Biology subjects

Schwarzacher, T.

Publications and source records attributed to Schwarzacher, T..

11 recordsLinked to original sources

bioRxiv2022

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C-into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding to through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.

plant biology↗

bioRxiv2022

The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris

Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in tropical and subtropical regions of Africa and Asia. In this work, we aim to investigate the genomic organization and characterize the nature of repetitive DNA sequences in this species. Because of the apomictic propagation, various aneuploid genotypes are found and we analysed here a 2n=4x+3=39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. About a third of Ty1-copia sites overlapped or spanned centromeric DAPI positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methycytosine signals, except some Ty3-gypsy on the arms of chromosomes which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. Probes developed from RepeatExplorer clusters gave strong signals mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris likely having different repeat sequence variants amplified before the genome came together in the tetraploid.

genomics↗

bioRxiv2022

Genome assembly and analysis of the flavonoid and phenylpropanoid biosynthetic pathways in Fingerroot ginger (Boesenbergia rotunda)

Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have high flavanone and chalcone content. Here we report genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which was assembled as 27,491 contigs with N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has 72% repeat content, with class I TEs occupying [~]67% of the assembled genome. Fluorescence In Situ Hybridization of the 18 chromosome pairs at metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. SSR analysis identified 238,441 gSSRs and 4,604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in leaf to 53% CpG, 18% CHG and 25% CHH in embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in watery callus. B rotunda has a relatively large genome with high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.

genomics↗

bioRxiv2022

Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses

BackgroundOat (Avena sativa, 2n=6x=42) is an important crop, and with its wild relatives including A. longiglumis (ALO, 2n=6x=14), has advantageous agronomic and nutritional traits. A de-novo chromosome-level ALO genome assembly was made to investigate diversity and structural genome variation between Avena species and other Poaceae in an evolutionary context, and develop genomic resources to identify the pangenome and economic traits within Pooideae. ResultsThe 3.85 gigabase ALO genome (seven pseudo-chromosomes), contained 40,845 protein-coding genes and 87% repetitive sequences (84.21% transposable elements). An LTR retrotransposon family was abundant at all chromosome centromeres, and genes were distributed without major terminal clusters. Comparisons of synteny with A. eriantha and A. strigosa showed evolutionary translocations of terminal segments including many genes. Comparison with rice (x=12) and the ancestral grass karyotype showed synteny and features of chromosome evolution including fusions, translocations and insertions of syntenic blocks across Pooideae species. With a genome size 10 times larger than rice, ALO showed relatively uniform expansion along the chromosome arms, with few gene-poor regions along arms, and no major duplications nor deletions. Linked gene networks were identified (mixed-linkage glucans and cellulose synthase genes), and CYP450 genes may be related to salt-tolerance. ConclusionsThe high-continuity genome assembly shows gene, chromosomal structural and copy number variation, providing a reference for the Avena pangenome, defining the full spectrum of diversity. Chromosomal rearrangements and genome expansion demonstrate features of evolution across the genus and grass BOP-clade, contributing to exploitation of gene and genome diversity through precision breeding.

genomics↗

bioRxiv2021

A chromosome-level reference genome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae

BackgroundEnsete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence of E. glaucum offers a vital genomic resource for functional and evolutionary studies of Ensete, the Musaceae, and more widely in the Zingiberales. FindingsUsing a combination of Illumina and Oxford Nanopore Technologies (ONT) sequencing, genome-wide chromosome conformation capture (Hi-C), and RNA survey sequence, we report a high-quality assembly of the 481.5Mb genome with 9 pseudochromosomes and 36,836 genes (BUSCO 94.7%). A total of 55% of the genome is composed of repetitive sequences with LTR-retroelements (37%) and DNA transposons (7%) predominant. The 5S and 45S rDNA were each present at one locus, and the 5S rDNA had an exceptionally long monomer length of c.1,056 bp, contrasting with the c. 450 bp monomer at multiple loci in Musa. A tandemly repeated c. 134 bp satellite, 1.1% of the genome (with no similar sequence in Musa), was present around all nine centromeres, with a LINE retroelement also found at Musa centromeres. The assembly, including centromeric positions, enabled us to characterize in detail the chromosomal rearrangements occurring between the x = 9 species and x = 11 species of Musa. Only one chromosome has the same gene content as M. acuminata (ma). Three ma chromosomes represent part of only one E. glaucum (eg) chromosome, while the remaining seven ma chromosomes are fusions of parts of two, three, or four eg chromosomes, demonstrating complex and multiple evolutionary rearrangements in the change between x = 9 and x = 11. ConclusionsThe advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly show how chromosome number evolves, and features of the rapid evolution of repetitive sequences.

