scholarly journals Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

2021 ◽  
Author(s):  
Paulina Tomaszewska ◽  
Maria S Vorontsova ◽  
Stephen A Renvoize ◽  
Sarah Z Ficinski ◽  
Joseph Tohme ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Single Species ◽  
Evolutionary Divergence ◽  
Forage Grass ◽  
Whole Genome ◽  
Marginal Lands ◽  
Geographical Patterns ◽  
Germplasm Collections ◽  
Genome Survey ◽  
Tropical Forage

Abstract Background and Aims Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment​, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. Methods Some 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima. Key Results Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs​. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. Conclusions We suggest a new coherent nomenclature for the genomes present​. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.

scholarly journals Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

2021 ◽  
Author(s):  
Paulina Tomaszewska ◽  
Maria S. Vorontsova ◽  
Stephen A. Renvoize ◽  
Sarah Z. Ficinski ◽  
Joseph Tohme ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Evolutionary Divergence ◽  
Forage Grass ◽  
Whole Genome ◽  
Marginal Lands ◽  
Geographical Patterns ◽  
Germplasm Collections ◽  
Genome Survey ◽  
Tropical Forage

AbstractBackground and AimsDiploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa and now planted worldwide are important for food security and the environment, often being planted in marginal lands. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species.MethodsSome 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis with in situ hybridization to chromosomes were used to identify chromosomes and genomes in Urochloa accessions belonging to the different agamic complexes.Key ResultsGenome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids.ConclusionsWe suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.

scholarly journals Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l.

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 957
Author(s):  
Paulina Tomaszewska ◽  
Till K. Pellny ◽  
Luis M. Hernández ◽  
Rowan A. C. Mitchell ◽  
Valheria Castiblanco ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Germplasm Collection ◽  
Forage Grass ◽  
Breeding Programs ◽  
Robust Identification ◽  
Ploidy Levels ◽  
Sustainable Improvement ◽  
Tropical Forage ◽  
Relative Differences

Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. We aimed to develop an optimized approach to determine ploidy of germplasm collection of this tropical forage grass group using dried leaf material, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Our methods enable robust identification of ploidy levels (coefficient of variation of G0/G1 peaks, CV, typically <5%). Ploidy of some 348 forage grass accessions (ploidy range from 2x to 9x), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes are used in the current breeding programs at CIAT and EMBRAPA: the ’brizantha’ and ’humidicola’ agamic complexes are variable, with multiple ploidy levels. Some U. brizantha accessions have odd level of ploidy (5x), and the relative differences in fluorescence values of the peak positions between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed aneuploidy.

scholarly journals Persistence of single species of symbionts across multiple closely-related host species

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jorge Doña ◽  
Carolina Osuna-Mascaró ◽  
Kevin P. Johnson ◽  
David Serrano ◽  
Raül Aymí ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Host Species ◽  
Population Genetic ◽  
Single Species ◽  
Mite Species ◽  
Evolutionary Divergence ◽  
Species Status ◽  
Limited Dispersal ◽  
Dispersal Events ◽  
Symbiont Species

AbstractSome symbiont species are highly host-specific, inhabiting only one or a very few host species, and typically have limited dispersal abilities. When they do occur on multiple host species, populations of such symbionts are expected to become genetically structured across these different host species, and this may eventually lead to new symbiont species over evolutionary timescales. However, a low number of dispersal events of symbionts between host species across time might be enough to prevent population structure and species divergence. Overall, processes of evolutionary divergence and the species status of most putative multi-host symbiont systems are yet to be investigated. Here, we used DNA metabarcoding data of 6,023 feather mites (a total of 2,225 OTU representative sequences) from 147 infracommunities (i.e., the assemblage consisting of all mites of different species collected from the same bird host individual) to investigate patterns of population genetic structure and species status of three different putative multi-host feather mite species Proctophyllodes macedo Vitzthum, 1922, Proctophyllodes motacillae Gaud, 1953, and Trouessartia jedliczkai (Zimmerman, 1894), each of which inhabits a variable number of different closely related wagtail host species (genus Motacilla). We show that mite populations from different host species represent a single species. This pattern was found in all the mite species, suggesting that each of these species is a multi-host species in which dispersal of mites among host species prevents species divergence. Also, we found evidence of limited evolutionary divergence manifested by a low but significant level of population genetic structure among symbiont populations inhabiting different host species. Our study agrees with previous studies showing a higher than expected colonization opportunities in host-specific symbionts. Indeed, our results support that these dispersal events would allow the persistence of multi-host species even in symbionts with limited dispersal capabilities, though additional factors such as the geographical structure of some bird populations may also play a role.

scholarly journals Whole Genome Survey of Copy Number Variation in the Spontaneously Hypertensive Rat

Hypertension ◽  
2010 ◽  
Vol 55 (5) ◽  
pp. 1231-1238 ◽  
Author(s):  
Fadi J. Charchar ◽  
Michael Kaiser ◽  
Andrew J. Bingham ◽  
Nina Fotinatos ◽  
Fahima Ahmady ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Spontaneously Hypertensive Rat ◽  
Whole Genome ◽  
Spontaneously Hypertensive ◽  
Genome Survey ◽  
Hypertensive Rat ◽  
Number Variation

Comprehensive whole genome survey analyses of male and female brown-spotted flathead fish Platycephalus sp.1

Genomics ◽  
2020 ◽  
Vol 112 (6) ◽  
pp. 4742-4748
Author(s):  
Shengyong Xu ◽  
Hao Zhang ◽  
Tianxiang Gao
Keyword(s):  
Whole Genome ◽  
Male And Female ◽  
Genome Survey ◽  
Survey Analyses

scholarly journals Genome survey and SSR analysis of Apocynum venetum

2019 ◽  
Vol 39 (6) ◽  
Author(s):  
Guo-qi Li ◽  
Li-xiao Song ◽  
Chang-qing Jin ◽  
Miao Li ◽  
Shi-pei Gong ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Size ◽  
Genome Sequencing ◽  
Repeated Sequences ◽  
Economic Plant ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Total Length ◽  
Genome Survey ◽  
Apocynum Venetum

AbstractApocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measure the genome size of A. venetum, and bioinformatics methods were employed for the evaluation of the genome size, heterozygosity ratio, repeated sequences, and GC content in order to provide a foundation for subsequent whole-genome sequencing. The sequencing analysis results indicated that the preliminary estimated genome size of A. venetum was 254.40 Mbp, and its heterozygosity ratio and percentage of repeated sequences were 0.63 and 40.87%, respectively, indicating that it has a complex genome. We used k-mer = 41 to carry out a preliminary assembly and obtained contig N50, which was 3841 bp with a total length of 223949699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227322054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous. We recommend the use of the ‘2+3’ (Illumina+PacBio) sequencing combination to supplement the Hi-C technique and resequencing technique in future whole-genome research in A. venetum.

scholarly journals Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 113 ◽  
Author(s):  
Pavel Kroupin ◽  
Victoria Kuznetsova ◽  
Dmitry Romanov ◽  
Alina Kocheshkova ◽  
Gennady Karlov ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Related Species ◽  
Evolutionary Divergence ◽  
Whole Genome ◽  
Target Genome ◽  
Target Species ◽  
Closely Related Species ◽  
Chromosome Markers

Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.

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