Skip to main content

Main menu

  • Home
  • Content
    • Current Issue
    • Archive
    • Preview Papers
  • Info for
    • Instructions for Authors
    • Submit a Manuscript
    • Advertisers
    • Librarians
    • Subscribers
  • About
    • Editorial Board and Staff
    • About the Journal
    • Terms & Privacy
  • More
    • Alerts
    • Contact Us
  • Other Publications
    • Plant Physiology
    • The Plant Cell
    • Plant Direct
    • The Arabidopsis Book
    • Teaching Tools in Plant Biology
    • ASPB
    • Plantae

User menu

  • My alerts
  • Log in

Search

  • Advanced search
Plant Cell
  • Other Publications
    • Plant Physiology
    • The Plant Cell
    • Plant Direct
    • The Arabidopsis Book
    • Teaching Tools in Plant Biology
    • ASPB
    • Plantae
  • My alerts
  • Log in
Plant Cell

Advanced Search

  • Home
  • Content
    • Current Issue
    • Archive
    • Preview Papers
  • Info for
    • Instructions for Authors
    • Submit a Manuscript
    • Advertisers
    • Librarians
    • Subscribers
  • About
    • Editorial Board and Staff
    • About the Journal
    • Terms & Privacy
  • More
    • Alerts
    • Contact Us
  • Follow PlantCell on Twitter
  • Visit PlantCell on Facebook
  • Visit Plantae
Research ArticleResearch Article
Open Access

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region from Phaseolus vulgaris

Jer-Young Lin, Robert M. Stupar, Christian Hans, David L. Hyten, Scott A. Jackson
Jer-Young Lin
Molecular and Evolutionary Genetics, Purdue University, West Lafayette, Indiana 47907
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert M. Stupar
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christian Hans
Molecular and Evolutionary Genetics, Purdue University, West Lafayette, Indiana 47907
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David L. Hyten
Soybean Genomics and Improvement Lab, U.S. Department of Agriculture–Agricultural Research Service, Beltsville, Maryland 20705
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Scott A. Jackson
Molecular and Evolutionary Genetics, Purdue University, West Lafayette, Indiana 47907
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: sjackson@purdue.edu

Published August 2010. DOI: https://doi.org/10.1105/tpc.110.074229

  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • Figure 1.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 1.

    Annotation Results of Chromosome Segments from Soybean (Gm8 and Gm15) and Phaseolus (Pv5).

    The two soybean homoeologous regions, Gm8 and Gm15, and orthologous Phaseolus region, Pv5, are shown. Black bars are sequence contigs. Gm8 has two physical gaps, and Pv5 has one. Pentagons represent genes. Orange genes have homoeologs and/or orthologs (collinear genes), connected by black lines. Yellow genes do not have homoeologs and orthologs (noncollinear genes). Triangles represent transposons: blue triangles are intact LTR retrotranspsons, pink triangles are solo LTRs, cyan triangles are truncated LTR retrotransposons, and green triangles are non-LTR retrotransposons. Shaded boxes show the duplication events: green boxes show segmental duplications. The purple box shows a tandem duplication. Black numbers are the gene number from annotation results. Insertion times of intact LTR retrotransposons are shown in red. Regions between the two pink dotted lines are physical gaps in Gm8 and their corresponding intervals in Gm15.

  • Figure 2.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 2.

    Distribution of Ks Values of Genes in Both Soybean Homoeologs and Phaseolus.

    Blue circles are Ks values from Pv5-Gm8; green triangles are Ks values from Pv5-Gm15; red boxes are Ks values from Gm8-Gm15. Different zones show the Ks from different homoeologous and orthologous counterparts. Zone I shows the Ks from the pairwise comparison of the two soybean homoeologs and one Phaseolus ortholog. Zone II shows the Ks from the sequence comparisons of Pv5 orthologs and Gm8 homoeologs. Zone III shows the Ks from Pv5 orthologs and Gm15 homoeolog comparisons. Zone IV shows the Ks from homoeologs between Gm8 and Gm15. Numbers below the plot are the annotated gene numbers. Ks value of gene114 (Pv5-Gm15) is ~2.8 due to extensive variation outside the conserved protein domain, and it is not shown here.

  • Figure 3.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 3.

    Heat Maps of Relative Transcript Abundance of Homoeologous Genes on Gm8 and Gm15 for Seven Different Tissue Types.

    The relative positions of 29 tested genes (top to bottom) are shown as colored rectangles along the Gm8 and Gm15 contigs. The numbers on the left are gene annotation results of the 29 tested genes. The transcription level of each gene is indicated as high (red) or low (blue) relative to the respective homoeologous counterpart. Homoeologs with approximately equal transcription levels are shown as black. The scale on the right indicates the coloration used to depict relative transcript proportions between homoeologous copies.

  • Figure 4.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 4.

    Assessment of Tissue-Specific Transcriptional Divergence between Homoeolog Pairs.

