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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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Cassava comparative genomes.(a) Venn diagram of SNVs/InDels diversity of the cassava genomes of W14, KU50 and CAS36 sequenced in this study with comparison to the AM560 genome sequences previously released. The number of SNVs is listed and the number of InDels is shown in parentheses. (b) Chromosome in situ hybridization showing the repeated occurrence of 45S (Nucleolus organizer, NOR), LTR and chromosome numbers (2n=36) of cultivar KU50. (c) A CirCOS (http://circos.ca/) figure showing synteny between three paralogous cassava genomic regions and their putative orthologues present in R. communis and A. thaliana genomes. Coloured lines connect the cassava scaffolds to the A. thaliana chromosomes and R. communis scaffolds. The line distances across different scaffolds denote the similarities of the segments, with a longer line indicating a higher similarity. (d) Gene tree showing the divergence time of the wild ancestor subspecies to cultivars, referenced to neighbour species in the Euphorbiaceae family inferred from sequence comparison to 71 chloroplast genes from eight different plant species. Mtr: Medicago truncatula, Csa: Cucumis sativus, Ptr: Populus trichocarpa, Pni: Populus nigra, Ptd: Populus trichocarpa x Populus deltoids, Rco: Ricinus communis, Ees: Euphorbia esula, Jcu: Jatropha curcas, Mef-W14: Manihot esculenta ssp. flabellifolia (W14), Mes-KU50: Manihot esculenta ssp. esculenta (KU50), Mes-AM560: Manihot esculenta ssp. esculenta (cultivar AM560).
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f1: Cassava comparative genomes.(a) Venn diagram of SNVs/InDels diversity of the cassava genomes of W14, KU50 and CAS36 sequenced in this study with comparison to the AM560 genome sequences previously released. The number of SNVs is listed and the number of InDels is shown in parentheses. (b) Chromosome in situ hybridization showing the repeated occurrence of 45S (Nucleolus organizer, NOR), LTR and chromosome numbers (2n=36) of cultivar KU50. (c) A CirCOS (http://circos.ca/) figure showing synteny between three paralogous cassava genomic regions and their putative orthologues present in R. communis and A. thaliana genomes. Coloured lines connect the cassava scaffolds to the A. thaliana chromosomes and R. communis scaffolds. The line distances across different scaffolds denote the similarities of the segments, with a longer line indicating a higher similarity. (d) Gene tree showing the divergence time of the wild ancestor subspecies to cultivars, referenced to neighbour species in the Euphorbiaceae family inferred from sequence comparison to 71 chloroplast genes from eight different plant species. Mtr: Medicago truncatula, Csa: Cucumis sativus, Ptr: Populus trichocarpa, Pni: Populus nigra, Ptd: Populus trichocarpa x Populus deltoids, Rco: Ricinus communis, Ees: Euphorbia esula, Jcu: Jatropha curcas, Mef-W14: Manihot esculenta ssp. flabellifolia (W14), Mes-KU50: Manihot esculenta ssp. esculenta (KU50), Mes-AM560: Manihot esculenta ssp. esculenta (cultivar AM560).

Mentions: The genome sequence assembly was searched for repetitive DNA using de novo approaches that identified 36.9% and 25.7% of the W14 and KU50 genomes as repetitive sequences, respectively. The majority of the repetitive elements were long interspersed nuclear elements and long-terminal repeat elements (LTRs, Supplementary Table 8). These results, in addition to the fact that around 35% of the genome could not be assembled, suggest that the cassava genome is highly heterochromatic. This was confirmed by chromosome in-situ hybridization using an LTR probe (Fig. 1b).


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)

Cassava comparative genomes.(a) Venn diagram of SNVs/InDels diversity of the cassava genomes of W14, KU50 and CAS36 sequenced in this study with comparison to the AM560 genome sequences previously released. The number of SNVs is listed and the number of InDels is shown in parentheses. (b) Chromosome in situ hybridization showing the repeated occurrence of 45S (Nucleolus organizer, NOR), LTR and chromosome numbers (2n=36) of cultivar KU50. (c) A CirCOS (http://circos.ca/) figure showing synteny between three paralogous cassava genomic regions and their putative orthologues present in R. communis and A. thaliana genomes. Coloured lines connect the cassava scaffolds to the A. thaliana chromosomes and R. communis scaffolds. The line distances across different scaffolds denote the similarities of the segments, with a longer line indicating a higher similarity. (d) Gene tree showing the divergence time of the wild ancestor subspecies to cultivars, referenced to neighbour species in the Euphorbiaceae family inferred from sequence comparison to 71 chloroplast genes from eight different plant species. Mtr: Medicago truncatula, Csa: Cucumis sativus, Ptr: Populus trichocarpa, Pni: Populus nigra, Ptd: Populus trichocarpa x Populus deltoids, Rco: Ricinus communis, Ees: Euphorbia esula, Jcu: Jatropha curcas, Mef-W14: Manihot esculenta ssp. flabellifolia (W14), Mes-KU50: Manihot esculenta ssp. esculenta (KU50), Mes-AM560: Manihot esculenta ssp. esculenta (cultivar AM560).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Cassava comparative genomes.(a) Venn diagram of SNVs/InDels diversity of the cassava genomes of W14, KU50 and CAS36 sequenced in this study with comparison to the AM560 genome sequences previously released. The number of SNVs is listed and the number of InDels is shown in parentheses. (b) Chromosome in situ hybridization showing the repeated occurrence of 45S (Nucleolus organizer, NOR), LTR and chromosome numbers (2n=36) of cultivar KU50. (c) A CirCOS (http://circos.ca/) figure showing synteny between three paralogous cassava genomic regions and their putative orthologues present in R. communis and A. thaliana genomes. Coloured lines connect the cassava scaffolds to the A. thaliana chromosomes and R. communis scaffolds. The line distances across different scaffolds denote the similarities of the segments, with a longer line indicating a higher similarity. (d) Gene tree showing the divergence time of the wild ancestor subspecies to cultivars, referenced to neighbour species in the Euphorbiaceae family inferred from sequence comparison to 71 chloroplast genes from eight different plant species. Mtr: Medicago truncatula, Csa: Cucumis sativus, Ptr: Populus trichocarpa, Pni: Populus nigra, Ptd: Populus trichocarpa x Populus deltoids, Rco: Ricinus communis, Ees: Euphorbia esula, Jcu: Jatropha curcas, Mef-W14: Manihot esculenta ssp. flabellifolia (W14), Mes-KU50: Manihot esculenta ssp. esculenta (KU50), Mes-AM560: Manihot esculenta ssp. esculenta (cultivar AM560).
Mentions: The genome sequence assembly was searched for repetitive DNA using de novo approaches that identified 36.9% and 25.7% of the W14 and KU50 genomes as repetitive sequences, respectively. The majority of the repetitive elements were long interspersed nuclear elements and long-terminal repeat elements (LTRs, Supplementary Table 8). These results, in addition to the fact that around 35% of the genome could not be assembled, suggest that the cassava genome is highly heterochromatic. This was confirmed by chromosome in-situ hybridization using an LTR probe (Fig. 1b).

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