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Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters.

Miao Z, Li D, Zhang Z, Dong J, Su Z, Wang T - BMC Genomics (2012)

Bottom Line: Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula.A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created.A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.

ABSTRACT

Background: Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula.

Description: The M. truncatula transporter database (MTDB) contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG) V3.5 V3 and the M. truncatula Gene Index (MTGI) V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments.

Conclusions: In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://bioinformatics.cau.edu.cn/MtTransporter/.

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Phylogenetic tree analysis of the Amt family. This figure shows the result of phylogenetic tree analysis of Amt, an example of the 162 families in the Medicago truncatula transporter database. Individual members of the Amt family were further clustered and color-coded based on the result of phylogenetic analysis and TC numbering system. M. truncatula Amts can be classified into two groups: Amt1 and Amt2. Green markers refer to Arabidopsis thaliana sequences. Red markers refer to M. truncatula sequences. Each group contains links to individual protein pages.
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Figure 2: Phylogenetic tree analysis of the Amt family. This figure shows the result of phylogenetic tree analysis of Amt, an example of the 162 families in the Medicago truncatula transporter database. Individual members of the Amt family were further clustered and color-coded based on the result of phylogenetic analysis and TC numbering system. M. truncatula Amts can be classified into two groups: Amt1 and Amt2. Green markers refer to Arabidopsis thaliana sequences. Red markers refer to M. truncatula sequences. Each group contains links to individual protein pages.

Mentions: We designed a user-friendly web site interface. Users can browse or search different functions of content classes based on various choices. Using the search function, for example, users can search for one type of putative transporter or specify certain information such as gene family, transporter name, or M. truncatula ID (MtID). In addition, a batch search function is achieved, through which users can search the transporter information by inputting a set of MtIDs. A brief summary on the page can provide users with a useful platform for searching. The MTDB supports a comprehensive treeview-like navigation interface. Users can browse the TC numbering system of every type of M. truncatula transporter with a collapsible function. The results are grouped by transporter family. To make browsing more convenient and scientific, we performed phylogenetic tree analysis of each family. Protein sequences in each family were used to generate a midpoint-rooted neighbor-joining tree. The trees were created by Mega 4.0[28] with the default parameters. Individual members of the families were further clustered into groups based on TC numbering system and evolutionary analysis [Figure 2 and Additional file 2]. Each group contains links to individual protein pages. Each putative transport protein is presented on separate web pages where users can find detailed information such as transporter function annotations; TC classifications; transmembrane segment predictions by TMHMM; genomic locus information; EST mapping results; domain annotation predictions by Pfam; 3D template predictions; expression annotations; and protein, cDNA, and genome sequences [Figure 3]. The protein and CDS sequences in MTDB are readily available for BLAST searches. Users can submit a single peptide or nucleotide sequence in the "BLAST" section. Location distribution maps, expression annotations, and 3D templates can also be browsed quickly using the "Advanced Tools" function [Figure 4].


Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters.

Miao Z, Li D, Zhang Z, Dong J, Su Z, Wang T - BMC Genomics (2012)

Phylogenetic tree analysis of the Amt family. This figure shows the result of phylogenetic tree analysis of Amt, an example of the 162 families in the Medicago truncatula transporter database. Individual members of the Amt family were further clustered and color-coded based on the result of phylogenetic analysis and TC numbering system. M. truncatula Amts can be classified into two groups: Amt1 and Amt2. Green markers refer to Arabidopsis thaliana sequences. Red markers refer to M. truncatula sequences. Each group contains links to individual protein pages.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3298476&req=5

Figure 2: Phylogenetic tree analysis of the Amt family. This figure shows the result of phylogenetic tree analysis of Amt, an example of the 162 families in the Medicago truncatula transporter database. Individual members of the Amt family were further clustered and color-coded based on the result of phylogenetic analysis and TC numbering system. M. truncatula Amts can be classified into two groups: Amt1 and Amt2. Green markers refer to Arabidopsis thaliana sequences. Red markers refer to M. truncatula sequences. Each group contains links to individual protein pages.
Mentions: We designed a user-friendly web site interface. Users can browse or search different functions of content classes based on various choices. Using the search function, for example, users can search for one type of putative transporter or specify certain information such as gene family, transporter name, or M. truncatula ID (MtID). In addition, a batch search function is achieved, through which users can search the transporter information by inputting a set of MtIDs. A brief summary on the page can provide users with a useful platform for searching. The MTDB supports a comprehensive treeview-like navigation interface. Users can browse the TC numbering system of every type of M. truncatula transporter with a collapsible function. The results are grouped by transporter family. To make browsing more convenient and scientific, we performed phylogenetic tree analysis of each family. Protein sequences in each family were used to generate a midpoint-rooted neighbor-joining tree. The trees were created by Mega 4.0[28] with the default parameters. Individual members of the families were further clustered into groups based on TC numbering system and evolutionary analysis [Figure 2 and Additional file 2]. Each group contains links to individual protein pages. Each putative transport protein is presented on separate web pages where users can find detailed information such as transporter function annotations; TC classifications; transmembrane segment predictions by TMHMM; genomic locus information; EST mapping results; domain annotation predictions by Pfam; 3D template predictions; expression annotations; and protein, cDNA, and genome sequences [Figure 3]. The protein and CDS sequences in MTDB are readily available for BLAST searches. Users can submit a single peptide or nucleotide sequence in the "BLAST" section. Location distribution maps, expression annotations, and 3D templates can also be browsed quickly using the "Advanced Tools" function [Figure 4].

Bottom Line: Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula.A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created.A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.

ABSTRACT

Background: Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula.

Description: The M. truncatula transporter database (MTDB) contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG) V3.5 V3 and the M. truncatula Gene Index (MTGI) V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments.

Conclusions: In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://bioinformatics.cau.edu.cn/MtTransporter/.

Show MeSH