Alignment of Rutaceae Genomes Reveals Lower Genome Fractionation Level Than Eudicot Genomes Affected by Extra Polyploidization.

Jiaqing Yuan,Shaoqi Shen,Chao Liu,Jin Zhang,Yangqin Xie,Yuhao Zhao,Zhikang Zhang,He Guo,Jinpeng Wang,Tariq Shehzad,Fanbo Meng,Pengchuan Sun,Jing Li,Xinyu Li,Jigao Yu,Chendan Wei,Xiyin Wang,Yayi Hou ,Xiaoyang Duan ,Shiqun Sun

doi:10.3389/fpls.2019.00986

Jiaqing Yuan, Shaoqi Shen + Show 18 more

Open Access

https://doi.org/10.3389/fpls.2019.00986

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Abstract

Owing to their nutritional and commercial values, the genomes of several citrus plants have been sequenced, and the genome of one close relative in the Rutaceae family, atalantia (Atalantia buxifolia), has also been sequenced. Here, we show a family-level comparative analysis of Rutaceae genomes. By using grape as the outgroup and checking cross-genome gene collinearity, we systematically performed a hierarchical and event-related alignment of Rutaceae genomes, and produced a gene list defining homologous regions based on ancestral polyploidization or speciation. We characterized genome fractionation resulting from gene loss or relocation, and found that erosion of gene collinearity could largely be described by a geometric distribution. Moreover, we found that well-assembled Rutaceae genomes retained significantly more genes (65–82%) than other eudicots affected by recursive polyploidization. Additionally, we showed divergent evolutionary rates among Rutaceae plants, with sweet orange evolving faster than others, and by performing evolutionary rate correction, re-dated major evolutionary events during their evolution. We deduced that the divergence between the Rutaceae family and grape occurred about 81.15–91.74 million years ago (mya), while the split between citrus and atalantia plants occurred <10 mya. In addition, we showed that polyploidization led to a copy number expansion of key gene families contributing to the biosynthesis of vitamin C. Overall, the present effort provides an important comparative genomics resource and lays a foundation to understand the evolution and functional innovation of Rutaceae genomes.

Highlights

The genus Citrus L., belonging to the subfamily Aurantioideae in the family Rutaceae, comprises many important fruit-producing plants
The high-quality clementine genome sequence produced by the International Citrus Genome Consortium (ICGC: http://www. citrus.genome.ucr.edu/) includes 301.4 Mb with 1,398 scaffolds and L50 reached to 31.4 MB (Wu et al, 2014)
Papeda and atalantia were assembled only to the scaffold level, we mapped their scaffolds onto sweet orange pseudo-chromosomes to construct their own likely pseudo-chromosomes

Summary

Introduction

The genus Citrus L., belonging to the subfamily Aurantioideae in the family Rutaceae, comprises many important fruit-producing plants. Citrus has undergone a complicated history of inbreeding and artificial breeding (Scora, 1975; Barrett and Rhodes, 1976; Nicolosi et al, 2000; Wu et al, 2014, 2018; Curk et al, 2016) For their economic importance, genome sequences of citrus plants and a close Rutaceae relative have been deciphered, including sweet orange, clementine, pummelo, papeda, citron, and atalantia (Xu et al, 2013; Wu et al, 2014; Wang et al, 2017b). The other 4 genomes were released by the same research group, including a highest-quality assembled pummelo genome with total scaffold length of about 301.95 Mb positioned to 117 scaffolds, and draft genomes of papeda, citron, and atalantia, which were not assembled to the chromosomal level yet (Wang et al, 2017b)

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