigned to the species whose members share with it the highest pairwise sequence identity.

  2. (2)

    The petromoalphasatellite should be classified as belonging to any species in which it shares ≥81% pairwise sequence identity with any existing member of that species, even if it has <81% pairwise sequence identity to other members of that species.

Concluding remarks

As more sequence data become available, more changes to Alphasatellitidae taxonomy will certainly occur. We would also like to inform the Alphasatellitidae research community that a standardized binomial species nomenclature, consisting of the genus name and a free-form species epithet, has been ratified by the International Committee on Taxonomy of Viruses (ICTV) [10]. This needs to be adopted for currently established species in the family Alphasatellitidae by the year 2023. Thus, we encourage the community to engage with the ICTV Geminiviridae and Tolecusatellitidae Study Group and the Nanoviridae Study Group to determine the binomial names for current and new species in the family Alphasatellitidae.