High throughput sRNA sequencing revealed gene regulatory role mediated by pathogen-derived small RNAs during Sri Lankan Cassava Mosaic Virus infection in Cassava

Abstract

Small RNA (sRNA) mediated gene regulation during Sri Lankan Cassava Mosaic Virus (SLCMV) infection was studied from the Indian Cassava Cultivar H226. Our study generated high throughput sRNA dataset of 23.64 million reads from the control and SLCMV infected H226 leaf libraries. mes-miR9386 was detected as the most prominent miRNA expressed in control and infected leaf. Among the differentially expressed miRNAs, mes-miR156, mes- miR395 and mes-miR535a/b showed significant down regulation in the infected leaf. Genome-wide analysis of the three small RNA profiles revealed critical role of virus-derived small RNAs (vsRNAs) from the infected leaf tissues of H226. The vsRNAs were mapped to the bipartite SLCMV genome and high expression of siRNAs generated from the virus genomic region encoding AV1/AV2 genes in the infected leaf pointed towards the susceptibility of H226 cultivars to SLCMV. Furthermore, the sRNA reads mapped to the antisense strand of the SLCMV ORFs was higher than the sense strand. These vsRNAs were potential to target key host genes involved in virus interaction such as aldehyde dehydrogenase, ADP-ribosylation factor1 and ARF1-like GTP-binding proteins. The sRNAome-assisted analysis also revealed the origin of virus-encoded miRNAs from the SLCMV genome in the infected leaf. These virus-derived miRNAs were predicted to have hair-pin like secondary structures, and have different isoforms. Moreover, our study revealed that the pathogen sRNAs play a critical role in the infection process in H226 plants.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-023-03494-2.

Keywords: Cassava; H226; Sri Lankan Cassava Mosaic virus; Virus-derived small RNAs; miRNAs.

Fig. 1

Symptomatology and molecular detection of SLCMV infection. a Symptoms of SLCMV infection in H226 cassava plants. b Molecular screening of SLCMV infection using SLCMV coat protein-specific primers

Fig. 2

Functional categorization of small RNAs into different RNAs

Fig. 3

Statistics of small RNAs mapped to the host genome Manihot esculenta

Fig. 4

Differentially expressed miRNAs among control and SLCMV infected leaf tissues of H226

Fig. 5

a Small RNA reads mapped to the SLCMV bipartite genome A and B. b Virus- derived sRNAs mapped to the sense and antisense polarity of SLCMV DNA- A genome. c Virus- derived sRNAs mapped to the sense and antisense polarity of SLCMV DNA- B genome

Fig. 6

Length distribution of sRNAs mapped at the SLCMV A and SLCMV B genome. a SLCMV A mapped sRNA reads from H226I1, b SLCMV B mapped sRNA reads from H226I1. c SLCMV A mapped sRNA reads from H226I2, d SLCMV B mapped sRNA reads from H226I2

Fig. 7

Virus derived small RNAs reads mapped to different ORFs encoded in SLCMV genome A and B. a The read distribution of H226I1sRNAs mapped among the SLCMV ORFs. b The read distribution of H226I2 sRNAs mapped among the SLCMV ORFs. c Total sRNA reads of H226I1 distributed among the sense and antisense strands of SLCMV ORFs. d Total sRNA reads of H226I2 distributed among the sense and antisense strands of SLCMV ORFs

Fig. 8

Virus-derived miRNAs predicted from SLCMV genome

Fig. 9

Different isoforms and variants of v-miRNAs detected in the cassava small RNA library of SLCMV infected H226 leaves. a miRNA isoforms and variants detected from av1/av2 as sRNA13 and b av1/av2 as sRNA1. c The sequence variation detected at the av1/av2 as sRNA13 mapped regions of the different SLCMV isolates from cassava