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Title: Manihot esculenta cultivar:W14 and KU50 : Cassava genome from a wild ancestor to cultivated variety      
keywords:
Genome sequencing and assembly
ID:
PRJNA236442
description:
Cassava is one of the most important food crops in Africa, South East Asia, and Latin America, and also has a huge potential for industrial uses, particularly in poor countries, where extreme environmental conditions, such as drought, are common. Cassava's high photosynthetic capacity and its superior water use efficiency make it not only a preferred crop in adverse conditions, but also an excellent model system to understand adaptation to tropical environments. Cassava (Manihot esculenta Crantz), a heterozygous diploid (2n=36) species in the Euphorbiaceae, is a major source of food in tropical and subtropical regions. Salient characteristics include a remarkable carbohydrate production potential and high adaptability to diverse environments. Here, we present two draft genome sequences of a wild ancestor W14 (M. esculenta ssp. flabellifolia) and a domesticated variety KU50, and compare them to each other and to the draft genome of the partial inbred line AM560. A total of 28,799 gene models across the three genomes were identified, of these 1,584 appeared uniquely in W14 whereas 1,678 were specific to the cultivated species. High heterozygosity and millions of single nucleotide variations were discovered. Selection pressure of homologous genes and comparative transcriptomics evidenced two contrasting evolution patterns. Genes involved in photosynthesis efficiency, starch accumulation, as well as heat and oxidative stress have been positively selected and their expression has been up regulated. In contrast, genes related to cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been subject to negative selection and down regulated. These events took place approximately 0.5 million years ago when the cultivated species diverged from its wild ancestor. Structural variation of miRNA genes and altered retrotransposon regulation between wild and domesticated varieties could explain a shift in carbon flux to an increased starch accumulation and minimization of cyanogenic glucoside content. These new cassava genome sequences and findings reported here will contribute to better understanding biology and ultimately lead to genetic improvement in cassava.
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA236442
authentication:
none
authorization:
none
dateReleased:
07-31-2014
name:
Manihot esculenta
ncbiID:
ncbitax:3983
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject