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Why Assembling Plant Genome Sequences Is So Challenging
Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain
Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain
* Author to whom correspondence should be addressed.
Received: 16 July 2012; in revised form: 5 September 2012 / Accepted: 6 September 2012 / Published: 18 September 2012
Abstract: In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed.
Keywords: plant sequencing; NGS; complexity; repeats; assemblers; polyploidy; bioinformatics
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Claros, M.G.; Bautista, R.; Guerrero-Fernández, D.; Benzerki, H.; Seoane, P.; Fernández-Pozo, N. Why Assembling Plant Genome Sequences Is So Challenging. Biology 2012, 1, 439-459.
Claros MG, Bautista R, Guerrero-Fernández D, Benzerki H, Seoane P, Fernández-Pozo N. Why Assembling Plant Genome Sequences Is So Challenging. Biology. 2012; 1(2):439-459.
Claros, Manuel Gonzalo; Bautista, Rocío; Guerrero-Fernández, Darío; Benzerki, Hicham; Seoane, Pedro; Fernández-Pozo, Noé. 2012. "Why Assembling Plant Genome Sequences Is So Challenging." Biology 1, no. 2: 439-459.