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High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources.

Perdereau AC, Douglas GC, Hodkinson TR, Kelleher CT - Biotechnol Biofuels (2013)

Bottom Line: However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions.The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus.This study characterises the variation in several lignocellulose gene markers for such purposes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Teagasc, Agriculture and Food Development Authority, Kinsealy Research Centre, Malahide Road, Dublin, D17, Ireland. perderea@tcd.ie.

ABSTRACT

Background: Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation.

Results: Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix.

Conclusions: The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes.

No MeSH data available.


Midpoint rooted, bootstrapped trees based on the eight genes analysed by direct sequencing (and the genotypes where most of the sequences were present)generated using maximum likelihood in PhyML with HKY85+G substitution model. Asterisks indicate nodes with 50% or higher bootstrap support. The three Salix subgenera (according to most authorities) are indicated. Trees are shown with the P. trichocarpa gene model and P. tremula sequences included (Figure 4A) or excluded (Figure 4B).
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Figure 4: Midpoint rooted, bootstrapped trees based on the eight genes analysed by direct sequencing (and the genotypes where most of the sequences were present)generated using maximum likelihood in PhyML with HKY85+G substitution model. Asterisks indicate nodes with 50% or higher bootstrap support. The three Salix subgenera (according to most authorities) are indicated. Trees are shown with the P. trichocarpa gene model and P. tremula sequences included (Figure 4A) or excluded (Figure 4B).

Mentions: In order to explore similarities or dissimilarities in the data, phylogenetic trees were generated with maximum parsimony in PAUP 4.0 and maximum likelihood in PhyML with HKY85+G. The two types of analysis gave the same results. Therefore only the trees from the PhyML analyses are shown (Figure 4). These trees are based on the eight genes analysed by direct sequencing and the genotypes where most of the sequences were present, with the P. trichocarpa gene model and P. tremula sequences included (Figure 4A) or excluded to improve resolution around the Salix samples (Figure 4B).


High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources.

Perdereau AC, Douglas GC, Hodkinson TR, Kelleher CT - Biotechnol Biofuels (2013)

Midpoint rooted, bootstrapped trees based on the eight genes analysed by direct sequencing (and the genotypes where most of the sequences were present)generated using maximum likelihood in PhyML with HKY85+G substitution model. Asterisks indicate nodes with 50% or higher bootstrap support. The three Salix subgenera (according to most authorities) are indicated. Trees are shown with the P. trichocarpa gene model and P. tremula sequences included (Figure 4A) or excluded (Figure 4B).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750764&req=5

Figure 4: Midpoint rooted, bootstrapped trees based on the eight genes analysed by direct sequencing (and the genotypes where most of the sequences were present)generated using maximum likelihood in PhyML with HKY85+G substitution model. Asterisks indicate nodes with 50% or higher bootstrap support. The three Salix subgenera (according to most authorities) are indicated. Trees are shown with the P. trichocarpa gene model and P. tremula sequences included (Figure 4A) or excluded (Figure 4B).
Mentions: In order to explore similarities or dissimilarities in the data, phylogenetic trees were generated with maximum parsimony in PAUP 4.0 and maximum likelihood in PhyML with HKY85+G. The two types of analysis gave the same results. Therefore only the trees from the PhyML analyses are shown (Figure 4). These trees are based on the eight genes analysed by direct sequencing and the genotypes where most of the sequences were present, with the P. trichocarpa gene model and P. tremula sequences included (Figure 4A) or excluded to improve resolution around the Salix samples (Figure 4B).

Bottom Line: However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions.The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus.This study characterises the variation in several lignocellulose gene markers for such purposes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Teagasc, Agriculture and Food Development Authority, Kinsealy Research Centre, Malahide Road, Dublin, D17, Ireland. perderea@tcd.ie.

ABSTRACT

Background: Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation.

Results: Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix.

Conclusions: The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes.

No MeSH data available.