Why Assembling Plant Genome Sequences Is So Challenging

Claros, M. Gonzalo; Bautista, Rocí­o; Guerrero-Fernández, Darío; Benzerki, Hicham; Seoane, Pedro; Fernández-Pozo, Noé

doi:10.3390/biology1020439

Cited by 123 publications

(110 citation statements)

References 104 publications

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“…Our repeat DNA analysis suggested that ∼70% of the genome is repetitive (Table 2). Repeat sequences are difficult to assemble because high-identity reads can derive from different portions of the genome, generating gaps, ambiguities, and collapses in alignment and assembly 89 , 90 . This high repeat DNA content is likely to explain the relatively low scaffold N50 (17,908 bp), even though the sequencing depth exceeds ×100.…”

Section: Resultsmentioning

confidence: 99%

The draft genome ofRuellia speciosa(Beautiful Wild Petunia: Acanthaceae)

Zhuang

Tripp

2017

DNA Res

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The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3′H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3′5′H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3′H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.

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Section: Resultsmentioning

confidence: 99%

The draft genome ofRuellia speciosa(Beautiful Wild Petunia: Acanthaceae)

Zhuang

Tripp

2017

DNA Res

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“…Understanding the biosynthetic pathways and mode of regulation of these compounds in non-model plants, including T. govanianum is difficult due to the lack of genomic information. However, the advent of NGS based high throughput transcriptome sequencing has aided to circumvent the difficulties in such plants3839. NGS approach has been successfully utilized to elucidate key genes and regulators of complex biosynthetic pathways in a number of non-model plants.…”

Section: Discussionmentioning

confidence: 99%

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum

Singh

Bhandawat

et al. 2017

Sci Rep

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Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the molecular level due to the non-availability of genomic resources. To facilitate the basic understanding of the key genes and regulatory mechanism of pharmaceutically important biosynthesis pathways, first spatial transcriptome sequencing of T. govanianum was performed. 151,622,376 (~11.5 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 69,174 transcripts. Functional annotation with multiple public databases identified array of genes involved in steroidal saponin biosynthesis and other secondary metabolite pathways including brassinosteroid, carotenoid, diterpenoid, flavonoid, phenylpropanoid, steroid and terpenoid backbone biosynthesis, and important TF families (bHLH, MYB related, NAC, FAR1, bZIP, B3 and WRKY). Differentially expressed large number of transcripts, together with CYPs and UGTs suggests involvement of these candidates in tissue specific expression. Combined transcriptome and expression analysis revealed that leaf and fruit tissues are the main site of steroidal saponin biosynthesis. In conclusion, comprehensive genomic dataset created in the current study will serve as a resource for identification of potential candidates for genetic manipulation of targeted bioactive metabolites and also contribute for development of functionally relevant molecular marker resource to expedite molecular breeding and conservation efforts in T. govanianum.

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“…When the average GC content was lower than 30%, it will cause the significantly affect in genome sequence quality, and the influence on accuracy larger than integrity. The GC content proportions in the CSG plants were content with the previous reports in mammalian [57], [58], the moderate GC content will not improve the difficult of genome sequencing, and not affect the genome short reads assemble, gene prediction from the genome sequences.…”

Section: Resultsmentioning

confidence: 56%

Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags

et al. 2013

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BackgroundWith the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. Advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. Despite this, genome sequence qualities of multiple plants have not been evaluated.Methodology/Principal FindingIntegrity and accuracy were calculated to evaluate the genome sequence quality of 32 plants. The integrity of a genome sequence is presented by the ratio of chromosome size and genome size (or between scaffold size and genome size), which ranged from 55.31% to nearly 100%. The accuracy of genome sequence was presented by the ratio between matched EST and selected ESTs where 52.93% ∼ 98.28% and 89.02% ∼ 98.85% of the randomly selected clean ESTs could be mapped to chromosome and scaffold sequences, respectively. According to the integrity, accuracy and other analysis of each plant species, thirteen plant species were divided into four levels. Arabidopsis thaliana, Oryza sativa and Zea mays had the highest quality, followed by Brachypodium distachyon, Populus trichocarpa, Vitis vinifera and Glycine max, Sorghum bicolor, Solanum lycopersicum and Fragaria vesca, and Lotus japonicus, Medicago truncatula and Malus × domestica in that order. Assembling the scaffold sequences into chromosome sequences should be the primary task for the remaining nineteen species. Low GC content and repeat DNA influences genome sequence assembly.ConclusionThe quality of plant genome sequences was found to be lower than envisaged and thus the rapid development of genome sequencing projects as well as research on bioinformatics tools and the algorithms of genome sequence assembly should provide increased processing and correction of genome sequences that have already been published.

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Why Assembling Plant Genome Sequences Is So Challenging

Cited by 123 publications

References 104 publications

The draft genome ofRuellia speciosa(Beautiful Wild Petunia: Acanthaceae)

The draft genome ofRuellia speciosa(Beautiful Wild Petunia: Acanthaceae)

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum

Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags

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