Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

Gitte Petersen,Benjamin M Anderson,Kirsten Krause

doi:10.1186/s12864-021-08105-z

Gitte Petersen, Benjamin M Anderson + Show 1 more

Open Access

https://doi.org/10.1186/s12864-021-08105-z

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Abstract

BackgroundThe intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus.ResultsThe mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT.ConclusionsThe lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

Highlights

The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants
Cases of detected HGT in plants [9, 10] were principally found in Anderson et al BMC Genomics (2021) 22:816 their mitochondrial genomes, possibly partly as a result of the greater sequence availability at the time compared to the nuclear genome
Excluding hits that occurred in the ribosomal genes or atp1, which are similar to plastid ribosomal genes and atpA, we found 8 regions with hits, representing approximately 0.6 and 1.1% of the mitogenomes of C. australis and C. campestris, respectively (Table 2)

Summary

Introduction

The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. Cases of detected HGT in plants [9, 10] were principally found in Anderson et al BMC Genomics (2021) 22:816 their mitochondrial genomes (mitogenomes), possibly partly as a result of the greater sequence availability at the time compared to the nuclear genome. Cellular mechanisms such as active DNA uptake [11] and organelle fusion and fission [12, 13] have been referenced to explain why HGT is more prevalent in the mitogenome, at least compared with the extensively sequenced chloroplast genome (plastome). While examples of HGT from nuclear genomes are accumulating, mitogenome examples still remain a substantial portion of the evidence for HGT in plants

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