Adaptive evolution driving the young duplications in six Rosaceae species

- Conclusions: The functional preference of the young duplicate genes in both the expansion types showed that they were inclined to respond to abiotic or biotic stimuli.
- Full list of author information is available at the end of the article.
- However, duplicate genes face three long- term fates: nonfunctionalization (or pseudogenization), characterized by one of the copies losing its function;.
- neofunctionalization reflected by one of the copies gain- ing a novel function.
- and subfunctionalization exhibited by duplicate copies inheriting parts of the original gene function [5].
- Nonfunctionalization/pseudogenization is the most widespread fate of the duplicate copies.
- The whole-genome sequencing of Fragaria vesca, Malus x domestica, Pyrus communis, Prunus persica, Rosa chinensis, and Rubus occidentalis provides us an opportunity to investigate the evolution of the recent duplicate genes among the six Rosaceae genomes.
- Young duplicate genes in the six Rosaceae species A total of 35,936 gene families were explored across the six Rosaceae species containing 21,650 young duplicate gene families, which indicated that young duplications occurred in 60.25% of the total gene families (Table 1 and Additional file 1: Table S1).
- That is, each of the six species has two or more gene members in each of the seven gene families.
- Duplication types of the young duplicate genes.
- In species-specific expansions, the gene numbers of tandem duplications were much higher than those of the other two duplication types in F.
- Accordingly, the highest percentages of the young duplicate genes came from tandem duplications were also detected in the five species.
- It was indicated that tandem duplica- tions played important roles in the young duplications after the speciation of the five plants.
- of the young duplicate genes were produced by tandem duplications in P.
- Lineage-specific expansions.
- b Corresponding species involved in the lineage-specific expansions.
- Number means number of the young duplicate genes from different duplication types in the two patterns of expansions in every species.
- Domain preference of the young duplicate genes.
- The protein domains of the young duplicates were ex- plored in the species-specific and lineage-specific expan- sions to uncover the functional preference of the duplicate genes among the six Rosaceae species..
- It is worth mentioning that of the domains appeared in only one species, indicating that approximately one half of the protein domains were uniquely encoded by species- specific duplicate genes in the six species.
- On the con- trary, only of the domains occurred simultaneously in all the six species.
- 1 Top 20 protein domains of the young duplicate genes in species-specific expansions.
- especially the domains of PPR, LRR, Pkinase, p450, and NB-ARC, shared by the species-specific duplicates of the six Rosaceae species..
- Clearly, only 5.20% of the protein domains were discovered in one species, such as B- lectin, Vicilin, and Trigger, demonstrating that a small amount of lineage-specific duplicate genes had exclusive domains in some species (Additional file 2: Table S2).
- In addition, 22.95% of the protein domains were found to co-occur in all the six species, with .
- Therefore, it may be con- cluded that the high-frequency duplicate domains in species-specific and lineage-specific expansions, involved in growth and development (Ribosomal, Ank, and Pep- tidase) or response to environmental stresses (PPR, NB- ARC, LRR, and Pkinase), might play a key role in the evolutionary processes of the six Rosaceae species..
- Duplication time of the young duplicate genes.
- In species-specific expansions, the average Ks values of the orthologs were higher than those of the paralogs only in P.
- 2 Top 20 protein domains of the young duplicate genes in lineage-specific expansions.
- illustrated that a considerable portion of the young du- plicate genes were generated at the very recent times.
- The observation proved that, in the period of the recent time, much more species- specific duplicate genes were produced than the lineage- specific ones.
- Moreover, the appreciable clustering of the Ks values around 0.2 in M.
- The nucleotide diversity of the young duplicate genes To deeper explore the evolutionary differences between paralogs and orthologs, we calculated the nucleotide di- versity values (Pi values) among species-specific and lineage-specific duplicate genes (Table 3)..
- In species-specific expansions, the paralogs had larger average Pi values than the orthologs in each of the six species.
- Moreover, t-test analysis were also operated be- tween the Pi values of paralogs and orthologs, showing Pi values of paralogs were significantly higher than those of orthologs in each of the six species (P <.
- However, the opposite results of paralogs with lower average Pi values than the orthologs were found in lineage-specific expansions of the studies species, except P.
- Selective pressure on young duplicate genes.
- In both species-specific and lineage-specific expan- sions, most of the gene pairs with Ka/Ks ratios smaller than 1 illustrated that a majority of the young duplicate genes were subject to purifying selection among the six Rosaceae species.
- Nevertheless, a fraction of the gene pairs showed Ka/Ks ratios greater than 1, suggesting that they underwent positive selection (Fig.
- These results indicated that paralogs were driven by weaker functional constraints and had faster evolutionary rates than orthologs in the young duplicate gene families of the six Rosaceae species..
- Ks values than the orthologs of the same family and are represented by the corresponding dots above the trend lines (blue lines: slope equal to 1).
- Chromosomal location of young duplicate genes.
- The physical location of the young duplicate genes, in both the species-specific and lineage-specific expansions, was uneven on the chromosomes in the six Rosaceae species.
- Accordingly, the trends of the gene densities were basically consistent with those of gene numbers in the six species..
- In species-specific expansions, four distribution pat- terns of the duplicate genes on the chromosomes in the six species were noticed (Additional files and 12: Figs.
- of the telomeres on each chromosome, such as in chro- mosomes and 16 of M.
