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• Claros, M
• Bautista, R
• Guerrero-Fernández, D
• Benzerki, H
• Seoane, P
• Fernández-Pozo, N
• [+] on Google Scholar
• Claros, M
• Bautista, R
• Guerrero-Fernández, D
• Benzerki, H
• Seoane, P
• Fernández-Pozo, N
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• Claros, M
• Bautista, R
• Guerrero-Fernández, D
• Benzerki, H
• Seoane, P
• Fernández-Pozo, N

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Biology 2012, 1(2), 439-459; doi:10.3390/biology1020439

Review

Why Assembling Plant Genome Sequences Is So Challenging

Manuel Gonzalo Claros ^1,2,* , Rocío Bautista ² , Darío Guerrero-Fernández ² , Hicham Benzerki ^1,2 , Pedro Seoane ¹  and Noé Fernández-Pozo ¹

¹ Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain ² 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

(This article belongs to the Special Issue Next Generation Sequencing Approaches in Biology)

Download PDF Full-Text [203 KB, uploaded 18 September 2012 11:55 CEST]

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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