CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes

Abstract

Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.

Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes

“…Despite their ubiquity and abundance, ECVs remain largely neglected features during plant genome annotation because of a lack of dedicated tools for their proper annotation, hampering the development of paleovirology approaches. CAULIFINDER, a bioinformatics tool, was recently developed for the automated detection and annotation of ECVs in plant genomes [99], jointly with databanks that can be used to help with the classification of repetitive elements produced by standard repeat annotation pipelines. Use of CAULIFINDER should improve ECV annotation in plant genomes, foster comparative analyses across caulimovirid genera and their hosts, and characterize candidate functional ECVs.…”

Introduction of Plant Transposon Annotation for Beginners

“…Endogenous pararetroviruses (EPRVs) are present in the genomes of a wide range of plants [55,56], and they encode polyproteins that share a high sequence similarity with Ty3/Gypsy LTR retrotransposons; thus, EPRVs were frequently misannotated as Ty3/Gypsy LTR retrotransposons or were ignored. All EPRVs identified thus far lack LTRs [7,8], which brings difficulties in annotating these pararetroviral sequences and accurately defining their boundaries. Recently, the bioinformatics pipeline CAULIFINDER has been developed for the automatic annotation and classification of EPRVs in plant genomes [7].…”

“…All EPRVs identified thus far lack LTRs [7,8], which brings difficulties in annotating these pararetroviral sequences and accurately defining their boundaries. Recently, the bioinformatics pipeline CAULIFINDER has been developed for the automatic annotation and classification of EPRVs in plant genomes [7].…”

“…However, only 16 superfamilies were found in the plant kingdom (Figure 1), including 2 superfamilies of long terminal repeat (LTR) retrotransposons, 3 superfamilies of long interspersed nuclear elements (LINEs), 1 superfamily of short interspersed nuclear elements (SINEs), and 9 DNA transposon superfamilies. Additionally, many plant genomes harbor endogenous plant pararetroviruses (EPRVs), which share similar core genes with LTR retroelements for reverse transcription but lack both functional integrase (INT) and LTRs [7,8]. Numerous elements can still be recognized as TEs as they show some typical features of transposons such as LTRs, terminal inverted repeats (TIRs), and flanking target site duplications (TSDs).…”

“…Biology 2023, 12, x FOR PEER REVIEW 2 of 18 (SINEs), and 9 DNA transposon superfamilies. Additionally, many plant genomes harbor endogenous plant pararetroviruses (EPRVs), which share similar core genes with LTR retroelements for reverse transcription but lack both functional integrase (INT) and LTRs [7,8]. Numerous elements can still be recognized as TEs as they show some typical features of transposons such as LTRs, terminal inverted repeats (TIRs), and flanking target site duplications (TSDs).…”