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Genome structure and mapping of genes in the U. ruziziensis chloroplast genome. The LSC, SSC, and IR regions are labeled accordingly. The inner circle depicts GC content. Genes on the outside of the map are in the forward strand, while genes on the inside are in the reverse strand. Genes are colored according to their functions as shown in the legend.
Source publication
Background
Forage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress tra...
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The eastern Australian temperate biota harbours many plants with fragmented geographic ranges distributed over 1000s of kilometres, yet the spatial genetic structure of their populations remains largely unstudied. In this study, we investigated genetic variation of the nuclear internal transcribed spacer (ITS) and chloroplast DNA sequences to disen...
Citations
... We used the U. ruziziensis reference genome to improve the quality and robustness of our map, as well as to look for evidence of synteny, because this is the species with the closest phylogenetic relationship to U. humidicola for which whole-genome sequencing information is available (Pessoa-Filho et al. 2019). Assigning the U. humidicola LGs to U. ruziziensis chromosomes revealed high collinearity (Supplementary Fig. 5), which was expected because the two species were classified in different but sister taxa (Pessoa-Filho et al. 2017). Major disruptions were observed in LG2, LG3 and LG6, each of which split into two different chromosomes in U. ruziziensis, and in LG4, where we observed an inversion, evidencing some genomic rearrangements. ...
Key message
We present the highest-density genetic map for the hexaploid Urochloa humidicola. SNP markers expose genetic organization, reproduction, and species origin, aiding polyploid and tropical forage research.
Abstract
Tropical forage grasses are an important food source for animal feeding, with Urochloa humidicola, also known as Koronivia grass, being one of the main pasture grasses for poorly drained soils in the tropics. However, genetic and genomic resources for this species are lacking due to its genomic complexity, including high heterozygosity, evidence of segmental allopolyploidy, and reproduction by apomixis. These complexities hinder the application of marker-assisted selection (MAS) in breeding programs. Here, we developed the highest-density linkage map currently available for the hexaploid tropical forage grass U. humidicola. This map was constructed using a biparental F1 population generated from a cross between the female parent H031 (CIAT 26146), the only known sexual genotype for the species, and the apomictic male parent H016 (BRS cv. Tupi). The linkage analysis included 4873 single nucleotide polymorphism (SNP) markers with allele dosage information. It allowed mapping of the ASGR locus and apospory phenotype to linkage group 3, in a region syntenic with chromosome 3 of Urochloa ruziziensis and chromosome 1 of Setaria italica. We also identified hexaploid haplotypes for all individuals, assessed the meiotic configuration, and estimated the level of preferential pairing in parents during the meiotic process, which revealed the autopolyploid origin of sexual H031 in contrast to apomictic H016, which presented allopolyploid behavior in preferential pairing analysis. These results provide new information regarding the genetic organization, mode of reproduction, and allopolyploid origin of U. humidicola, potential SNPs markers associated with apomixis for MAS and resources for research on polyploids and tropical forage grasses.
... We used the U. ruziziensis reference genome to improve the quality and robustness of our map, as well as to look for evidence of synteny, because this is the species with the closest phylogenetic relationship to U. humidicola for which whole-genome sequencing information is available (Pessoa-Filho et al. 2019). Assigning the U. humidicola LGs to U. ruziziensis chromosomes revealed high collinearity (Supplementary Fig. 5), which was expected because the two species were classified in different but sister taxa (Pessoa-Filho et al. 2017). Major disruptions were observed in LG2, LG3 and LG6, each of which split into two different chromosomes in U. ruziziensis, and in LG4, where we observed an inversion, evidencing some genomic rearrangements. ...
