The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 1943 coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these,~28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other~5.4-21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C39H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

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17The emergence of a novel coronavirus, SARS-CoV-2, resulted in a pandemic. Here, we used X-ray 18 structures of human ACE2 bound to the receptor-binding domain (RBD) of the spike protein (S) from 19 SARS-CoV-2 to predict its binding to ACE2 proteins from different animals, including pets, farm animals, 20 and putative intermediate hosts of SARS-CoV-2. Comparing the interaction sites of ACE2 proteins 21 known to serve or not serve as receptor allows to define residues important for binding. From the 20 22 amino acids in ACE2 that contact S up to seven can be replaced and ACE2 can still function as the SARS-23CoV-2 receptor. These variable amino acids are clustered at certain positions, mostly at the periphery 24 of the binding site, while changes of the invariable residues prevent S-binding or infection of the 25 respective animal. Some ACE2 proteins even tolerate the loss or the acquisition of N-glycosylation sites 26 located near the S-interface. Of note, Pigs and dogs, which are not or not effectively infected and have 27 only a few changes in the binding site, exhibit relatively low levels of ACE2 in the respiratory tract. 28Comparison of the RBD of S of SARS-CoV-2 with viruses from Bat-CoV-RaTG13 and Pangolin-CoV 29 revealed that the latter contains only one substitution, whereas the Bat-CoV-RaTG13 exhibits five. 30However, ACE2 of pangolin exhibit seven changes relative to human ACE2, a similar number of 31 substitutions is present in ACE2 of bats, raccoon, and civet suggesting that SARS-CoV-2 may not 32 especially adapted to ACE2 of any of its putative intermediate hosts. These analyses provide new 33 insight into the receptor usage and animal source/origin of SARS-CoV-2. 34 IMPORTANCE 35 SARS-CoV-2 is threatening people worldwide and there are no drugs or vaccines available to mitigate 36 its spread. The origin of the virus is still unclear and whether pets and livestock can be infected and 37 transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host 38 receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis 39 provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from 40 species known to support SARS-CoV-2 infection tolerate many amino acid changes indicating that the 41 species barrier might be low. An exception are dogs and especially pigs, which, however, revealed 42

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BackgroundLeucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively.ResultsAll LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%.ConclusionsOur results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4155-y) contains supplementary material, which is available to authorized users.