Potato (Solanum tuberosum L.) is the world’s most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production1–4. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

1Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely 2 related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and 3 RmYN02. However, there is a segment of high amino acid similarity between human CoV-2 and a pangolin isolated strain, GD410721, in the receptor binding domain (RBD) of 5 the spike protein, a pattern that can be caused by either recombination or by convergent 6 amino acid evolution driven by natural selection. We perform a detailed analysis of the 7 synonymous divergence, which is less likely to be affected by selection than amino acid 8 divergence, between human SARS-CoV-2 and related strains. We show that the 9 synonymous divergence between the bat derived viruses and SARS-CoV-2 is larger than 10 between GD410721 and SARS-CoV-2 in the RBD, providing strong additional support for 11 the recombination hypothesis. However, the synonymous divergence between pangolin 12 strain and SARS-CoV-2 is also relatively high, which is not consistent with a recent 13 recombination between them, instead it suggests a recombination into RaTG13. We also 14 find a 14-fold increase in the d N /d S ratio from the lineage leading to SARS-CoV-2 to the 15 strains of the current pandemic, suggesting that the vast majority of non-synonymous 16 mutations currently segregating within the human strains have a negative impact on viral 17fitness. Finally, we estimate that the time to the most recent common ancestor of SARS-18CoV-2 and RaTG13 or RmYN02 based on synonymous divergence, is 51.71 years (95% 19 C.I., 28.11-75.31) and 37.02 years (95% C.I., 18.19-55.85), respectively. 20 21 a coronavirus (Lu, et al. 2020; Zhang and Holmes 2020), Severe acute respiratory syndrome 1 coronavirus 2 (SARS-CoV-2), an RNA virus with a 29,891 bp genome consisting of four major 2 structural genes (Wu, et al. 2020; Zhou, Yang, et al. 2020). Of particular relevance to this study 3 is the spike protein which is responsible for binding to the primary receptor for the virus, 4 angiotensin-converting enzyme 2 (ACE2) (Wan, et al. 2020; Wu, et al. 2020; Zhou, Yang, et al. 5 2020). 6Human SARS-CoV-2 is related to a coronavirus (RaTG13) isolated from the bat 7Rhinolophus affinis from Yunnan province of China (Zhou, Yang, et al. 2020). RaTG13 and the 8 human strain reference sequence (Genbank accession number MN996532) are 96.2% identical 9and it was first argued that, throughout the genome, RaTG13 is the closest relative to human 10 SARS-CoV-2 (Zhou, et al. 2020). Zhang, et al. 2020 showed that RaTG13 and SARS-CoV-2 11 were 91.02% and 90.55% identical ,respectively, to coronaviruses isolated from pangolins 12 (Pangolin-CoV), which therefore form a close outgroup to the SARS-CoV-2+RaTG13 clade . 13 Furthermore, five key amino acids in the receptor-binding domain (RBD) of spike were identical 14 between SARS-CoV-2 and Pangolin-CoV, but differed between those two strains and RaTG13. 15 (Lam, et al. 2020) independently made similar observations and additionally showed that when 16 analyzing...

Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and RmYN02. However, there is a segment of high amino acid similarity between human SARS-CoV-2 and a pangolin-isolated strain, GD410721, in the receptor-binding domain (RBD) of the spike protein, a pattern that can be caused by either recombination or by convergent amino acid evolution driven by natural selection. We perform a detailed analysis of the synonymous divergence, which is less likely to be affected by selection than amino acid divergence, between human SARS-CoV-2 and related strains. We show that the synonymous divergence between the bat-derived viruses and SARS-CoV-2 is larger than between GD410721 and SARS-CoV-2 in the RBD, providing strong additional support for the recombination hypothesis. However, the synonymous divergence between pangolin strain and SARS-CoV-2 is also relatively high, which is not consistent with a recent recombination between them, instead, it suggests a recombination into RaTG13. We also find a 14-fold increase in the dN/dS ratio from the lineage leading to SARS-CoV-2 to the strains of the current pandemic, suggesting that the vast majority of nonsynonymous mutations currently segregating within the human strains have a negative impact on viral fitness. Finally, we estimate that the time to the most recent common ancestor of SARS-CoV-2 and RaTG13 or RmYN02 based on synonymous divergence is 51.71 years (95% CI, 28.11–75.31) and 37.02 years (95% CI, 18.19–55.85), respectively.