The genome of cowpea (Vigna unguiculata [L.] Walp.) Lonardi, Stefano; Muñoz‐Amatriaín, María; Liang, Qihua ...
The Plant journal : for cell and molecular biology,
June 2019, Letnik:
98, Številka:
5
Journal Article
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Summary
Cowpea (Vigna unguiculata L. Walp.) is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. An ...assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single‐molecule real‐time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination‐poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high‐recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS‐LRR and the SAUR‐like auxin superfamilies compared with other warm‐season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.
Significance Statement
State‐of‐the‐art technologies and assembly methods were used to generate a reference genome sequence of cowpea, a drought‐resilient crop on which millions of people in sub‐Saharan Africa depend as a source of protein. This sequence facilitated the identification of: repetitive elements and gene families expanded in cowpea compared with other closely related legumes; a large and apparently rare chromosomal inversion; and an interesting candidate gene that is associated with several domestication‐related traits.
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum
but even so there remains a need to further clarify relationships ...within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
The class
is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ...ecological importance.
classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000
and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
Theory of prokaryotic genome evolution Sela, Itamar; Wolf, Yuri I.; Koonin, Eugene V.
Proceedings of the National Academy of Sciences - PNAS,
10/2016, Letnik:
113, Številka:
41
Journal Article
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Bacteria and archaea typically possess small genomes that are tightly packed with protein-coding genes. The compactness of prokaryotic genomes is commonly perceived as evidence of adaptive genome ...streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. Here, by fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. These results suggest that the number of genes in prokaryotic genomes reflects the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias (i.e., the rate of deletion of genetic material being slightly greater than the rate of acquisition). Thus, new genes acquired by microbial genomes, on average, appear to be adaptive. The tight spacing of protein-coding genes likely results from a combination of the deletion bias and purifying selection that efficiently eliminates nonfunctional, noncoding sequences.
Mutation dictates the tempo and mode of evolution, and like all traits, the mutation rate is subject to evolutionary modification. Here, we report refined estimates of the mutation rate for a ...prokaryote with an exceptionally small genome and for a unicellular eukaryote with a large genome. Combined with prior results, these estimates provide the basis for a potentially unifying explanation for the wide range in mutation rates that exists among organisms. Natural selection appears to reduce the mutation rate of a species to a level that scales negatively with both the effective population size (N ₑ), which imposes a drift barrier to the evolution of molecular refinements, and the genomic content of coding DNA, which is proportional to the target size for deleterious mutations. As a consequence of an expansion in genome size, some microbial eukaryotes with large N ₑ appear to have evolved mutation rates that are lower than those known to occur in prokaryotes, but multicellular eukaryotes have experienced elevations in the genome-wide deleterious mutation rate because of substantial reductions in N ₑ.
•The main cultivar of Jerusalem artichokes, has an estimated genome size of 21.36 Gb.•Jerusalem artichokes genome is highly heterozygous.•Gene size is not uniform within Jerusalem artichokes ...species.•Yield and genome size of Jerusalem artichokes are highly correlated.
Genome survey technology The Jerusalem artichoke (Helianthus tuberosus L.) holds great significance as a crop for inulin production. However, the absence of a sequenced Jerusalem artichoke genome has hindered the advancement of genetic resources and molecular research regarding this plant. Furthermore, no research the investigations into potential variations in genome size among Jerusalem artichoke species and their impact on agronomic traits have not been conducted. This study endeavors to explore the genome size of Jerusalem artichoke and its interaction with the plant's agronomy. To estimate the genome size of Jerusalem artichoke, the cultivar JA1155 underwent genome analysis using flow cytometry and K-mers. Additionally, flow cytometry was employed to determine the genome size of eight remaining Jerusalem artichoke germplasms and establish a correlation with their phenotypic characteristics. The results of flow cytometry revealed an estimated genome size (2C) of 21.96 Gb for JA1155. Moreover, the Genome Survey results indicated that the genome size of JA1155 (2C) was estimated to be 21.36 Gb, mirroring the findings of flow cytometry. The heterozygosity rate of the JA1155 gene set was 1.21%, with a duplication rate of 92.25%. Following the initial genome assembly, the contig N50 reached 165 bp, encompassing a total length of 10,616.86 Mbp, while the scaffold N50 was 172 bp, totaling 10,772.62 Mbp in length. Flow cytometry results demonstrated a wide range of genome sizes among the measured Jerusalem artichoke genomes, ranging from 20.51 to 23.23 Gb (2C). Additionally, we discovered significant correlations between genome size and several agronomic traits in Jerusalem artichoke, namely total tuber weight (p<0.01, r=0.474), leaf length (p<0.01, r=0.319), plant height (p<0.01, r=0.267), and aboveground weight (p<0.05, r=0.229). This study not only aids in completing the genome sequencing of Jerusalem artichoke but also offers valuable insights into the connection between genome size and agronomic traits. Future research should address the interplay of these mechanisms by tackling various related inquiries.
• Background and Aims Plant nuclear genomes vary tremendously in DNA content, mostly due to differences in ancestral ploidy and variation in the degree of transposon amplification. These processes ...can increase genome size, but little is known about mechanisms of genome shrinkage and the degree to which these can attenuate or reverse genome expansion. This research focuses on characterizing DNA removal from the rice and Arabidopsis genomes, and discusses whether loss of DNA has effectively competed with amplification in these species. • Methods Retrotransposons were analyzed for sequence variation within several element families in rice and Arabidopsis. Nucleotide sequence changes in the two termini of individual retrotransposons were used to date their time of insertion. • Key Results An accumulation of small deletions was found in both species, caused by unequal homologous recombination and illegitimate recombination. The relative contribution of unequal homologous recombination compared to illegitimate recombination was higher in rice than in Arabidopsis. However, retrotransposons are rapidly removed in both species, as evidenced by the similar apparent ages of intact elements (most less than 3 million years old) in these two plants and all other investigated plant species. • Conclusions Differences in the activity of mechanisms for retrotransposon regulation or deletion generation between species could explain current genome size variation without any requirement for natural selection to act on this trait, although the results do not preclude selection as a contributing factor. The simplest model suggests that significant genome size variation is generated by lineage-specific differences in the molecular mechanisms of DNA amplification and removal, creating major variation in nuclear DNA content that can then serve as the substrate for fitness-based selection.
We consider the rapidly advancing discipline of plant evolutionary genomics, with a focus on the evolution of polyploid genomes. In many lineages, polyploidy is followed by ‘biased fractionation’, ...the unequal loss of genes from ancestral progenitor genomes. Mechanistically, it has been proposed that biased fractionation results from changes in the epigenetic landscape near genes, likely mediated by transposable elements. These epigenetic changes result in unequal gene expression between duplicates, establishing differential fitness that leads to biased gene loss with respect to ancestral genomes. We propose a unifying conceptual framework and a set of testable hypotheses based on this model, relating genome size, the proximity of transposable elements to genes, epigenetic reprogramming, chromatin accessibility, and gene expression.
Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA ...(transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size.
Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria.
We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal.
Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.
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