Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum
Identifieur interne : 000046 ( Main/Merge ); précédent : 000045; suivant : 000047Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum
Auteurs : Qing Zhang [République populaire de Chine] ; Weichang Hu [République populaire de Chine] ; Fan Zhu [États-Unis] ; Liming Wang [République populaire de Chine] ; Qingyi Yu [États-Unis] ; Ray Ming [République populaire de Chine, États-Unis] ; Jisen Zhang [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
Sugarcane is an economically important crop contributing to about 80 % of the world sugar production. Increasing efforts in molecular biological studies have been performed for improving the sugar yield and other relevant important agronomic traits. However, due to sugarcane’s complicated genomes, it is still challenging to study the genetic basis of traits, such as sucrose accumulation. Sucrose transporters (SUTs) are critical for both phloem loading in source tissue and sucrose uptaking in sink tissue, and are considered to be the control points for regulating sucrose storage. However, no genomic study for sugarcane sucrose transporter (SsSUT) families has been reported up to date.
By using comparative genomics and bacterial artificial chromosomes (BACs), six SUT genes were identified and characterized in
In this study, we presented the first comprehensive genomic study for a whole gene family, the SUT family, in
The online version of this article (doi:10.1186/s12864-016-2419-6) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-2419-6
PubMed: 26830680
PubMed Central: 4736615
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<author><name sortKey="Zhang, Jisen" sort="Zhang, Jisen" uniqKey="Zhang J" first="Jisen" last="Zhang">Jisen Zhang</name>
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<wicri:regionArea>Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou</wicri:regionArea>
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<wicri:regionArea>College of Life Sciences, Fujian Normal University, Fuzhou</wicri:regionArea>
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<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2016">2016</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Sugarcane is an economically important crop contributing to about 80 % of the world sugar production. Increasing efforts in molecular biological studies have been performed for improving the sugar yield and other relevant important agronomic traits. However, due to sugarcane’s complicated genomes, it is still challenging to study the genetic basis of traits, such as sucrose accumulation. Sucrose transporters (SUTs) are critical for both phloem loading in source tissue and sucrose uptaking in sink tissue, and are considered to be the control points for regulating sucrose storage. However, no genomic study for sugarcane sucrose transporter (SsSUT) families has been reported up to date.</p>
</sec>
<sec><title>Results</title>
<p>By using comparative genomics and bacterial artificial chromosomes (BACs), six SUT genes were identified and characterized in <italic>S. spontaenum</italic>
. Phylogenetic analyses revealed that the two pairs <italic>SsSUTs</italic>
(<italic>SsSUT1</italic>
/<italic>SsSUT3</italic>
and <italic>SsSUT5</italic>
/<italic>SsSUT6</italic>
) could be clustered together into two separate monocot specific SUT groups, while <italic>SsSUT2</italic>
and <italic>SsSUT4</italic>
were separated into the other two groups, with members from both dicot and monocot species. Gene structure comparison demonstrated that the number and position of exons/introns in <italic>SUTs</italic>
were highly conserved among the close orthologs; in contrast, there were variations among the paralogous <italic>SUTs</italic>
in <italic>Sacchuarm</italic>
. Though with the high polyploidy level, gene allelic haplotype comparative analysis showed that the examined four <italic>SsSUT</italic>
member<italic>s</italic>
exhibited conservations of gene structures and amino acid sequences among the allelic haplotypes accompanied by variations of intron sizes. Gene expression analyses were performed for tissues from seedlings under drought stress and mature plants of three <italic>Saccharum</italic>
species (<italic>S.officinarnum</italic>
, <italic>S.spotaneum</italic>
and <italic>S.robustum</italic>
). Both <italic>SUT1</italic>
and <italic>SUT4</italic>
expressed abundantly at different conditions. <italic>SUT2</italic>
had similar expression level in all of the examined tissues, but <italic>SUT3</italic>
was undetectable. Both of <italic>SUT5</italic>
and <italic>SUT6</italic>
had lower expression level than other gene member, and expressed stronger in source leaves and are likely to play roles in phloem loading. In the seeding plant leave under water stress, four genes <italic>SUT1</italic>
, <italic>SUT2</italic>
, <italic>SUT4</italic>
and <italic>SUT5</italic>
were detectable. In these detectable genes, <italic>SUT1</italic>
and <italic>SUT4</italic>
were down regulated, while, <italic>SUT2</italic>
and <italic>SUT5</italic>
were up regulated.</p>
</sec>
<sec><title>Conclusions</title>
<p>In this study, we presented the first comprehensive genomic study for a whole gene family, the SUT family, in <italic>Saccharum</italic>
. We speculated that there were six <italic>SUT</italic>
members in the <italic>S. spotaneum</italic>
genome. Out of the six members, <italic>SsSUTs</italic>
, <italic>SsSUT5</italic>
and <italic>SsSUT6</italic>
were recent duplication genes accompanied by rapid evolution, while, <italic>SsSUT2</italic>
and <italic>SsSUT4</italic>
were the ancient members in the families. Despite the high polypoidy genome, functional redundancy may not exist among the SUTs allelic haplotypes supported by the evidence of strong purifying selection of the gene allele. <italic>SUT3</italic>
could be a low active member in the family because it is undetectable in our study, but it might not be a pseudogene because it harbored integrated gene structure. <italic>SUT1</italic>
and <italic>SUT4</italic>
were the main members for the sucrose transporter, while, these <italic>SUTs</italic>
had sub-functional divergence in response to sucrose accumulation and plant development in <italic>Saccharum</italic>
.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12864-016-2419-6) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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<author><name sortKey="Beyhl, D" uniqKey="Beyhl D">D Beyhl</name>
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<author><name sortKey="Marten, I" uniqKey="Marten I">I Marten</name>
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<author><name sortKey="Wormit, A" uniqKey="Wormit A">A Wormit</name>
</author>
<author><name sortKey="Neuhaus, E" uniqKey="Neuhaus E">E Neuhaus</name>
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<author><name sortKey="Poschet, G" uniqKey="Poschet G">G Poschet</name>
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<author><name sortKey="Dealtry, G" uniqKey="Dealtry G">G Dealtry</name>
</author>
<author><name sortKey="Roux, S" uniqKey="Roux S">S Roux</name>
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<author><name sortKey="Bradley, G" uniqKey="Bradley G">G Bradley</name>
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