RNase‐based self‐incompatibility in cacti

Abstract

Summary Approximately one‐half of all flowering plants express genetically based physiological mechanisms that prevent self‐fertilisation. One such mechanism, termed RNase‐based self‐incompatibility, employs ribonucleases as the pistil component. Although it is widespread, it has only been characterised in a handful of distantly related families, partly due to the difficulties presented by life history traits of many plants, which complicate genetic research. Many species in the cactus family are known to express self‐incompatibility but the underlying mechanisms remain unknown. We demonstrate the utility of a candidate‐based RNA‐seq approach, combined with some unusual features of self‐incompatibility‐causing genes, which we use to uncover the genetic basis of the underlying mechanisms. Specifically, we assembled transcriptomes from Schlumbergera truncata (crab cactus or false Christmas cactus), and interrogated them for tissue‐specific expression of candidate genes, structural characteristics, correlation with expressed phenotype(s), and phylogenetic placement. The results were consistent with operation of the RNase‐based self‐incompatibility mechanism in Cactaceae. The finding yields additional evidence that the ancestor of nearly all eudicots possessed RNase‐based self‐incompatibility, as well as a clear path to better conservation practices for one of the most charismatic plant families.

The snapdragon genomes reveal the evolutionary dynamics of theSlocus supergene

“…After examining SLFs and S - RNase expression of two haplotypes, we found that S 7 - RNase and S 8 - RNase expressed indiscriminately and fairly high in AhS 7 S 8 style (Table S18), which is consistent with the situation in crab cactus(Ramanauskas and Igić 2021), and they are nearly undetectable in leaf and petal. Those two gene only expressed in style of AhS 7 S C and AhS 8 S C respectively as expect, yet at higher level than AhS 7 S 8 style.…”

“…After examining SLFs and S-RNase expression of two haplotypes, we found that S 7 -RNase and S 8 -RNase expressed indiscriminately and fairly high in AhS 7 S 8 pistil (Table S18), which is consistent with the situation in crab cactus 33 , and they are nearly undetectable in leaf and petal. 7B).…”

“…Besides, 27 of 32 SLFs are intron-less, suggesting SLFs proliferated most likely through retroelement-mediated way. With the estimated Antirrhinum mutation rate, the peak value of SLFs paralogs Ks distribution (range from 1.35 to 1.40) corresponding 122 Mya 31 , indicated the S -locus structure is a very conserved and long lived remnants 32 33 survived from long-term balancing selection (Fig. 4B).…”

Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects

“…The RNA-Seq method has been used in the family for different purposes ( Table S3 ). For instance, Walker et al [ 151 ] and Wang et al [ 152 ] used this kind of dataset for phylogenomic and evolutionary studies, while other authors tested differential gene expression in cactus species under distinct ecological stress, drought event conditions, RNase-based self-incompatibility, gene expression in root development, and genes under positive selection into specific clades [ 30 , 153 , 154 , 155 , 156 , 157 , 158 ] ( Table S3 ). Thus, the application of transcriptome methodologies to study ecological and environmental stresses may provide new evidence to understand cacti adaptations [ 30 , 159 ].…”

kakapo: Easy extraction and annotation of genes from raw RNA-seq reads

“…Without additional intervention, it stores intermediate results and does not repeat previously completed analyses. We have already employed kakapo in published work (Sánchez-Cabrera et al 2021; Ramanauskas and Igić 2021). Here, we describe the implementation of key steps in the pipeline, and provide readily reproducible examples, which showcase its modular features.…”