Tropical forage grasses are an important food source for animal feeding, with Urochloa humidicol a, also known as Koronivia grass, being one of the main pasture grasses for poorly drained soils in the tropics. However, genetic and genomic resources for this species are lacking due to its genomic complexity, including high heterozygosity, evidence of segmental allopolyploidy, and reproduction by apomixis. These complexities hinder the application of marker-assisted selection (MAS) in breeding programs. Here, we developed the highest-density linkage map currently available for the hexaploid tropical forage grass U. humidicola . This map was constructed using a biparental F1 population generated from a cross between the female parent H031 (CIAT 26146), the only known sexual genotype for the species, and the apomictic male parent H016 (BRS cv. Tupi). The linkage analysis included 4,873 single nucleotide polymorphism (SNP) markers with allele dosage information. It allowed mapping of the apospory locus and phenotype to linkage group 3, in a region syntenic with chromosome 3 of Urochloa ruziziensis and chromosome 1 of Setaria italica . We also identified hexaploid haplotypes for all individuals, assessed the meiotic configuration, and estimated the level of preferential pairing in parents during the meiotic process, which revealed the autopolyploid origin of sexual H031 in contrast to H016, which presented allopolyploid behavior in preferential pairing analysis. These results provide new information regarding the genetic organization, mode of reproduction, and allopolyploid origin of U. humidicola , potential SNPs markers associated to apomixes for MAS and resources for research on polyploids and tropical forage grasses.
Key message
We present the highest-density genetic map for the hexaploid Urochloa humidicola . SNP markers expose genetic organization, reproduction, and species origin, aiding polyploid and tropical forage research.
... We used the RelTime-JA method with little bootstraps ( Figure 2B) to analyze six phylogenomic datasets (Pessoa-Filho et al., 2017;Johnson et al., 2018;Ran et al., 2018;Sann et al., 2018;Kuntner et al., 2019;Álvarez-Carretero et al., 2022), which ...
... We analyzed the apoid and five other phylogenomic datasets (Pessoa-Filho et al., 2017;Johnson et al., 2018;Ran et al., 2018;Sann et al., 2018;Kuntner et al., 2019;Álvarez-Carretero et al., 2022) applying only a root calibration, which is critical to directly assess the impact of applying SA or JA methods on time estimates without topological and time constraints. RelTime-JA generated very similar node times and CIs to RelTime-SA (Figure 4) because phylogenetic uncertainty was small for the analyzed phylogenomic datasets. ...
A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result.
... (Bie et al., 2006). Additionally, R8s was used to calibrate the divergence time (Taylor and Berbee, 2006) according to the following constraints: (1) the divergence time for A. thaliana and O. sativa was 152 Mya (Magalloán and Sanderson, 2010), and (2) the divergence time for Z. mays and S. italica was 23.4 Mya (Pessoa-Filho et al., 2017). An orthogroup with 50%-70% of its genes lacking introns was inferred to be an orthogroup of IGs. ...
Intronless genes (IGs), which are a feature of prokaryotes, are a fascinating group of genes that are also present in eukaryotes. In the current study, a comparison of Poaceae genomes revealed that the origin of IGs may have involved ancient intronic splicing, reverse transcription, and retrotranspositions. Additionally, IGs exhibit the typical features of rapid evolution, including recent duplications, variable copy numbers, low divergence between paralogs, and high non-synonymous to synonymous substitution ratios. By tracing IG families along the phylogenetic tree, we determined that the evolutionary dynamics of IGs differed among Poaceae subfamilies. IG families developed rapidly before the divergence of Pooideae and Oryzoideae and expanded slowly after the divergence. In contrast, they emerged gradually and consistently in the Chloridoideae and Panicoideae clades during evolution. Furthermore, IGs are expressed at low levels. Under relaxed selection pressure, retrotranspositions, intron loss, and gene duplications and conversions may promote the evolution of IGs. The comprehensive characterization of IGs is critical for in-depth studies on intron functions and evolution as well as for assessing the importance of introns in eukaryotes.
... Moreover, this technique has been used on different taxonomic levels of grasses (Wang et al. 2017), in addition to studies concerning molecular discrimination and identification (Diamante et al. 2020). The use of DNA chloroplast (cpDNA) allows the identification of structural and sequence polymorphisms, which may be useful for genetic studies, as well as contributing to phylogenetic reconstruction and estimation of the divergence time between species (Salariato et al. 2010;Silva et al. 2015;Machado et al. 2016;Pessoa-Filho et al. 2017) in addition to providing insights into plants population genetics and their evolution (Moore et al. 2010). ...