    The relative transcriptional proportions of the Gm8 homoeologs are shown for 29 tested gene pairs. The mean Gm8 proportion across two biological replicates is shown in the plot for each gene pair across seven tissue types. The percentage of statistically significant (P < 0.05) tissue × tissue differences detected in a factorial pairwise comparison of the homoeolog proportions among seven tissue types is shown below each gene pair number. There was a wide range (2 to 67%) of transcription variations among homoeolog pairs. The genes are ordered from lowest to highest percentage of tissue × tissue differences among the seven tissue types. Therefore, the gene pairs on the left infrequently exhibited significant tissue-specific transcriptional variation, and the genes on the right frequently exhibited significant tissue-specific transcriptional variation. The red number shown below each percentage indicates the number of informative assays for each homoeolog pair.

Tables

  • Figures
  • Additional Files
    • View popup
    Table 1.

    Number of Transposons (LTR Retrotransposon, Non-LTR Retrotransposon, and DNA Transposon) in the Two Soybean Homoeologous Regions, Gm15 and Gm8

    Classes of TransposonsGm8Gm15
    LTR retrotransposon
        Intact elements16
        Intact elements without TSDs02
        Solo LTRs57
        Solo LTRs without TSDs02
    Truncated element
        Both LTRs partially deleted with TSDs20
        Both LTRs partially deleted without TSDs34
        One LTR deleted, another partially deleted43
    Remnant
        Remnants from insert712
        Remnants from LTR711
    Total2947
    Non-LTR retrotransposon LINE1517
    DNA transposon54
    • View popup
    Table 2.

    Analyses of Genes with Transposon Insertions in Gm8, Gm15, and Pv5

    Features of Genes with Transposon InsertionsGm8Gm15Pv5
    Number of genes with transposon insertions131110
    Percentage of genes with transposon insertions10.0%12.5%9.6%
    Number of transposons inserted into a gene
        Genes with one transposon959
        Genes with two transposons361
        Genes with three transposons100
    Classes of inserted transposons
        LTR retrotransposons899
        Solo LTRs230
        Non-LTR retrotransposons852
    Insertion site in gene
        5′ End010
        Exon663
        Intron12107
        3′ End001
    Insertions into genes with homoeologs
        One homoeolog with transposon insertion67NAa
        Both homoeologs with transposon insertions22NAa
    Insertions into genes with orthologs
        Number of genes with orthologs that have insertions553
        One homoeolog and ortholog with insertions202
        Both homoeologs and ortholog with insertions111
    • ↵a Not applicable.

Additional Files

  • Figures
  • Tables
  • Supplemental Data

    Files in this Data Supplement:

    • Supplemental Figures and Tables
    • Supplemental Dataset 1
    • Supplemental Dataset 2
    • Supplemental Dataset 3
    • Supplemental Dataset 4
    • Supplemental Dataset 5
    • Supplemental Dataset 6
PreviousNext
Back to top

Table of Contents

Print
Download PDF
Article Alerts
Sign In to Email Alerts with your Email Address
Email Article

Thank you for your interest in spreading the word on Plant Cell.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region from Phaseolus vulgaris
(Your Name) has sent you a message from Plant Cell
(Your Name) thought you would like to see the Plant Cell web site.
Citation Tools
Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region from Phaseolus vulgaris
Jer-Young Lin, Robert M. Stupar, Christian Hans, David L. Hyten, Scott A. Jackson
The Plant Cell Aug 2010, 22 (8) 2545-2561; DOI: 10.1105/tpc.110.074229

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region from Phaseolus vulgaris
Jer-Young Lin, Robert M. Stupar, Christian Hans, David L. Hyten, Scott A. Jackson
The Plant Cell Aug 2010, 22 (8) 2545-2561; DOI: 10.1105/tpc.110.074229
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Jump to section

  • Article
    • Abstract
    • INTRODUCTION
    • RESULTS
    • DISCUSSION
    • Conclusions
    • METHODS
    • Acknowledgments
    • Footnotes
    • References
  • Figures & Data
  • Info & Metrics
  • PDF

In this issue

The Plant Cell Online: 22 (8)
The Plant Cell
Vol. 22, Issue 8
Aug 2010
  • Table of Contents
  • Table of Contents (PDF)
  • About the Cover
  • Index by author
  • Advertising (PDF)
  • Front Matter (PDF)
View this article with LENS

More in this TOC Section

  • Metabolically Distinct Pools of Phosphatidylcholine Are Involved in Trafficking of Fatty Acids out of and into the Chloroplast for Membrane Production
  • The Formation of a Camalexin Biosynthetic Metabolon
  • OsCASP1 Is Required for Casparian Strip Formation at Endodermal Cells of Rice Roots for Selective Uptake of Mineral Elements
Show more RESEARCH ARTICLES

Similar Articles

Our Content

  • Home
  • Current Issue
  • Plant Cell Preview
  • Archive
  • Teaching Tools in Plant Biology
  • Plant Physiology
  • Plant Direct
  • Plantae
  • ASPB

For Authors

  • Instructions
  • Submit a Manuscript
  • Editorial Board and Staff
  • Policies
  • Recognizing our Authors

For Reviewers

  • Instructions
  • Peer Review Reports
  • Journal Miles
  • Transfer of reviews to Plant Direct
  • Policies

Other Services

  • Permissions
  • Librarian resources
  • Advertise in our journals
  • Alerts
  • RSS Feeds
  • Contact Us

Copyright © 2019 by The American Society of Plant Biologists

Powered by HighWire