Viroid-derived polynucleotides for modification of plants

(canceled)

3:

• The method of claim 1, wherein the composition is provided to a plant, plant tissue, or plant cell, or a processed product thereof, and wherein the eukaryote consumes or contacts the plant, plant tissue, or plant cell, or processed product thereof, whereby the effector is delivered to the eukaryote.

4:

• The method of claim 1, wherein (a) the ssRNA viroid sequence is a viroid genome or a derivative thereof or (b) the ssRNA viroid sequence is a viroid genome fragment or a derivative thereof.

5:

• The method of claim 1, wherein the ssRNA viroid sequence is a sequence of a viroid from the family Pospiviroidae or Avsunviroidae.

6:

• The method of claim 1, wherein the viroid is potato spindle tuber viroid (PSTVd) or eggplant latent viroid (ELVd).

7:

• The method of claim 1, wherein the ssRNA viroid sequence has at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NOs:51-54, SEQ ID NOs:65-66, SEQ ID NO:68, SEQ ID NO:75, SEQ ID NOs:77-79, SEQ ID NOs:84-96, SEQ ID NOs:98-107, SEQ ID NOs:123-124, SEQ ID NOs:126-132, SEQ ID NO:134, SEQ ID NOs:136-143, SEQ ID NOs:145-150, SEQ ID NOs:153-154, SEQ ID NO:159, SEQ ID NO:166, SEQ ID NO:168, SEQ ID NO:196, SEQ ID NO:242, SEQ ID NO:268, SEQ ID NO:274, SEQ ID NO:276, SEQ ID NO:289, SEQ ID NO:451, SEQ ID NOs:458-459, and SEQ ID NO:467.

8:

• The method of claim 1, wherein the ssRNA viroid sequence has at least 90% sequence identity to SEQ ID NO:51 or SEQ ID NO:50.

9:

• The method of claim 1, wherein the ssRNA viroid sequence does not contain a pathogenicity domain.

10:

• The method of claim 1, wherein the RNA sequence comprising or encoding the effector is not a viroid sequence and (a) has a biological effect on a plant or (b) has a biological effect on an animal or fungus that consumes or contacts the plant.

11:

• The method of claim 1, wherein the effector comprises or is encoded by an ssRNA sequence.

12:

• The method of claim 1, wherein the effector is an siRNA, miRNA, or pre-miRNA.

13:

• The method of claim 1, wherein the heterologous RNA sequence comprises coding RNA, non-coding RNA, or both coding and non-coding RNA.

14:

• The method of claim 1, wherein the effector comprises coding RNA, non-coding RNA, or both coding and non-coding RNA.

15:

• The method of claim 1 wherein the effector comprises non-coding RNA comprising at least one regulatory RNA or at least one interfering RNA that regulates a target gene or its transcript in a target cell.

16:

• The method of claim 15, wherein the target cell is selected from the group consisting of a plant cell, an animal cell, and a fungal cell.

17:

• The method of claim 15, wherein the effector modifies a trait, phenotype, or genotype in the target cell, optionally wherein the trait is pest resistance, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, or insect resistance.

20:

• The method of claim 1, wherein the recombinant polynucleotide lacks free ends and/or is circular.

21:

• The method of claim 1, wherein the composition is topically delivered to a plant a scion, or a rootstock, and wherein the topical delivery is spraying, leaf rubbing, soaking, coating, injecting, seed coating, or delivery through root uptake.

22:

• A composition comprising a recombinant polynucleotide comprising:
• (a) a single-stranded RNA (ssRNA) viroid sequence that is a viroid genome or a derivative thereof or a viroid genome fragment or a derivative thereof, and (b) a heterologous RNA sequence that is not a viroid sequence and comprises or encodes an effector.

23:

• The composition of claim 22, wherein the viroid genome is (a) a genome of a viroid from the family Pospiviroidae or Avsunviroidae, or (b) a genome of potato spindle tuber viroid (PSTVd) or eggplant latent viroid (ELVd).

24:

• The composition of claim 22, wherein the ssRNA viroid sequence has at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NOs:51-54, SEQ ID NOs:65-66, SEQ ID NO:68, SEQ ID NO:75, SEQ ID NOs:77-79, SEQ ID NOs:84-96, SEQ ID NOs:98-107, SEQ ID NOs:123-124, SEQ ID NOs:126-132, SEQ ID NO:134, SEQ ID NOs:136-143, SEQ ID NOs:145-150, SEQ ID NOs:153-154, SEQ ID NO:159, SEQ ID NO:166, SEQ ID NO:168, SEQ ID NO:196, SEQ ID NO:242, SEQ ID NO:268, SEQ ID NO:274, SEQ ID NO:276, SEQ ID NO:289, SEQ ID NO:451, SEQ ID NOs:458-459, and SEQ ID NO:467.

25:

• The composition of claim 22, wherein the ssRNA viroid sequence has at least 90% sequence identity to SEQ ID NO:51 or SEQ ID NO:50.

26:

• The composition of claim 22, wherein the effector comprises non-coding RNA comprising at least one regulatory RNA or at least one interfering RNA or at least one guide RNA that regulates or modifies a target gene or its transcript in a target cell, wherein the target cell is a plant cell, an animal cell, or a fungal cell.

27:

• The composition of claim 22, wherein the effector (a) modifies expression of a target gene in a eukaryotic cell;
• or (b) has a biological effect on a plant or on an animal or fungus that consumes or contacts the plant.

28:

• The composition of claim 22, wherein the composition is (a) formulated for delivery to a plant or to the environment in which the plant grows;
• or (b) formulated for delivery to an animal or fungus.