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Cassava genome from a wild ancestor to cultivated varieties.

Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, Møller BL, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJ, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, Jørgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, López-Lavalle LA, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K, Peng M - Nat Commun (2014)

Bottom Line: Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication.Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava.These results may contribute to genetic improvement of cassava through better understanding of its biology.

View Article: PubMed Central - PubMed

Affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.

ABSTRACT
Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.

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Selection pressure and carbon flux diversification in cassava.(a) Chart for synonymous substitution (Ks) and nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) between wild W14 and cultivated variety (WC) and between cultivated varieties (CC). Ka/Ks=1 indicates genes with neutral selection, Ka/Ks>1 indicates positive selection and Ka/Ks<1 indicates negative selection. (b) The differential expression patterns of genes involved in photosynthesis, Calvin cycle, sugar transport and starch synthesis in storage roots and leaves between cultivated varieties (KU50 and Arg7) and wild ancestor (W14) revealed by digital transcriptome sequencing. (c) A model of high-efficient starch accumulation in the tuber roots of domesticated cassava. Red arrows present the carbon flux directions in cultivar and blue arrows indicate the carbon flux directions in wild W14. The width of the arrow indicates the strength of carbon flux. The gene symbol marked in red shows genes with copy number expansion in cultivars. cPGM, cytoplasmic phosphor-glucomutase; GPI, glucose-6-phosphate isomerase; G6PT, glucose-6-phosphate/phosphate translocator; pPGM, phospho-glucomutase; SBE, starch branching enzyme; SS, starch synthase; SUT, sucrose transporter; TPT, triosephosphate translocator; UTP, uridine triphosphate.
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f2: Selection pressure and carbon flux diversification in cassava.(a) Chart for synonymous substitution (Ks) and nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) between wild W14 and cultivated variety (WC) and between cultivated varieties (CC). Ka/Ks=1 indicates genes with neutral selection, Ka/Ks>1 indicates positive selection and Ka/Ks<1 indicates negative selection. (b) The differential expression patterns of genes involved in photosynthesis, Calvin cycle, sugar transport and starch synthesis in storage roots and leaves between cultivated varieties (KU50 and Arg7) and wild ancestor (W14) revealed by digital transcriptome sequencing. (c) A model of high-efficient starch accumulation in the tuber roots of domesticated cassava. Red arrows present the carbon flux directions in cultivar and blue arrows indicate the carbon flux directions in wild W14. The width of the arrow indicates the strength of carbon flux. The gene symbol marked in red shows genes with copy number expansion in cultivars. cPGM, cytoplasmic phosphor-glucomutase; GPI, glucose-6-phosphate isomerase; G6PT, glucose-6-phosphate/phosphate translocator; pPGM, phospho-glucomutase; SBE, starch branching enzyme; SS, starch synthase; SUT, sucrose transporter; TPT, triosephosphate translocator; UTP, uridine triphosphate.

Mentions: The synonymous (Ks) and nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) of the gene set were used to describe evolutionary signatures of the cassava genome3536 (Supplementary Note 16, Supplementary Fig. 26). Approximately 2,818 genes were strictly positively selected (Fig. 2a, Ka/Ks>1), 436 genes were negatively selected (Fig. 2a, Ka/Ks<1) and 9,298 genes were selection-neutral (Fig. 2a, Ka/Ks=1) during evolution of cultivated varieties, whereas 6,342 genes exhibited lack of neutral or selected divergence between cultivars (Fig. 2a, Ka=Ks=0, Ka=0, Ks>0 and Ka>0, Ks=0) (Supplementary Tables 13, 14 and 15). By comparison, we found that 1,133 genes have been heavily selected in the domesticated cultivar, indicating a selective sweep. Analyses of GO functional categories indicated that those genes were mainly enriched in four categories: (i) ‘developmental process’ including cell differentiation and organ development such as leaf, stem, storage root and fruit; (ii) ‘metabolic process’ centred around cell wall polysaccharide synthesis, secondary metabolites and fatty acid metabolism; (iii) ‘biological regulation’ involved in regulation of cell size, cellular metabolism, immune and transcription; (iv) ‘response to stimulus’ including abiotic stresses such as light, temperature, water and oxygen, and biotic stresses caused by viral, bacterial and fungal, and response to hormones such as abscisic acid, ethylene, jasmonic acid and brassinosteroids (Supplementary Fig. 27). The enrichments in such GO categories suggested that those genes that underwent selection cover nearly every aspect of phenotypic variations necessary for cassava cultivation.