Poaceae has numerous species that are highly invasive thorough the planet. Urochloa, native to Africa, stands out in terms of invasion and impacts in South America. However, the correct identification of the species included in this genus is complex due to their morphological similarity with other species and there is a lack of studies involving the genetic variability of some species in Brazil, which is important for understanding the invasion mechanisms and planning control measures. In this study, we evaluated the genetic variability of the invasive exotic Poaceae Urochloa arrecta in different Brazilian regions, by using the nuclear marker ITS and the intergenetic chloroplast marker trnL-trnF. The sequences obtained were compared with those available in GenBank (NCBI). The results indicated a low genetic differentiation among the sampled populations. Seven and ten distinct haplotypes were identified for ITS and trnL-trnF, respectively, and most specimens shared a single haplotype. These results indicate that a limited number of propagules were introduced in the invasive range and/or that this species reproduces mainly through asexual reproduction. This last possibility is suggested by the great regeneration and colonization rates of asexual propagules of this species. The data obtained are useful for understanding the invasion mechanisms of the group in the region.
... Although more conserved in the terms of structures and organization of gene content than nuclear genome in plants, the chloroplast DNA sequences have suffered many mutation events throughout the evolution of vascular plants, including InDels, substitutions, and inversions [36]. Therefore, it is imperative to employ the complete chloroplast genome sequences to resolve the genetic diversity and phylogenetic analysis at high taxonomical levels, and even in lower taxa [37,38]. ...
The taxonomy of an ancient gymnosperm genus Taxus, with high value in horticulture and medicine, is perplexing because of few reliable morphological characters for diagnosing species. Here, we performed a comprehensive investigation of the evolutionary dynamics of Taxus chloroplast genomes and estimated phylogenetic relationships, divergence times, and ancestral distributions of Taxus species by comparing 18 complete chloroplast genomes. The variations across the chloroplast genome of different Taxus species indicated that remarkably varied genome variations across lineages have reshaped the genome architecture. Our well-resolved phylogeny supported that T. brevifolia Nutt. was basal lineages followed by the other North America lineages. Divergence time estimation and ancestral range reconstruction suggested that the Taxus species originated in North America in the Late Cretaceous and revealed that extant Taxus species shared a common ancestor whose ancestral distribution area was probably in North America and afterwards the earliest members expanded to Southeast Asia from where Chinese Taxus species originated. The predominant European species have more closer relationship with the Eastern Asian species and the speciation of Eurasia species arose from several dispersal and vicariance events in the Miocene. Genome-wide scanning revealed 18 positively selected genes that were involved in translation and photosynthesis system in Taxus, which might be related to the adaptive evolution of Taxus species. The availability of these complete chloroplast genomes not only enhances our understanding of the elusive phylogenetic relationships and chloroplast genome evolution such as conservation, diversity, and gene selection within Taxus genus but also provides excellent templates and genetic bases for further exploration of evolution of related lineages as well as for plant breeding and improvement.
... Two findings, the shared ancestry but strong genetic differentiation of 'brizantha-1' and the interspecific U. decumbens/U. brizantha subpopulation, support an evolutionary scenario where a single polyploidization event established both the tetraploid U. brizantha and U. decumbens, as previously proposed by Pessoa-Filho et al. (2017) and Tomaszewska et al. (2021b) based on chromosomal and repetitive DNA analysis. This would be followed by the divergence of 'brizantha-1' by evolutionary processes putatively driven by adaptation and its facultative apomictic nature. ...
Background:
Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. We aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction.
Methods:
We explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-seq to generate 1.1 million SNP loci. We employed genetic admixture, principal component, and phylogenetic analysis for defining subpopulations.
Results:
We observed three highly differentiated subpopulations in U. brizantha, which were unrelated to ploidy; one intermixed with U. decumbens, and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola, unrelated to ploidy; one subpopulation had fewer accessions but included the only characterised sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima.
Conclusions:
Polyploid U. decumbens are more related to polyploid U. brizantha than to diploid U. decumbens, which supports the divergence of both polyploid groups from a common tetraploid ancestor and evidences of the hybridisation barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can be likely utilised in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha, U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual-apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas.
