The flax genome reveals orbitide diversity

Ziliang Song; Connor Burbridge; David J Schneider; Timothy F Sharbel; Martin J T Reaney

doi:10.1186/s12864-022-08735-x

The flax genome reveals orbitide diversity

BMC Genomics. 2022 Jul 23;23(1):534. doi: 10.1186/s12864-022-08735-x.

Authors

Ziliang Song¹, Connor Burbridge², David J Schneider³, Timothy F Sharbel¹, Martin J T Reaney^{4

5}

Affiliations

¹ Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.
² Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada.
³ School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada.
⁴ Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. martin.reaney@usask.ca.
⁵ Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, Guangzhou, Guangdong, 510632, China. martin.reaney@usask.ca.

Abstract

Background: Ribosomally-synthesized cyclic peptides are widely found in plants and exhibit useful bioactivities for humans. The identification of cyclic peptide sequences and their precursor proteins is facilitated by the growing number of sequenced genomes. While previous research largely focused on the chemical diversity of these peptides across various species, there is little attention to a broader range of potential peptides that are not chemically identified.

Results: A pioneering study was initiated to explore the genetic diversity of linusorbs, a group of cyclic peptides uniquely occurring in cultivated flax (Linum usitatissimum). Phylogenetic analysis clustered the 5 known linusorb precursor proteins into two clades and one singleton. Preliminary tBLASTn search of the published flax genome using the whole protein sequence as query could only retrieve its homologues within the same clade. This limitation was overcome using a profile-based mining strategy. After genome reannotation, a hidden Markov Model (HMM)-based approach identified 58 repeats homologous to the linusorb-embedded repeats in 8 novel proteins, implying that they share common ancestry with the linusorb-embedded repeats. Subsequently, we developed a customized profile composed of a random linusorb-like domain (LLD) flanked by 5 conserved sites and used it for string search of the proteome, which extracted 281 LLD-containing repeats (LLDRs) in 25 proteins. Comparative analysis of different repeat categories suggested that the 5 conserved flanking sites among the non-homologous repeats have undergone convergent evolution driven by functional selection.

Conclusions: The profile-based mining approach is suitable for analyzing repetitive sequences. The 25 LLDR proteins identified herein represent the potential diversity of cyclic peptides within the flax genome and lay a foundation for further studies on the functions and evolution of these protein tandem repeats.

Keywords: Diversity; Linum usitatissimum; Mining; Orbitide; Protein tandem repeats.

MeSH terms

Base Sequence
Flax* / genetics
Genome, Plant
Humans
Peptides, Cyclic / genetics
Phylogeny

Substances

Peptides, Cyclic