The genome sequence ofHirschfeldia incana, a new Brassicaceae model to improve photosynthetic light‐use efficiency

Abstract

SUMMARY Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C3 plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light‐use efficiency at high irradiance as identified in a small number of exceptional C3 species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light‐use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light‐saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species‐specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light‐use efficiency and enhancing photosynthetic rates in crop species.

A genomic panel for studying C3‐C4 intermediate photosynthesis in the Brassiceae tribe

“…To resolve the phylogenetic relationships of the two H. incana accessions HIR1 and HIR3 from our study and another accession, NIJ, previously reported in Garassino et al (2022), we constructed phylogenetic trees. Our phylogenetic tree based on the LSC regions of 14 Brassiceae chloroplast genomes had high support values for all nodes (SH‐aLRT/bootstrap >70%).…”

“…Our phylogenetic tree based on the LSC regions of 14 Brassiceae chloroplast genomes was consistent with the topology reported in previous studies (Arias & Pires, 2012; Koch & Lemmel, 2019). In this tree, the two H. incana accessions were placed together with the NIJ accession (Garassino et al, 2022)⁠ on the same branch. However, our result suggests that HIR3 is genetically different from the HIR1 and NIJ accessions (Figure 6a).…”

“…In addition, the assembly of D. muralis reached satisfactory contiguity after two generations of selfing. Coincidentally, an assembly for H. incana (Nijmegen) with six generations of selfing has just been released (Garassino et al, 2022) with an N50 value of 5.1 Mb, which is considerably longer compared to our assemblies with N50s of 885 and 663 Kb for H. incana HIR1 and H. incana HIR3 accessions, respectively, that were sequenced without prior selfing.…”

“…To ascertain the phylogenetic placement of the two H. incana accessions HIR1 and HIR3, in relation to other species in the Brassiceae tribe and also to another accession Nijmegen (NIJ, Garassino et al, 2022), we first assembled their chloroplast genomes using whole-genome sequencing data from our study. Raw reads were trimmed for adapter contamination, quality and length using Trimmomatic v0.39 (Bolger et al, 2014) with the following parameters: "ILLUMINACLIP: 2:20:10 SLIDINGWIN-DOW:4:15 LEADING:5 TRAILING:5 MINLEN:50".…”

Exploring the unexplored : Unravelling the cyto-nuclear interactions in Arabidopsis thaliana to improve photosynthesis

“…This means while both the physiological and genetic potential for increased photosynthesis is present, in nature plants perform at an optimum determined by the constraints of the environmental conditions. environments, with low competition and low biotic disease pressure, they show close to maximal photosynthesis (Mooney et al, 1976;Ehleringer, 1983;Garassino et al, 2022;Taylor et al, 2022).…”