Nan Wang, Chaochao Li, Lihua Kuang, Xiaomeng Wu, Kaidong Xie, Andan Zhu, Qiang Xu, Robert M. Larkin, Yongfeng Zhou, Xiuxin Deng, and Wenwu Guo

PNAS October 19, 2022; 119 (43) e2206076119

Significance

We found that evolutionary conflicts between the cytoplasmic and nuclear genomes have persistent effects on citrus genetics and breeding, based on an analysis of a citrus pan-mitogenome and population genomics. This conflict conferred a prominent divergence and increased the genetic load on the mitochondrial genome during diversification and domestication. Deficiencies in inheritance, the levels of heteroplasmy that occurred from paternal leakage, and mitochondrial–nuclear interactions were examined in hybrids. The data are consistent with two candidate chimeric open reading frames (ORFs) serving as species-specific cytoplasmic male sterility/restorer-of-fertility (CMS/Rf) genes. These findings on the cytoplasmic genomes expand our understanding of crop breeding.

Abstract

Although interactions between the cytoplasmic and nuclear genomes occurred during diversification of many plants, the evolutionary conflicts due to cytonuclear interactions are poorly understood in crop breeding. Here, we constructed a pan-mitogenome and identified chimeric open reading frames (ORFs) generated by extensive structural variations (SVs). Meanwhile, short reads from 184 accessions of citrus species were combined to construct three variation maps for the nuclear, mitochondrial, and chloroplast genomes. The population genomic data showed discordant topologies between the cytoplasmic and nuclear genomes because of differences in mutation rates and levels of heteroplasmy from paternal leakage. An analysis of species-specific SVs indicated that mitochondrial heteroplasmy was common and that chloroplast heteroplasmy was undetectable. Interestingly, we found a prominent divergence in the mitogenomes and the highest genetic load in the, which may provide the basis for cytoplasmic male sterility (CMS) and thus influence the reshuffling of the cytoplasmic and nuclear genomes during hybridization. Using cytoplasmic replacement experiments, we identified a type of species-specific CMS in mandarin related to two chimeric mitochondrial genes. Our analyses indicate that cytoplasmic genomes from mandarin have rarely been maintained in hybrids and that paternal leakage produced very low levels of mitochondrial heteroplasmy in mandarin. A genome-wide association study (GWAS) provided evidence for three nuclear genes that encode pentatricopeptide repeat (PPR) proteins contributing to the cytonuclear interactions in the Citrus genus. Our study demonstrates the occurrence of evolutionary conflicts between cytoplasmic and nuclear genomes in citrus and has important implications for genetics and breeding.

See https://www.pnas.org/doi/full/10.1073/pnas.2206076119

Figure 1: SVs and chimeric ORFs in the citrus super pan-mitogenome. (A) Summary of the 12 de novo mitochondrial assemblies and 2 previously published mitochondrial genomes. The previously published sequences are highlighted with asterisks. (B) 70- to 120-kb regions identified based on the coverage depth of long-read mapping containing >5-kb deletions from five groups. The mitogenomic regions are shown on the x-axis. The different levels of coverage are indicated on the y-axis. (C) Chimeric ORFs related to conserved genes in the intergenic regions of 14 citrus mitochondrial genomes. The heatmap includes two previously reported mitochondrial genomes, mandarin G1 and pummelo HBP. (D) Circular representation of the mitochondrial pan-genome. The conserved gene structure was annotated for the forward strand (I) and the reverse strand (II). The heatmap indicates the distribution of SNPs and indels among the 184 accessions of citrus, with the mitochondrial genome from kumquat used as a reference (III). The diversity of SNPs and indels in the mitochondrial genomes in 184 citrus accessions is indicated (IV). The mitochondrial pan-genome is indicated with a schematic drawing (V).