Contrasting genetic variation and positive selection followed the divergence of NBSencoding genes in Asian and European pears

- Contrasting genetic variation and positive selection followed the divergence of NBS- encoding genes in Asian and European pears.
- Previous studies have identified NBS-encoding genes in Pyrus bretschneideri.
- Results: In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes..
- We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance.
- Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear.
- Conclusion: Proximal duplication mainly led to the different number of NBS-encoding genes in P.
- This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear..
- Interestingly, the QTL region for black spot disease resistance contained two NBS-encoding genes [13], which were up-regulated after infection with A.
- Recently, a range of NBS-encoding genes have been identified in different rosaceae species.
- For instance, the number of NBS-encoding genes varies from 346 to 1303 in strawberry and apple, respectively [26].
- In addition, NBS-encoding genes show a strong signa- ture of selection, but the nature of selection differs across these genes [31].
- Some NBS-encoding genes evolve rapidly through copy number variation and high ratio of non-synonymous to synonymous substitutions, but other genes evolve at a slower rate [31]..
- bretsch- neideri [1], an accurate characterization of NBS-encoding genes and their comparative analysis with P.
- Since the selection and evolution of NBS-encoding genes is yet unclear, the genome se- quence information provides chances to explore their di- versity and evolution in wild and cultivated groups in Asian and European pear..
- In this study, we identified NBS-encoding genes and compared them across the genomes of P.
- We further used re-sequencing data from 131 pear accessions to characterize genetic vari- ation and selection signatures on NBS-encoding genes in wild and domesticated Asian and European pear popula- tions.
- In addition, NBS-encoding genes in disease resist- ance QTL were identified in Asian and European pears..
- These findings will provide additional resources for fu- ture research of NBS-encoding gene function and dis- ease resistance in pear..
- Identification and phylogenetic analysis of NBS-encoding genes in P.
- In this study, a total of 338 and 412 NBS-encoding genes were identified in the ~ 510 Mb P.
- The NBS-encoding genes were divided into six types including CC-NBS-LRR, TIR-NBS-LRR and four truncated NBS-LRR (Table 1), three of which (TIR- NBS-LRR, CC-NBS-LRR, NBS) determine the majority of the difference in the number of NBS-encoding genes between Asian and European pears.
- The position, num- ber, and length of LRR domains were comparatively more variable in NBS-encoding genes.
- Many species-specific genes and the differences in the numbers of NBS-encoding genes might have appeared after the divergence of Asian and European pears [3]..
- 1500 bp) analysis identified 128 different kinds of cis-elements in the NBS-encoding gene families of P.
- The CAAT-box, TATA-box, and MYC cis-elements showed highest enrichment in the pro- moters of NBS-encoding genes of both P.
- Genome-wide distribution and duplication of NBS- encoding genes.
- bretschneideri, a total of 265 NBS-encoding genes were mapped to the 17 chromosomes and the remaining 73 genes were placed on scaffolds (Additional file 2).
- communis, 408 NBS-encoding genes were mapped onto the 17 chromosomes, while 4 genes were on the Table 1 Classification of NBS-encoding genes in ‘ Dangshansuli.
- bretschneideri, four chromo- somes, Chr2 (52), Chr5 (42), Chr7 (58), Chr11 (41), had the highest proportion of the total NBS-encoding genes (Fig.
- A set of NBS-encoding genes on Chr2 co-localized with the previously detected fire blight disease resistance QTL of P.
- (15/50) NBS-encoding genes on Chr11 were located within the black spot disease resistance QTL of P..
- To detect the potential mechanism of expansion, we analyzed the duplication events of NBS-encoding genes in the P.
- However, only 23.96% of NBS- encoding genes in P.
- These results indicated that the percentage of NBS-encoding genes derived from dispersed and prox- imal duplication were 27.81 and 28.11% in P.
- Time of duplication events and selection pressure in NBS- encoding genes.
- communis had 61 dupli- cated NBS-encoding gene pairs (Fig.
- 1 The maximum likelihood (ML) Phylogenetic analysis of NBS-encoding genes from P.
- The phylogenetic tree was obtained using the IQ-TREE software on the basis of amino-acid sequences of NBS-encoding genes with ultrafast bootstrap 1000.
- ② The six classes of NBS-encoding genes are marked by different colors.
- We further estimated the ratio of non-synonymous (Ka) and synonymous substitutions per site (Ks) to in- vestigate the role of positive and purifying selection in the evolution of NBS-encoding genes.
- In addition, the Ka/Ks Table 2 Frequency of cis-elements identified in the promoter regions of NBS-encoding genes in two pear species.
- 2 Chromosome location of NBS-encoding genes in P.
- Different colors represent different types of NBS- encoding genes.
- These results indicated that about 35.21% NBS-encoding genes of P.
- Genetic diversity and selection across NBS-encoding genes in Asian and European pear.
- The average nucleotide diversity across NBS-encoding genes was 6.02E-03 and 5.65E-03 in the Asian and Euro- pean populations, and 5.92E-03 and 6.88E-03 in the wild and cultivated groups (Additional file 8), respectively.
- A similar trend was observed when analysis was repeated using only the coding regions from NBS-encoding genes (Table 3).
- A comparison of cultivated and wild populations revealed that average nucleotide diversity across NBS-encoding genes reduced after do- mestication in Asian pears, but contrasting results were observed in the European population (Table 3).
- Similarly, 17.2% of NBS-encoding re- gions had 4-fold genetic diversity loss during domestica- tion in European pear.
