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

Why Assembling Plant Genome Sequences Is So Challenging

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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)
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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
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.


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