... Both approaches are widely used, and their authors have tested them against comparable methods using empirical and simulated data (Stadler 2011;Höhna et al. 2016). We analyzed 15 timetrees spanning the diversity of life: plants (Pessoa-Filho et al. 2017;Ran et al. 2018;Barrera-Redondo et al. 2019), vertebrates (Kappas et al. 2016;Feng et al. 2017;Wu et al. 2017;Alfaro et al. 2018;Hughes et al. 2018;Delsuc et al. 2019;Harvey et al. 2020), and invertebrates (Blaimer et al. 2016;Fernández et al. 2018;Sann et al. 2018;Chazot et al. 2019;Kuntner et al. 2019) (Table 1). They cover time depths from 45-718 million years and include 11-1,939 species with alignments of 6,257-4,246,454 sites. ...
Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic datasets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study.
... In addition, the analysis showed that U. brizantha, U. decumbens, and U. ruziziensis were genetically closer to each other than to U. humidicola. This finding has also been observed in later studies using SSR markers (Jungmann et al., 2009a;Silva et al., 2013;Santos et al., 2015a;Ferreira et al., 2016;Triviño et al., 2017;Pessoa-Filho et al., 2017;Souza et al., 2018). Nitthaisong et al. (2016) assessed the genetic diversity of 11 Urochloa species using 10 ISSR markers and found high polymorphism between the genotypes. ...
... Therefore, these results were different from those found by Torres González and Morton (2005), who included U. decumbens in another group based on molecular and morphological data. Pessoa-Filho et al. (2017) evaluated the phylogenetic divergence between Urochloa species based on complete chloroplast genomes and observed that most of the polymorphisms between the species were located in intergenic regions, reflecting their phylogenetic distances. The phylogenetic analysis of this study yielded well-supported clades, and the results corroborated the findings reported by Salariato et al. (2009Salariato et al. ( , 2010: U. humidicola is a sister taxon of the U. ruziziensis, U. brizantha, and U. decumbens clades. ...
... The findings indicate U. ruziziensis as the ancestral donor of genome B 2 , while the origin of genomes B and B 1 remains unknown, but eligible candidates would be diploid genotypes of U. brizantha and U. decumbens. The probes used in GISH experiments reveal the homology between the three genomes (B, B 1 and B 2 ) and highlight the greater proximity between all three species, as previously suggested (Pessoa-Filho et al., 2017;Triviño et al., 2017). ...
Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.
... In addition, the analysis showed that U. brizantha, U. decumbens, and U. ruziziensis were genetically closer to each other than to U. humidicola. This finding has also been observed in later studies using SSR markers (Jungmann et al., 2009a;Silva et al., 2013;Santos et al., 2015a;Ferreira et al., 2016;Triviño et al., 2017;Pessoa-Filho et al., 2017;Souza et al., 2018). Nitthaisong et al. (2016) assessed the genetic diversity of 11 Urochloa species using 10 ISSR markers and found high polymorphism between the genotypes. ...
... Therefore, these results were different from those found by Torres González and Morton (2005), who included U. decumbens in another group based on molecular and morphological data. Pessoa-Filho et al. (2017) evaluated the phylogenetic divergence between Urochloa species based on complete chloroplast genomes and observed that most of the polymorphisms between the species were located in intergenic regions, reflecting their phylogenetic distances. The phylogenetic analysis of this study yielded well-supported clades, and the results corroborated the findings reported by Salariato et al. (2009Salariato et al. ( , 2010: U. humidicola is a sister taxon of the U. ruziziensis, U. brizantha, and U. decumbens clades. ...
... The findings indicate U. ruziziensis as the ancestral donor of genome B 2 , while the origin of genomes B and B 1 remains unknown, but eligible candidates would be diploid genotypes of U. brizantha and U. decumbens. The probes used in GISH experiments reveal the homology between the three genomes (B, B 1 and B 2 ) and highlight the greater proximity between all three species, as previously suggested (Pessoa-Filho et al., 2017;Triviño et al., 2017). ...
Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.
