The genome of the pear (Pyrus bretschneideri Rehd.)

Abstract

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 194× 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, C3'H, 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.

Figure 1.

Distribution of basic genomic elements of pear. (A) Chromosome karyotype. Colored segments are in accordance with the Rosaceous ancestor. (B) Gene density. The rate of sites within gene region per 100 kb ranges from a minimum of 0 to a maximum of 0.8, illustrated by red line. (C) DNA transposon element (TE) density. The rate of sites within the DNA TE region per 100 kb ranges from 0 to 0.65, illustrated by blue line. (D) Retrotransposon element (RT TE) density. The rate of sites within the RT TE regions ranges from 0 to 1, illustrated by purple. (E) SNP density. The rate of SNP per 100 kb ranges from 0 to 0.03, illustrated by green. (F) GC content. The rate of GC content ranges from 0.25 to 0.45, illustrated by black. Circos (Krzywinski et al. 2009) (http://circos.ca) was used for constructing this diagram.

Figure 2.

Comparisons between apple and pear for repetitive elements. The major repeats in apple and pear revealed that genome size differences of apple and pear were mainly attributed to repeat sequences.

Figure 3.

Distribution of fourfold degenerate site (4dTv) distances of duplicate gene pairs in pear, apple, and strawberry. A total of 1085 synteny blocks in pear (726 in apple and 262 in strawberry) are selected to calculate 4dTv values. The distribution of 4dTv values in pear (in blue) and those of apple (in red) are similar, while those of strawberry (in black) are different, with a single peak around 0.65, suggesting that there is no recent whole-genome duplication (WGD) in strawberry. (Green groups) Synteny blocks (557) between pear and apple, revealing that these groups are closer to the y-axis, and suggesting a more recent divergence event must have occurred between pear and apple.

Figure 4.

The evolutionary scenario of nine chromosomes of the Rosaceae ancestor. Pear and apple have the same chromosome karyotypes and same chromosomal evolution mode. The Pyreae tribe went through a recent WGD. The Amygdaleae tribe, such as strawberry in the Rosoideae subfamily, has no recent WGD but has chromosome fragmentation and recombination from nine to seven. It is estimated that the ancestor of Rosaceae had nine chromosomes. To demonstrate the evolutionary process from the eudicot ancestor to the Rosaceae ancestor, strawberry was compared with grape.

Figure 5.

Genes and repeat sequences surrounding candidate S-RNase genes in pear, apple, strawberry, and potato. The dashed line with dot endpoints connects candidate SFB genes of pear and apple that share the highest sequence identity (which are shown in Supplemental Table 10). (Gray arrow) Genes supported by experimental evidence. The vertex of the triangles is the 3′ orientation of the particular gene: (red) candidate S-RNase gene; (purple) candidate SFB gene; (blue) other genes in the neighboring regions; (green) repeat sequence.

Figure 6.

(A) The phenylpropanoid biosynthesis pathway in pear that influences the conformation of stone cells in fruit. (Red box) Genes that had detectable expression; (light red shaded ovals) important intermediate compounds in lignin pathway; (green text and arrows) pathways with minor expression; (blue boxes) three important end-product compounds in pear fruit; and green-boxed compound cannot be detected. (B) Transcript ratio distribution of all enzymes related to lignin. Three stages of fruit development (S422, early development; S627, middle development; and S830, near ripening) were assessed. The ratio of S422 and S627 is shown along the x-axis, and the ratio of S830 and S627 is shown along the y-axis. For points, different colors correspond to different enzymes, while different shapes correspond to different conditions of false-discovery rate (FDR) values. Abbreviations of genes involved in phenylpropanoid biosynthesis pathway are as follows: LP, L-phenylalanine; CAN, cinnamic acid; PCA, P-coumaric acid; CA, caffeic acid; FA, ferulic acid; 5HA, 5-hydroxyferulate acid; SA, sinapic acid; CNC, cinnamoyl-CoA; PCC, p-coumaroyl-CoA; CFC, caffeoyl-CoA; FC, feruloyl-CoA; 5HC, 5-hydroxyferuloyl-CoA; SC, sinapoyl-CoA; PCouA, p-coumar aldehyde; CafA, caffeyl aldehyde; ConA, conifer aldehyde; 5HydA, 5-hydroxyconifer aldehyde; SinA, sinapoyl aldehyde; PCAlc, p-coumaryl alcohol; CFAlc, caffeyl alcohol; CNAlc, coniferyl alcohol; 5HydAlc, 5-hydroxyconiferyl alcohol; SinAlc, sinapyl alcohol; PHL, p-hydroxyphenyl lignin; GL, guaiacyl lignin; 5GL, 5-hydroxy-guaiacyl lignin; SL, syringyl lignin; PAL, phenylalanine ammonia-lyase; C4H, trans-cinnamate 4-monooxygenase; 4CL, 4-coumarate-CoA ligase; HCT, shikimate O-hydroxycinnamoyltransferase; C3′H, coumaroylquinate 3′-monooxygenase; COMT, caffeic acid 3-O-methyltransferase; CCOMT, caffeoyl-CoA O-methyltransferase; F5H, ferulate-5-hydroxylase; CCR, cinnamoyl-CoA reductase; CAD, cinnamyl-alcohol dehydrogenase; and POD, peroxidase.

Figure 7.

Phylogenetic relationships, distribution patterns, and transcriptional expression of S6PDH genes. The phylogenetic tree was constructed using the maximum likelihood method with Mega 5.0 software (Tamura et al. 2011). Heatmaps of expression patterns were drawn using Cluster 3.0 (de Hoon et al. 2004) along with expression levels (fragments per kilobase per million mapped reads [FPKM]) of each of the S6PDH genes. Different colors have been used for different species. S422, S627, and S830 are three different stages of development. Dotted lines between circles correspond to deleted non-S6PDH genes.