Sequential Paleotetraploidization shaped the carrot genome

Ying Liu,Yuxian Li,Jin Zhang,Jigao Yu,Chendan Wei,Jinpeng Wang,Xiuqing Li,He Guo,Xiyin Wang

doi:10.1186/s12870-020-2235-7

Abstract

BackgroundCarrot (Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrences, and nature of these events are not clearly defined.ResultsUsing a previously published comparative genomics pipeline, we reanalysed the carrot genome and characterized genomic fractionation, as well as gene loss and retention, after each of the two tetraploidization events and inferred a dominant and sensitive subgenome for each event. In particular, we found strong evidence of two sequential tetraploidization events, with one (Dc-α) approximately 46–52 million years ago (Mya) and the other (Dc-β) approximately 77–87 Mya, both likely allotetraploidization in nature. The Dc-β event was likely common to all Apiales plants, occurring around the divergence of Apiales-Bruniales and after the divergence of Apiales-Asterales, likely playing an important role in the derivation and divergence of Apiales species. Furthermore, we found that rounds of polyploidy events contributed to the expansion of gene families responsible for plastidial methylerythritol phosphate (MEP), the precursor of carotenoid accumulation, and shaped underlying regulatory pathways. The alignment of orthologous and paralogous genes related to different events of polyploidization and speciation constitutes a comparative genomics platform for studying Apiales, Asterales, and many other related species.ConclusionsHierarchical inference of homology revealed two tetraploidization events that shaped the carrot genome, which likely contributed to the successful establishment of Apiales plants and the expansion of MEP, upstream of the carotenoid accumulation pathway.

Highlights

Carrot (Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome
Homologous gene collinearity We inferred collinear genes within each genome and between carrot and coffee or grape reference genomes using ColinearScan [20], which provides a function for evaluating the statistical significance of blocks of collinear genes (Additional file 2: Tables S1 and S2)
For the blocks with four or more collinear genes, we found the highest number of duplicated genes in carrot

Summary

Introduction

Carrot (Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome. Carota L.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrences, and nature of these events are not clearly defined. Carota belongs to the Apiaceae family within the order Apiales, within the Campanulids clade, which includes the order Asterales (with key species such as Lactuca sativa L. or Helianthus annuus L.) [3]. The Lamiids, a close sister clade of Campanulids, encompasses many species of agricultural importance. Ancient polyploidization events have played important roles in the evolution of land plants, contributing to their origin and diversification [6,7,8,9,10]. It was stated that the carrot genome may have been affected by two polyploidization events, previously referred to as Dc-α and Dc-β, likely resulting in a whole-genome triplication (× 3) and a whole-genome duplication event (× 2) [11], respectively.

Methods

Results

Discussion

Conclusion