An analysis of synteny of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>sheds new light on the structure, stability and evolution of legume genomes
<p>Abstract</p> <p>Background</p> <p>Most agriculturally important legumes fall within two sub-clades of the Papilionoid legumes: the Phaseoloids and Galegoids, which diverged about 50 Mya. The Phaseoloids are mostly tropical and include crops such as common bean and so...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-01-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/10/45 |
| _version_ | 1818485312106528768 |
|---|---|
| author | Nielsen Anna M Schauser Leif Fredslund Jakob Hougaard Birgit K Guimarães Patricia M Leal-Bertioli Soraya CM Sandal Niels Madsen Lene H Moretzsohn Marcio C Bertioli David J Sato Shusei Tabata Satoshi Cannon Steven B Stougaard Jens |
| author_facet | Nielsen Anna M Schauser Leif Fredslund Jakob Hougaard Birgit K Guimarães Patricia M Leal-Bertioli Soraya CM Sandal Niels Madsen Lene H Moretzsohn Marcio C Bertioli David J Sato Shusei Tabata Satoshi Cannon Steven B Stougaard Jens |
| author_sort | Nielsen Anna M |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Most agriculturally important legumes fall within two sub-clades of the Papilionoid legumes: the Phaseoloids and Galegoids, which diverged about 50 Mya. The Phaseoloids are mostly tropical and include crops such as common bean and soybean. The Galegoids are mostly temperate and include clover, fava bean and the model legumes <it>Lotus </it>and <it>Medicago </it>(both with substantially sequenced genomes). In contrast, peanut (<it>Arachis hypogaea</it>) falls in the Dalbergioid clade which is more basal in its divergence within the Papilionoids. The aim of this work was to integrate the genetic map of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>and improve our understanding of the <it>Arachis </it>genome and legume genomes in general. To do this we placed on the <it>Arachis </it>map, comparative anchor markers defined using a previously described bioinformatics pipeline. Also we investigated the possible role of transposons in the patterns of synteny that were observed.</p> <p>Results</p> <p>The <it>Arachis </it>genetic map was substantially aligned with <it>Lotus </it>and <it>Medicago </it>with most synteny blocks presenting a single main affinity to each genome. This indicates that the last common whole genome duplication within the Papilionoid legumes predated the divergence of <it>Arachis </it>from the Galegoids and Phaseoloids sufficiently that the common ancestral genome was substantially diploidized. The <it>Arachis </it>and model legume genomes comparison made here, together with a previously published comparison of <it>Lotus </it>and <it>Medicago </it>allowed all possible <it>Arachis-Lotus-Medicago </it>species by species comparisons to be made and genome syntenies observed. Distinct conserved synteny blocks and non-conserved regions were present in all genome comparisons, implying that certain legume genomic regions are consistently more stable during evolution than others. We found that in <it>Medicago </it>and possibly also in <it>Lotus</it>, retrotransposons tend to be more frequent in the variable regions. Furthermore, while these variable regions generally have lower densities of single copy genes than the more conserved regions, some harbor high densities of the fast evolving disease resistance genes.</p> <p>Conclusion</p> <p>We suggest that gene space in Papilionoids may be divided into two broadly defined components: more conserved regions which tend to have low retrotransposon densities and are relatively stable during evolution; and variable regions that tend to have high retrotransposon densities, and whose frequent restructuring may fuel the evolution of some gene families.</p> |
| first_indexed | 2024-12-10T16:06:58Z |
| format | Article |
| id | doaj.art-e907931980ab4ee9b60c84ab0100d038 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T16:06:58Z |
| publishDate | 2009-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e907931980ab4ee9b60c84ab0100d0382022-12-22T01:42:13ZengBMCBMC Genomics1471-21642009-01-011014510.1186/1471-2164-10-45An analysis of synteny of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>sheds new light on the structure, stability and evolution of legume genomesNielsen Anna MSchauser LeifFredslund JakobHougaard Birgit KGuimarães Patricia MLeal-Bertioli Soraya CMSandal NielsMadsen Lene HMoretzsohn Marcio CBertioli David JSato ShuseiTabata SatoshiCannon Steven BStougaard Jens<p>Abstract</p> <p>Background</p> <p>Most agriculturally important legumes fall within two sub-clades of the Papilionoid legumes: the Phaseoloids and Galegoids, which diverged about 50 Mya. The Phaseoloids are mostly tropical and include crops such as common bean and soybean. The Galegoids are mostly temperate and include clover, fava bean and the model legumes <it>Lotus </it>and <it>Medicago </it>(both with substantially sequenced genomes). In contrast, peanut (<it>Arachis hypogaea</it>) falls in the Dalbergioid clade which is more basal in its divergence within the Papilionoids. The aim of this work was to integrate the genetic map of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>and improve our understanding of the <it>Arachis </it>genome and legume genomes in general. To do this we placed on the <it>Arachis </it>map, comparative anchor markers defined using a previously described bioinformatics pipeline. Also we investigated the possible role of transposons in the patterns of synteny that were observed.