- In the third pattern, there was a relative mean distribution of the young duplicate genes on the chromosomes, such as on all chromosomes of P.
- In the fourth pattern, the peaks of the duplicate genes were located on the non-telomere regions of the chromosomes, such as in chromosomes 1 and 2 of P.
- Most of the chromosomes belonged to the first, third and forth patterns showed the gene densities consistent with the distribution pat- tern of the young duplicate numbers.
- Similarly, the four distribution patterns of the dupli- cate genes were also detected in lineage-specific expan- sions (Additional files and 12: Figs.
- 4 The Ka / Ks ratios of young duplicate genes in the two types of expansions.
- The small square and the line in the box represent average and median values of the Ka / Ks values, respectively.
- The distribution tendency of the third pattern was revealed by all the chromosomes of F.
- Therefore, the results indicated that the distribution patterns of young duplicate genes on the same chromosomes be- tween the species-specific and lineage-specific expan- sions were similar on some of the chromosomes among the six species..
- To further verify the relationship of gene locations be- tween the two expansion types, we calculated the correl- ation coefficients of the young duplicate gene numbers between species-specific and lineage-specific expansions on the same chromosome in the six species (Add- itional file 4: Table S4).
- Most of the correlation coeffi- cients of M.
- Collinearity between young duplicate genes.
- For exploring the evolutionary history of the young du- plicate genes, the collinearity block analysis was per- formed among the young duplicate genes of lineage- specific expansions co-occurred in the six species.
- Although the collinearity blocks located in different chromosomes among the six species, the young dupli- cate genes of the four families with collinearity relation- ships were frequently found distributed in the chromosome 3 in F.
- These in- dicated that these chromosomal regions might originate from the ancestral chromosomes of the common.
- The family members along with the related neighbouring genes exhibited these ancestral regions, which were conserved and retained in the chromosomes of the six modern Rosaceae species after experiencing series of evolutionary events, including the young duplications..
- To retrospect the history of the Rosaceae family, it could be better discovered the characteristics of young dupli- cate genes reflected by the evolutionary processes of the six species..
- A recent WGD shared by the modern Rosaceae species of Malus and Pyrus is also reported, which might be one of the main factor leading to the large numbers of young dupli- cate families in the lineage of M.
- Be- sides, the duplication time of the young duplicate genes in M.
- Especially, many of the leucine-rich repeat receptor-like kinase (LRR-RLK) genes are part of the disease resistance gene family in plants [16].
- Adaptive evolution of young duplicate genes.
- Based on the divergence ana- lysis of the Ka/Ks (or dN/dS) ratios, it has been previ- ously reported that many gene families in plants are driven by adaptive evolution.
- The results demonstrated that the species-specific duplications mainly contributed to the recent expansions of the six species.
- All results showed that functional bias of the young duplicate genes was related to environmental stimuli response.
- in the six Rosaceae species.
- Identification of young duplicate gene families.
- The whole genome sequences and annotations of the six Rosaceae species, F.
- An all-vs.-all BLASTN search was performed among the nucleotide sequences (CDSs) of the six species (e-value<.
- Phylogenetic tree of young duplicate genes.
- For the accuracy of sequence alignments, CDSs of the seven young duplicate gene families involved in the six species were firstly translated into proteins, which expe- rienced the alignments by using the MUSCLE program with default options in MEGA7 [85].
- Duplication types of young duplicate genes.
- Moreover, chromosomal locations of whole-genome genes were achieved from the annotation files of the six species..
- Domain preference of young duplicate genes.
- Then, the domain numbers of the young duplicate genes were counted by Excel according to the Pfam results..
- The physical positions of young duplicate genes and whole-genome genes were available from the annotation information of the six species.
- Syntenic analysis of young duplicate genes between species.
- The syntenic relationships between the genes of the six species were detected at genome-wide levels by using TBtools [88] and MCScanX [89].
- The correlation coefficients of the young duplicate gene numbers between species-specific and lineage-specific expansions on the same chromosome..
- Chromosomal locations of young duplicate genes in the two types of expansions in F.
- Chromosomal locations of young duplicate genes in the two types of expansions in M.
- Chromosomal locations of young duplicate genes in the two types of expansions in P.
- Chromosomal locations of young duplicate genes in the two types of expansions in R.
- The directions of the triangles mean the transcriptional directions of the genes.
- Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics..
- Duplication and adaptive evolution of the chalcone synthase genes of dendranthema (Asteraceae)..
- The genome of the domesticated apple (Malus x domestica Borkh.
- The genome of the pear (Pyrus bretschneideri Rehd.)..
- Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae).
- Adaptation to drought in two wild tomato species: the evolution of the Asr gene family.
- Amplification of prolamin storage protein genes in different subfamilies of the Poaceae.
- Signature of diversifying selection on members of the Pentatricopeptide repeat protein family in Arabidopsis lyrata.
- Evolutionary dynamics of the Leucine-rich repeat receptor-like kinase (LRR-RLK) subfamily in angiosperms.
- Disease resistance signature of the leucine-rich repeat receptor-like kinase genes in four plant species.
- Adaptive and degenerative evolution of the S-phase kinase-associated protein 1-like family in Arabidopsis thaliana.
- Expressed sequence tag analysis of the response of apple (Malus x domestica 'Royal Gala') to low temperature and water deficit

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