Image_2.TIFF

<p>Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don] is a commercially important fruit crop in China, but its structure patterns and domestication history remain imprecise. To address these questions, we estimated the genetic structure and domestication history of Chinese cherry using 19 nuclear microsatellite markers and 650 representative accessions (including 118 Cerasus relatives) selected throughout their natural eco-geographical distributions. Our structure analyses detected no genetic contribution from Cerasus relatives to the evolution history of Chinese cherry. A separate genetic structure was detected in wild Chinese cherries and rough geographical structures were observed in cultivated Chinese cherries. One wild (wild Chinese cherry, WC) and two cultivated (cultivated Chinese cherry, CC₁ and CC₂) genetic clusters were defined. Our approximate Bayesian computation analyses supported an independent domestication history with two domestication events for CC₁ and CC₂, happening about 3900 and 2200 years ago, respectively. Moderate loss of genetic diversity, over 1000-year domestication bottlenecks and divergent domestication in fruit traits were also detected in cultivated Chinese cherries, which is highly correlated to long-term clonal propagation and different domestication trends and preferences. Our study is the first to comprehensively and systematically investigate the structure patterns and domestication history for Chinese cherry, providing important references for revealing the evolution and domestication history of perennial woody fruit trees.</p

Statistical analysis of <i>Cocos nucifera</i> unigenes with sequence matches against public protein databases.

<p>Statistical analysis of <i>Cocos nucifera</i> unigenes with sequence matches against public protein databases.</p

Summary of the nucleotide BLAST results between the <i>de novo</i>-assembled unigenes and EST sequences from <i>Cocos nucifera</i> and <i>Elaeis guineensis</i>.

<p>(A) Percentage of unigenes matched with EST sequences from <i>Cocos nucifera</i>. (B) Percentage of unigenes matched with EST sequences from <i>Elaeis guineensis</i>. (C) Percentage of EST sequences from <i>Cocos nucifera</i> matched with unigenes. (D) Percentage of EST sequences from <i>Elaeis guineensis</i> matched with unigenes. (E) E-values of unigene matches with cDNA sequences from <i>Cocos nucifera</i>. (F) E-values of unigene matches with cDNA sequences from <i>Elaeis guineensis</i>. (G) Unigene similarities to cDNA sequences from <i>Cocos nucifera</i>. (H) Unigene similarities to cDNA sequences from <i>Elaeis guineensis.</i></p

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<p>Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don] is a commercially important fruit crop in China, but its structure patterns and domestication history remain imprecise. To address these questions, we estimated the genetic structure and domestication history of Chinese cherry using 19 nuclear microsatellite markers and 650 representative accessions (including 118 Cerasus relatives) selected throughout their natural eco-geographical distributions. Our structure analyses detected no genetic contribution from Cerasus relatives to the evolution history of Chinese cherry. A separate genetic structure was detected in wild Chinese cherries and rough geographical structures were observed in cultivated Chinese cherries. One wild (wild Chinese cherry, WC) and two cultivated (cultivated Chinese cherry, CC₁ and CC₂) genetic clusters were defined. Our approximate Bayesian computation analyses supported an independent domestication history with two domestication events for CC₁ and CC₂, happening about 3900 and 2200 years ago, respectively. Moderate loss of genetic diversity, over 1000-year domestication bottlenecks and divergent domestication in fruit traits were also detected in cultivated Chinese cherries, which is highly correlated to long-term clonal propagation and different domestication trends and preferences. Our study is the first to comprehensively and systematically investigate the structure patterns and domestication history for Chinese cherry, providing important references for revealing the evolution and domestication history of perennial woody fruit trees.</p

Image_1.TIFF

<p>Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don] is a commercially important fruit crop in China, but its structure patterns and domestication history remain imprecise. To address these questions, we estimated the genetic structure and domestication history of Chinese cherry using 19 nuclear microsatellite markers and 650 representative accessions (including 118 Cerasus relatives) selected throughout their natural eco-geographical distributions. Our structure analyses detected no genetic contribution from Cerasus relatives to the evolution history of Chinese cherry. A separate genetic structure was detected in wild Chinese cherries and rough geographical structures were observed in cultivated Chinese cherries. One wild (wild Chinese cherry, WC) and two cultivated (cultivated Chinese cherry, CC₁ and CC₂) genetic clusters were defined. Our approximate Bayesian computation analyses supported an independent domestication history with two domestication events for CC₁ and CC₂, happening about 3900 and 2200 years ago, respectively. Moderate loss of genetic diversity, over 1000-year domestication bottlenecks and divergent domestication in fruit traits were also detected in cultivated Chinese cherries, which is highly correlated to long-term clonal propagation and different domestication trends and preferences. Our study is the first to comprehensively and systematically investigate the structure patterns and domestication history for Chinese cherry, providing important references for revealing the evolution and domestication history of perennial woody fruit trees.</p

Histogram of cluster of COG classification of <i>Cocos nucifera</i> sequences deposited in the NCBI database and <i>de novo</i> assembled unigenes.

<p>14,741 assembled unigenes were annotated, falling into 25 clusters.</p

Summary of RNA-Seq and <i>de novo</i> assembly of <i>Cocos nucifera</i> results.

<p>Summary of RNA-Seq and <i>de novo</i> assembly of <i>Cocos nucifera</i> results.</p

Histogram of GO classifications of assembled <i>Cocos nucifera</i> unigenes.

<p>Results are summarized for three main GO categories: biological process, cellular component and molecular function.</p

Statistical analysis of a <i>de novo</i> assembly of <i>Cocos nucifera</i> short reads generated by Illumina Hiseq™ 2000 sequencing.

<p>The distribution of assembled contigs and unigene lengths is shown (127,952 contigs and 57,304 unigenes were generated in the study).</p

Classification of 347 unigenes involved in fatty acid biosynthesis and metabolism.

<p>Classification of 347 unigenes involved in fatty acid biosynthesis and metabolism.</p