The Loss of the Inverted Repeat in the Putranjivoid Clade of Malpighiales.

Dong-Min Jin,Jun-Bo Yang,Lu Gan,Ting-Shuang Yi,Jian-Jun Jin,Susann Wicke

doi:10.3389/fpls.2020.00942

Abstract

The typical plastid genome (plastome) of photosynthetic angiosperms comprises a pair of Inverted Repeat regions (IRs), which separate a Large Single Copy region (LSC) from a Small Single Copy region (SSC). The independent losses of IRs have been documented in only a few distinct plant lineages. The majority of these taxa show uncommonly high levels of plastome structural variations, while a few have otherwise conserved plastomes. For a better understanding of the function of IRs in stabilizing plastome structure, more taxa that have lost IRs need to be investigated. We analyzed the plastomes of eight species from two genera of the putranjivoid clade of Malpighiales using Illumina paired-end sequencing, the de novo assembly strategy GetOrganelle, as well as a combination of two annotation methods. We found that all eight plastomes of the putranjivoid clade have lost their IRB, representing the fifth case of IR loss within autotrophic angiosperms. Coinciding with the loss of the IR, plastomes of the putranjivoid clade have experienced significant structural variations including gene and intron losses, multiple large inversions, as well as the translocation and duplication of plastome segments. However, Balanopaceae, one of the close relatives of the putranjivoid clade, exhibit a relatively conserved plastome organization with canonical IRs. Our results corroborate earlier reports that the IR loss and additional structural reorganizations are closely linked, hinting at a shared mechanism that underpins structural disturbances.

Highlights

Plastids, such as chloroplasts, chromoplasts, and leucoplasts, are the place for photosynthesis and the major organelle for organic product storage in plants
Our analyses focused on exploring the structural variation of plastomes and revealed that all plastomes of the putranjivoid calde have lost the IRB entirely and experienced extensive additional structural rearrangements
Plastomes from the putranjivoid clade are relatively small compared to their sister family Balanopaceae (Figure 1; Table 1)

Summary

INTRODUCTION

Plastids, such as chloroplasts, chromoplasts, and leucoplasts, are the place for photosynthesis and the major organelle for organic product storage in plants. Plastomes of the IRLC, C. gigantea (Sanderson et al, 2015), Tahina spectabilis (Barrett et al, 2016) showed significant higher rearrangement degrees compared to their sister clade, while species in a lineage of Erodium that has lost one IR exhibit an otherwise conserved plastome structure (Blazier et al, 2016). Previous studies have revealed significant structural variations in the plastomes of multiple taxa in this order. Two recent studies detected an inversion in the LSC, significant variation in length reduction of the IRs, gene loss and pseudogenization events in plastomes of Podostemaceae (Bedoya et al, 2019; Jin et al, 2020). Previous studies suggested that multiple lineages of Malpighiales have experienced plastome structural variations, but knowledge of plastomes evolution in this large order is still limited. The plastomes of the two Balanopaceae species retain a relatively conserved plastome structure, indicating an evolutionary shift after the split of both lineages

MATERIALS AND METHODS

RESULTS AND DISCUSSION

DATA AVAILABILITY STATEMENT