Characterization of paralogous protein families in rice

doi:10.1186/1471-2229-8-18

BMC Plant Biology

Volume 8

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Lin H
Ouyang S
Egan A
Nobuta K
Haas BJ
Zhu W
Gu X
Silva JC
Meyers BC
Buell CR

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Ouyang S
Egan A
Nobuta K
Haas BJ
Zhu W
Gu X
Silva JC
Meyers BC
Buell CR
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Research article

Characterization of paralogous protein families in rice

Haining Lin¹^,3^,7 , Shu Ouyang¹ , Amy Egan¹^,6 , Kan Nobuta² , Brian J Haas¹^,5 , Wei Zhu¹ , Xun Gu³^,4 , Joana C Silva¹^,6 , Blake C Meyers² and C Robin Buell¹^,7

¹The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA and J.Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA

²Department of Plant and Soil Sciences & Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA

³Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA

⁴Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA

⁵The Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA

⁶Institute for Genome Sciences & Department of Microbiology & Immunology, University of Maryland, Baltimore, School of Medicine, HSF-II, Rm S-445, 20 Penn St., Baltimore, MD 21201, USA

⁷Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA

author email corresponding author email

BMC Plant Biology 2008, 8:18doi:10.1186/1471-2229-8-18


Published:	19 February 2008

Additional files

Additional File 1:

Putative paralogous protein families within the rice genome.

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Additional File 2:

Rice paralogous protein families with more than one hundred member proteins.

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Additional File 3:

Distribution of non-transposable element-related genes in rice and Arabidopsis. In panel A, the 12 rice chromosomes are shown with paralogous gene family members plotted in blue while single copy genes are plotted in red. Segmental duplicated blocks are indicated in green and centromeres are denoted by a white box. In panel B, the five Arabidopsis chromosomes are shown with paralogous gene family members plotted in blue while single copy genes are plotted in red.

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Additional File 4:

The age distribution of rice paralogous protein families. A) an expanded view of the age distribution. B) the enlarged distribution of rice paralogous protein families with largest ds ≤ 1.5.

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Additional File 5:

Distribution of modal values under d_S≤ 1.5 across rice paralogous protein families. Of all 3,865 paralogous protein families, 2,388 showed a peak under 1.5 in the distribution of all pairwise d_Svalues and are plotted.

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Additional File 6:

Pearson's correlation coefficient (r) versus ds values. A) 0 <d_S≤ 0.1; B) 0.4 <d_S≤ 0.5; C) 1.0 <d_S≤ 1.1; D) 1.4 <d_S≤ 1.5.

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Additional File 7:

Schematic illustration of the domain composition of three related rice paralogous protein families: Family 3722, Family 3193, and Family 3856.

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Additional File 8:

Expression abundance of the rice prolamin genes from Family 3722 and Family 3193 in 18 libraries which were associated with unique, reliable, and significant MPSS tags.

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Additional File 9:

Expression abundance of genes from rice paralogous protein family Family 3856 (contained PF00234) in 18 libraries which were associated with unique, reliable, and significant MPSS tags.

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Additional File 10:

Genome Browser view of the genes encoding rice prolamin proteins with TE-related genes inserted between putative tandem duplications.

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Additional File 11:

Schematic illustration of the domain composition of two rice BBI-related paralogous protein families which have Pfam domain PF00228: Family 3328 and Family 1493.

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Additional File 12:

Neighbor-Joining tree of the rice Bowman-Birk inhibitor protein family Family 3328.

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Additional File 13:

Genome Browser view of the rice genes encoding BBI proteins on chromosome 1.

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