</p> <p>Results</p> <p>The <it>Arachis </it>genetic map was substantially aligned with <it>Lotus </it>and <it>Medicago </it>with most synteny blocks presenting a single main affinity to each genome. This indicates that the last common whole genome duplication within the Papilionoid legumes predated the divergence of <it>Arachis </it>from the Galegoids and Phaseoloids sufficiently that the common ancestral genome was substantially diploidized. The <it>Arachis </it>and model legume genomes comparison made here, together with a previously published comparison of <it>Lotus </it>and <it>Medicago </it>allowed all possible <it>Arachis-Lotus-Medicago </it>species by species comparisons to be made and genome syntenies observed. Distinct conserved synteny blocks and non-conserved regions were present in all genome comparisons, implying that certain legume genomic regions are consistently more stable during evolution than others. We found that in <it>Medicago </it>and possibly also in <it>Lotus</it>, retrotransposons tend to be more frequent in the variable regions. Furthermore, while these variable regions generally have lower densities of single copy genes than the more conserved regions, some harbor high densities of the fast evolving disease resistance genes.</p> <p>Conclusion</p> <p>We suggest that gene space in Papilionoids may be divided into two broadly defined components: more conserved regions which tend to have low retrotransposon densities and are relatively stable during evolution; and variable regions that tend to have high retrotransposon densities, and whose frequent restructuring may fuel the evolution of some gene families.</p>http://www.biomedcentral.com/1471-2164/10/45 |
| spellingShingle | Nielsen Anna M Schauser Leif Fredslund Jakob Hougaard Birgit K Guimarães Patricia M Leal-Bertioli Soraya CM Sandal Niels Madsen Lene H Moretzsohn Marcio C Bertioli David J Sato Shusei Tabata Satoshi Cannon Steven B Stougaard Jens An analysis of synteny of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>sheds new light on the structure, stability and evolution of legume genomes BMC Genomics |
| title | An analysis of synteny of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>sheds new light on the structure, stability and evolution of legume genomes |
| title_full | An analysis of synteny of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>sheds new light on the structure, stability and evolution of legume genomes |
| title_fullStr | An analysis of synteny of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>sheds new light on the structure, stability and evolution of legume genomes |
| title_full_unstemmed | An analysis of synteny of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>sheds new light on the structure, stability and evolution of legume genomes |
| title_short | An analysis of synteny of <it>Arachis </it>with <it>Lotus </it>and <it>Medicago </it>sheds new light on the structure, stability and evolution of legume genomes |
| title_sort | analysis of synteny of it arachis it with it lotus it and it medicago it sheds new light on the structure stability and evolution of legume genomes |
| url | http://www.biomedcentral.com/1471-2164/10/45 |
| work_keys_str_mv | AT nielsenannam ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT schauserleif ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT fredslundjakob ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT hougaardbirgitk ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT guimaraespatriciam ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT lealbertiolisorayacm ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT sandalniels ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT madsenleneh ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT moretzsohnmarcioc ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT bertiolidavidj ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT satoshusei ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT tabatasatoshi ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT cannonstevenb ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT stougaardjens ananalysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT nielsenannam analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT schauserleif analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT fredslundjakob analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT hougaardbirgitk analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT guimaraespatriciam analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT lealbertiolisorayacm analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT sandalniels analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT madsenleneh analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT moretzsohnmarcioc analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT bertiolidavidj analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT satoshusei analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT tabatasatoshi analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT cannonstevenb analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes AT stougaardjens analysisofsyntenyofitarachisitwithitlotusitanditmedicagoitshedsnewlightonthestructurestabilityandevolutionoflegumegenomes |