- A total of 41 NBS-encoding genomic windows having reduction in genetic diversity were common in Asian and European populations (Add- itional file 8).
- We further calculated the Ka/Ks ratio to investigate positive selection in the 338 NBS-encoding genes.
- 4 Synteny analysis of the NBS-encoding genes between P.
- The NBS-encoding gene, Pbr003344.1, under black spot dis- ease resistance QTL also had up-regulated.
- A model to identify putative disease resistance in pear In order to detect the putative formation of resistance in wild and cultivated pear accessions, we combined the analysis of genetic variants, diversity, selection pressure and expression patterns in NBS-encoding genes.
- It was found that NBS-encoding gene of Pbr025269.1 had 36 significantly (chi-square test p-value <.
- In this study, we observed a simi- larity in the distribution patterns and cis-elements types of NBS-encoding genes in P.
- The number of NBS-encoding genes in P.
- communis were considerably different (338 vs 412), and only 64.79% orthologous NBS-encoding genes were present between them.
- In contrast, the higher nucleotide diversity in NBS-encoding genes of cultivated groups in Europe might have occurred due to distinct selection pressure imposed by the cultivated habitats [41].
- A recent study has shown that several regions with NBS-encoding genes had higher nucleotide diversity in landraces than the wild pear group [42].
- The level of differentiation of NBS-encoding genes be- tween wild and cultivated groups between two pear spe- cies also differs significantly from some other annual species.
- For instance, only 6 and 5 NBS-encoding genes show high divergence (F ST value >.
- Positive selection drives the evolution and selection of NBS-encoding genes in Asian and European pears Ka/Ks ratio of several paralogous gene pairs were greater than one, indicating a positive selection on NBS-.
- b Distribution of F ST values across the whole NBS- encoding gene family of Asian pears.
- bretschneideri, with the lat- ter showing comparatively stronger selection and more rapid evolution of NBS-encoding genes.
- The NBS- encoding genes also exhibited positive selection and rapid evolution in other species [26, 45].
- 6 Expression profiles of 17 NBS-encoding genes in four pear accessions at enlarged stage by RT-qPCR analysis and RNA-seq data.
- The relative expression levels of each individual NBS-encoding genes were normalized by the Pyrus GAPDH gene.
- NBS-encoding genes and disease resistance in pear The presence of 41 NBS-encoding genes in the previously identified disease-related QTL regions indicated their im- portant roles in defense against these diseases.
- Similarly, 15 NBS-encoding genes were located under the black spot re- sistance QTL on chromosome 11 of P.
- Three NBS-encoding genes (Pbr023226.1, Pbr023227.1, Pbr003344.1) in the black spot QTL regions showed >.
- The NBS-encoding gene family evolved through duplica- tion events in P.
- communis, and proximal duplication has resulted in different numbers of NBS-encoding genes in these two pear species.
- Moreover, several NBS-encoding genes were located under disease resistance QTL regions, indicating their potential role in disease resistance or susceptibility in pear.
- Identification and classification of NBS-encoding genes For identification of NBS-encoding genes, the Chinese white pear (P.
- Also, we selected the candi- date NBS-encoding genes (e-value <1E-20) as query sequence and used BLASTP [56] to search NBS- encoding genes separately in both the genomes.
- The same strategy was used to identify the NBS- encoding genes in P.
- The amino acid sequences of all 750 NBS-encoding genes in P.
- Cis-elements analysis of NBS-encoding genes.
- Promoters in the upstream 1500 bp regions of NBS- encoding genes were obtained from the pear annotation database [1] and phytozome database (https://phytozome.jgi..
- The same strategy was used to identify the cis- elements in NBS-encoding genes family of P.
- Detection of NBS-encoding genes in disease resistance QTL.
- Finally, NBS-encoding genes in these QTL flanking regions were identified for further analysis..
- Diversity of NBS-encoding genes in four groups.
- To measure genetic diversity of the NBS-encoding gene family in pear, nucleotide diversity (π) and fixation index (F ST ) were used as population-differentiation statistics..
- In brief, 338 NBS-encoding genes were combined to form a single sequence scaffold with the sorted order (Additional file 14), and SNPs were identified across them using the above defined methods..
- The resulting SNPs were used to calculate the π and F ST with a 1000 bp sliding window and a step size of 500 bp across the linear sequence of all 338 NBS-encoding genes.
- To identify signatures of selection, we calculated the Ka/Ks ratio of all orthologous NBS-encoding gene pairs to identify signatures of positive selection on them.
- Genome-wide expression analysis of the NBS-encoding genes.
- To investigate the expression changes of the NBS-encoding genes after inoculation with A..
- RPKM value was used to measure the expression level of NBS- encoding genes.
- The expression level of selected NBS- encoding genes was calculated by using 2 –ΔΔ Ct method and normalized to the Pyrus GAPDH gene [42]..
- The information of all NBS-encoding genes in P..
- NBS-encoding genes in pear disease resistance QTL regions.
- Duplication categories of NBS-encoding genes in P..
- The RPKM values of 338 NBS-encoding genes in four Asian pear accessions at three fruit stages.
- The expression patterns of 338 NBS-encoding genes ’ expression in P.
- NBS-encoding genes in a sorted physical genome order.
- Extreme expansion of NBS- encoding genes in Rosaceae.
- Genome-Wide Identification and Expression Analysis of NBS-Encoding Genes in Malus x domestica and Expansion of NBS Genes Family in Rosaceae

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