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16 results for “legume genomes”
Discordant population structure among rhizobium divided genomes and their legume hosts
<p>Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprised of multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole-genome resequencing of a hierarchically-structured sample of 191 strains of <em>Sinorhizobium meliloti</em> collected from 21 locations in southern Europe to characterize the population structures of this bacterial symbiont and its host plant <em>Medicago truncatula</em>. <em>Sinorhizobium meliloti</em> genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. The differences in population structure may result from among-replicon differences in the extent of horizontal gene transfer, although given limited recombination of the chromosome, different levels of purifying or positive selection may also contribute to among-replicon differences. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.</p>
The genome of the mimosoid legume Prosopis cineraria, a desert tree
<p>The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions. Unlike the better studied Papilionoideae, there are few genomic resources within this legume group. The tree <em>Prosopis cineraria</em> native to the Near East and Indian subcontinent, where it thrives in very hot desert environments. To develop a tool to better understand desert plant adaptation mechanisms, we sequenced the <em>P. cineraria</em> genome to near-chromosome assembly, with a total sequence length of ~691 Mb. We predicted 77,579 gene models (76,554 CDS, 361 rRNAs and 664 tRNAs) from the assembled genome, among them 55,325 (~72%) protein-coding genes that were functionally annotated. This genome was found to consist of over 58% repeat sequences, primarily long terminal repeats (LTR-) -retrotransposons. We find an expansion of terpenoid metabolism genes in <em>P. cineraria</em> and its relative <em>P. alba</em>, but not in other legumes. We also observed an amplification of NBS-LRR disease resistance genes correlated with LTR-associated retrotransposition, and identified 410 retrogenes with an active burst of chimeric retrogene creation that approximately occurred at the same time of divergence of <em>P. cineraria</em> from a common lineage with <em>P. alba</em> ~23 Mya. These retrogenes include many for biotic defense response and abiotic stress stimulus response, as well as the early Nodulin 93 gene. Nodulin 93 gene amplification is consistent with an adaptive response of the species to low nitrogen in arid desert soil. </p>
Discordant population structure among rhizobium divided genomes and their legume hosts
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Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis
<p>The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host <em>Medicago truncatula</em> with a community of 88 <em>Ensifer meliloti</em> strains. Multi-strain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, <em>i.e.</em>, genotype-by-genotype, effects on rhizobia fitness and some annotated rhizobia genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multi-strain contexts.</p>
Genomic relationships of Glycine remota, a recently discovered perennial relative of soybean, within the legume genus Glycine
<p><span>The legume genus, <em>Glycine</em>, which includes the Asian annual cultivated soybean, also includes a group of Australian perennial species comprising the subgenus <em>Glycine</em>. Because the subgenus <em>Glycine</em> represents the tertiary gene pool for one of the world's most important crops, the group has been the target of collection and study for decades, resulting in a steady growth in the number of formally recognized species, from six in the 1970s to over 20 at present, as well as a number of additional informal taxa. These studies have also produced a system of nuclear diploid "genome groups" corresponding to clades in molecular phylogenies. The aptly named <em>G</em>. <em>remota</em> is known only from a single isolated population in the Kimberley region of northwestern Australia and was named only in 2015. The species is unique within <em>Glycine</em> in having unifoliolate leaves; its discoverers hypothesized that <em>G</em>. <em>remota</em>, if diploid, is related to species of the I-genome that are also native to the Kimberley region. We produced low-coverage short-read genome sequencing data from an herbarium specimen of <em>G</em>. <em>remota</em>. Genome size estimates from the sequencing data suggest that <em>G</em>. <em>remota</em> is a diploid, while ploidy estimation is inconclusive likely due to the history of whole genome duplication in <em>Glycine</em>. Phylogenomic analyses of genome-wide SNPs, as well as phylogenetic analyses of the low copy nuclear gene (histone H3D), the entire ribosomal RNA cistron, and the internal transcribed spacer all placed the species unequivocally in the diploid I-genome clade. A complete plastome sequence was also generated and its placement with a plastome phylogeny is also consistent with membership in the I-genome.</span></p>
Genomic relationships of Glycine remota, a recently discovered perennial relative of soybean, within the legume genus Glycine
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Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis
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Data from: Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism
In the legume-rhizobia mutualism, the benefit each partner derives from the other depends on the genetic identity of both host and rhizobial symbiont. To gain insight into the extent of genome x genome interactions on hosts at the molecular level and to identify potential mechanisms responsible for the variation, we examined host gene expression within nodules (the plant organ where the symbiosis occurs) of four genotypes of Medicago truncatula grown with either Ensifer meliloti or E. medicae symbionts. These host x symbiont combinations show significant variation in nodule and biomass phenotypes. Likewise, combinations differ in their transcriptomes: host, symbiont, and host x symbiont affected the expression of 70%, 27% and 21%, respectively, of the approximately 27,000 host genes expressed in nodules. Genes with the highest levels of expression often varied between hosts and/or symbiont strain and include leghemoglobins that modulate oxygen availability and hundreds of Nodule Cysteine-Rich (NCR) peptides involved in symbiont differentiation and viability in nodules. Genes with host x symbiont dependent expression were enriched for functions related to resource exchange between partners (sugar/sulfate/iron/amino acid transport and dicarboxylate/amino acid synthesis). These enrichments suggest mechanisms for host control of the currencies of the mutualism. The transcriptome of M. truncatula accession HM101 (A17), the reference genome used for most molecular research, was less affected by symbiont identity than the other hosts. These findings underscore the importance of assessing the molecular basis of variation in ecologically important traits, particularly those involved in biotic interactions, in multiple genetic contexts.
Data from: Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism
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Data from: Genomic evidence of genetic variation with pleiotropic effects on caterpillar fitness and plant traits in a model legume
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Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy region. Our study also indicates that rps16 has been independently lost at least five times in legumes, with additional gene and intron losses scattered among the papilionoids. Additionally, genera from two distinct lineages within the papilionoids, Lupinus and Robinia, have a parallel inversion of 36 kb and 39 kb, respectively. This parallel inversion is novel as it appears to be caused by a 29 bp repeat within two trnS genes. This repeat is present in all available legume plastid genomes indicating that there is the potential for this inversion to be present in more species. This case of a homoplasious inversion is also evidence that some inversion events may not be reliable phylogenetic markers.
Data from: Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50–75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and <15% of the variation in either synonymous rates (dS) or dN:dS. Among putative targets of selection were genes involved in defence against pathogens and herbivores, genes with roles in mediating the relationship with rhizobial symbionts and one-third of annotated histone-lysine methyltransferases. Adaptive evolution of the methyltransferases suggests that positive selection in gene expression may have occurred through evolution of enzymes involved in epigenetic modification.
Data from: Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes
Background: Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be diverse transcriptional regulators, playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. Results: In this study, we identified 428 bZIP genes encoding 585 distinct proteins in six legumes, Glycine max, Medicago truncatula,Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Lotus japonicus. The legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. Four kinds of intron patterns (a–d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. We predicted the DNA-binding patterns and the dimerization properties, based on the characteristic features in the basic and hinge regions and the Leu zipper, respectively, which indicated that some highly conserved amino acid residues existed across each major group. The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. We also detected several key legume bZIP genes involved in drought- and salt-responses by comparing fold changes of expression values in drought-stressed or salt-stressed roots and leaves. Conclusions: In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses.
Data from: Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes
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Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
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Data from: Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula
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