Genome-Enabled Insights into Legume Biology - University of ...

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Annu. Rev. Plant Biol. 2012.63:283-305. Downloaded from www.annualreviews.org by University of Minnesota - Twin Cities - Wilson Library on 05/07/12. For personal use only. Contents INTRODUCTION.................. 284 SEQUENCING LEGUME GENOMES....................... 284 Reference Legume Genomes . . . . . . . 284 What Can We Learn from Sequenced Legume Genomes? . . 286 Sequencing in Nonreference Legumes....................... 287 From Genome Sequencing toResequencing................ 288 COMPARATIVE GENOMICS AND THE SEARCH FOR THE PRIMORDIAL LEGUME GENOME........................ 289 Strategies for Comparative Genomic Analysis . . . . . . . . . . . . . . . 289 Comparing Legume Genomes . . . . . . 290 Envisioning the Ancestral LegumeGenome............... 294 GENOME DUPLICATIONS IN LEGUME BIOLOGY . . . . . . . . . 294 Whole-Genome Duplication Events in the History of Legumes. . . . . . . 294 THE AFTERMATH OF GENOME DUPLICATION AND ITS IMPACT ON LEGUME BIOLOGY........................ 296 The Fates of Duplicated Genes . . . . . 296 Impacts of Genome Duplication on Legume Biology . . . . . . . . . . . . . 297 Genome Duplication and the Evolution of Nodulation . . . . . . . . 298 PERSPECTIVES ON LEGUME GENOMICS...................... 299 INTRODUCTION Legumes (Fabaceae or Leguminosae) are the third-largest family of flowering plants and the second-most-important plant family in agriculture. They are especially interesting because most have the capacity to fix atmospheric nitrogen through mutualistic interactions with rhizobial soil bacteria, a trait that is both ecologically and agriculturally important (32). Indeed, without the nitrogen fixed each year by legumes, humans would need to consume 288 billion kg of additional fuel in the Haber- Bosch process to generate anhydrous ammonia for agriculture (47). Given their importance to people, legumes are now the target of extensive sequence-based genomics research, which is revolutionizing our understanding of legume evolution and its connection to biologically important traits. Of particular significance are the recently completed and annotated genomes of three legume species—Glycine max (soybean) (Gm) (81), Medicago truncatula (Mt) (100), and Lotus japonicus (Lj) (79). This review focuses on genomics research carried out in legume biology, emphasizing comparisons among legume genomes and the critical role of genome duplication and its aftermath in shaping present-day legume genomes and traits. With the recent publication of three legume genome sequences—and, very recently, a fourth (76)—and the rapid development of genomics tools for multiple legume species, there are already several excellent scientific reviews available to researchers. These reviews have emphasized the structural analyses of legume genomes (13, 78), translational opportunities provided by reference genome sequences (101), and the prospects for extending genome sequence data to less studied “orphan” legume species (13, 95). Therefore, we endeavor here to complement and expand the scope of these existing reviews with our focus on genome evolution and genome duplication, and on their impact on legume biology. SEQUENCING LEGUME GENOMES Reference Legume Genomes The genome sequences of Gm, Mt, and Lj form the foundation for much of our current understanding about legume genomics. All three species are members of Papilionoideae, a subfamily that diverged from the two other legume subfamilies (Mimosoideae and 284 Young·Bharti
Annu. Rev. Plant Biol. 2012.63:283-305. Downloaded from www.annualreviews.org by University of Minnesota - Twin Cities - Wilson Library on 05/07/12. For personal use only. Caesalpinoideae) approximately 60 Mya (52). Most cultivated legumes are found within two sister clades of the papilionoids: the millettoid/phaseoloid clade [warm-season legumes, including Gm, pigeon pea (Cajanus cajan), common bean (Phaseolus vulgaris), mung bean (Vigna radiata), and cowpea (Vigna unguiculata)] and the temperate galegoid clade [cool-season legumes, including Mt, Lj, and species such as alfalfa (Medicago sativa), chickpea (Cicer arietinum), clover (Trifolium sp.), lentil (Lens sp.), and garden pea (Pisum sativum)]. Papilionoideae also includes two minor clades: the genistoid (lupin, Lupinus sp.) and the dalbergioid (peanut, Arachis hypogaea). Because all these species are reasonably close phylogenetically, insights from the Gm, Mt, and Lj genomes should be highly relevant when transferred among cultivated legume crops. However, the current emphasis on papilionoids also means that many interesting legume species—especially mimosoids (Mimosa, Acacia, Prosopis, and Chamaecrista, for example) and caesalpinioids (Caesalpinia, Senna, and tamarind, for example)—are quite distant evolutionarily from the nexus of genomics research. Researchers have noted this previously and highlighted the importance of developing genomics resources in additional nodes throughout the legume evolutionary tree (87). The Gm genome sequence, published in 2010, is currently the most thoroughly characterized legume genome (81). More than 950 million base pairs (Mb) of the overall 1,115-Mb genome were completed through the use of 8x Sanger whole-genome shotgun (WGS) sequencing. Many of the resulting pseudomolecules extend all the way from centromeres (as indicated by scaffolds extending into centromeric repeats) out to telomeres (with scaffolds extending into telomeric repeats). The Gm sequence is also impressive for the very large size of the resulting sequence scaffolds. These are the physically defined assemblies of sequence contigs that are built into Gm’s 20 chromosome pseudomolecules. In Gm assembly Glyma 1.0, the so-called L50 (a common metric to describe scaffold size that is calculated by summing the lengths of all scaffolds from longest to shortest and then finding the scaffold size where you reach 50% of the overall length) is 47.8 Mb. By comparison, nearly all other published WGS plant genome sequences have notably shorter L50s [with the notable exception of Sorghum bicolor (70), another very high-quality assembly]. It is especially noteworthy that nearly all of the published Gm sequence (98%) could be anchored to specific chromosomal positions. The Mt genome was sequenced by a combination of Sanger-based bacterial artificial chromosome (BAC) clones (with genomic inserts approximately 80–120 kb in length) and ∼40x Illumina WGS (100). In this case, the sequencing effort was focused on euchromatic arms outside centromeric regions through the use of fluorescence in situ hybridization (FISH) (49) and optical mapping (104) to define physical location. Altogether, 367 Mb of the approximately 470-Mb Mt genome (http://data. kew.org/cvalues) is included in the published assembly. Because of the emphasis on BAC-based sequencing, the quality in BACsequenced regions is quite high, although scaffolds tend to be relatively short (overall L50 of 1.27 Mb) and only the BAC-based portion of the sequence (245 Mb, or 67%) could be anchored to specific chromosomal locations. Another 17 Mb of BAC-based sequence could not be anchored. The remaining portion of the Mt sequence consists of Illumina WGS (104 Mb), with the Illumina contigs being quite short (L50 of 2.4 kb, largest 31 kb) and primarily useful as a way to recover missing portions of the genome for gene discovery. Still, Mt chromosome 5 is noteworthy in being a nearly intact BAC-based pseudomolecule that is complete on either side of the centromere. Throughout the entire pseudomolecule of Mt chromosome 5, there are just four sequence gaps, which is comparable in quality to the Arabidopsis thaliana (3) or Oryza sativa (40) genomes. One surprising result of the Mt sequencing project was the discovery of a large chromosomal translocation in the accession used as a template for sequencing ( Jemalong-A17) compared with other Mt www.annualreviews.org • Genome-Enabled Insights into Legume Biology 285
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