Cassava genome from a wild ancestor to cultivated varieties.

Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, Møller BL, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJ, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, Jørgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, López-Lavalle LA, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K, Peng M - Nat Commun (2014)

Selection pressure and carbon flux diversification in cassava.(a) Chart for synonymous substitution (Ks) and nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) between wild W14 and cultivated variety (WC) and between cultivated varieties (CC). Ka/Ks=1 indicates genes with neutral selection, Ka/Ks>1 indicates positive selection and Ka/Ks<1 indicates negative selection. (b) The differential expression patterns of genes involved in photosynthesis, Calvin cycle, sugar transport and starch synthesis in storage roots and leaves between cultivated varieties (KU50 and Arg7) and wild ancestor (W14) revealed by digital transcriptome sequencing. (c) A model of high-efficient starch accumulation in the tuber roots of domesticated cassava. Red arrows present the carbon flux directions in cultivar and blue arrows indicate the carbon flux directions in wild W14. The width of the arrow indicates the strength of carbon flux. The gene symbol marked in red shows genes with copy number expansion in cultivars. cPGM, cytoplasmic phosphor-glucomutase; GPI, glucose-6-phosphate isomerase; G6PT, glucose-6-phosphate/phosphate translocator; pPGM, phospho-glucomutase; SBE, starch branching enzyme; SS, starch synthase; SUT, sucrose transporter; TPT, triosephosphate translocator; UTP, uridine triphosphate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4214410&req=5

f2: Selection pressure and carbon flux diversification in cassava.(a) Chart for synonymous substitution (Ks) and nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) between wild W14 and cultivated variety (WC) and between cultivated varieties (CC). Ka/Ks=1 indicates genes with neutral selection, Ka/Ks>1 indicates positive selection and Ka/Ks<1 indicates negative selection. (b) The differential expression patterns of genes involved in photosynthesis, Calvin cycle, sugar transport and starch synthesis in storage roots and leaves between cultivated varieties (KU50 and Arg7) and wild ancestor (W14) revealed by digital transcriptome sequencing. (c) A model of high-efficient starch accumulation in the tuber roots of domesticated cassava. Red arrows present the carbon flux directions in cultivar and blue arrows indicate the carbon flux directions in wild W14. The width of the arrow indicates the strength of carbon flux. The gene symbol marked in red shows genes with copy number expansion in cultivars. cPGM, cytoplasmic phosphor-glucomutase; GPI, glucose-6-phosphate isomerase; G6PT, glucose-6-phosphate/phosphate translocator; pPGM, phospho-glucomutase; SBE, starch branching enzyme; SS, starch synthase; SUT, sucrose transporter; TPT, triosephosphate translocator; UTP, uridine triphosphate.
Mentions: The synonymous (Ks) and nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) of the gene set were used to describe evolutionary signatures of the cassava genome3536 (Supplementary Note 16, Supplementary Fig. 26). Approximately 2,818 genes were strictly positively selected (Fig. 2a, Ka/Ks>1), 436 genes were negatively selected (Fig. 2a, Ka/Ks<1) and 9,298 genes were selection-neutral (Fig. 2a, Ka/Ks=1) during evolution of cultivated varieties, whereas 6,342 genes exhibited lack of neutral or selected divergence between cultivars (Fig. 2a, Ka=Ks=0, Ka=0, Ks>0 and Ka>0, Ks=0) (Supplementary Tables 13, 14 and 15). By comparison, we found that 1,133 genes have been heavily selected in the domesticated cultivar, indicating a selective sweep. Analyses of GO functional categories indicated that those genes were mainly enriched in four categories: (i) ‘developmental process’ including cell differentiation and organ development such as leaf, stem, storage root and fruit; (ii) ‘metabolic process’ centred around cell wall polysaccharide synthesis, secondary metabolites and fatty acid metabolism; (iii) ‘biological regulation’ involved in regulation of cell size, cellular metabolism, immune and transcription; (iv) ‘response to stimulus’ including abiotic stresses such as light, temperature, water and oxygen, and biotic stresses caused by viral, bacterial and fungal, and response to hormones such as abscisic acid, ethylene, jasmonic acid and brassinosteroids (Supplementary Fig. 27). The enrichments in such GO categories suggested that those genes that underwent selection cover nearly every aspect of phenotypic variations necessary for cassava cultivation.

Bottom Line: Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication.Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava.These results may contribute to genetic improvement of cassava through better understanding of its biology.

View Article: PubMed Central - PubMed

Affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.

ABSTRACT
Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.

Show MeSH