plant biology↗

bioRxiv2021

The five Urochola spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

Background and AimsUrochloa (syn. Brachiaria, and including some Panicum and Megathyrus) is a genus of tropical and subtropical grasses widely sown as forage to feed ruminants in the tropics. A better understanding of the diversity among Urochloa spp. allow us to leverage its varying ploidy levels and genome composition to accelerate its improvement, following the example from other crop genera. MethodsWe explored the genetic make-up and population structure in 111 accessions, which comprise the five Urochloa species used for the development of commercial cultivars. These accessions are conserved from wild materials from collection sites at their centre of origin in Africa. We used RNA-seq, averaging 40M reads per accession, to generate 1,167,542 stringently selected SNP markers that tentatively encompassed the complete Urochloa gene pool used in breeding. Key ResultsWe identified ten subpopulations, which had no relation with geographical origin and represented ten independent gene pools, and two groups of admixed accessions. Our results support a division in U. decumbens by ploidy, with a diploid subpopulation closely related to U. ruziziensis, and a tetraploid subpopulation closely related to U. brizantha. We observed highly differentiated gene pools in U. brizantha, which were not related with origin or ploidy. Particularly, one U. brizantha subpopulation clustered distant from the other U. brizantha and U. decumbens subpopulations, so likely containing unexplored alleles. We also identified a well-supported subpopulation containing both polyploid U. decumbens and U. brizantha accessions; this was the only group containing more than one species and tentatively constitutes an independent "mixed" gene pool for both species. We observed two gene pools in U. humidicola. One subpopulation, "humidicola-2", was much less common but likely includes the only known sexual accession in the species. ConclusionsOur results offered a definitive picture of the available diversity in Urochloa to inform breeding and resolve questions raised by previous studies. It also allowed us identifying prospective founders to enrich the breeding gene pool and to develop genotyping and genotype-phenotype association mapping experiments. HIGHLIGHTWe clarified the genetic make-up and population structure of 111 Urochloa spp. forage grasses to inform cultivar development.

plant biology↗

bioRxiv2021

Flow cytometry-based determination of ploidy from dried leaf specimens in genomically complex collections of the tropical forage grass Urochloa s. l.

We aimed to develop an optimized approach to determine ploidy for dried leaf material in a germplasm collection of a tropical forage grass group, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. 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. The methods enable robust identification of ploidy levels (coefficient of variation, CV, typically <5%). Ploidy of some 353 forage grass accessions (ploidy range from 2 to 9), 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 used in the current breeding programs at CIAT and EMBRAPA: the brizantha and humidicola agamic complexes are variable, with multiple ploidy levels and DNA content. U. brizantha has odd level of ploidy (x=5), and the relative differences in nuclear DNA content between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed some aneuploidy.

genomics↗

bioRxiv2021

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

Background 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.

genomics↗

bioRxiv2020

Broken, silent, and in hiding: Tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris)

Background and AimsEndogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. MethodsUsing next- and third-generation sequencing data and the genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRV families (beetEPRVs) in the B. vulgaris genome. Focusing on the canonical family beetEPRV3, we investigated its chromosomal localization, abundance, and distribution by fluorescent in situ and Southern hybridization. Key ResultsBeetEPRVs range between 7.5 and 10.7 kb (0.3 % of the B. vulgaris genome) and are heterogeneous in structure and sequence. Although all three beetEPRV families were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different degrees of fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that target beetEPRVs in a family-specific manner, indicating stringent epigenetic suppression. We localized beetEPRV3 on all 18 sugar beet chromosomes, occurring preferentially in clusters and associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 variants also exist in the genomes of related wild species, indicating an initial beetEPRV3 integration 13.4 to 7.2 million years ago. ConclusionsOur study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing imply possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.

plant biology↗

bioRxiv2020

Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes): evolutionary relationships and a repetitive element in the Control Region (D-loop)

We are presenting the complete mitogenomes of eight fish species/cytotypes from Neotropical region belonging to the Astyanax and Psalidodon genus: A. aeneus, A. altiparanae, P. fasciatus (from two locations - Upper Parana and Sao Francisco river basins), A. lacustris, P. rivularis (two cytotypes) and P. rioparanaibano. We perform the whole-genome sequencing for six of these species in a Novaseq 6000 - by Illumina, meanwhile two genomes were assembled from raw data available in databases. Plus, we reassembled and annotated the mitochondrial genomes for A. mexicanus and P. paranae, both already described and with raw data available online. All the genomes presented the same organization, with 13 protein-coding genes, 22 tRNA genes and two rRNA genes. Aiming to contribute to the understanding of the several cryptic species complexes and phylogeny of the genus, we perform Bayesian analysis using the 13 protein-coding genes from these species, plus Deuterodon giton and using a Brycon species as outgroup.

genomics↗

bioRxiv2020

The genotypic and genetic diversity of enset (Ensete ventricosum) landraces used in traditional medicine is similar to the diversity found in starchy landraces

BackgroundEnset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed and fiber. It contributes to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. Socio-economic changes and the loss of indigenous knowledge might lead to the decline of important medicinal landraces and their associated genetic diversity. However, it is currently unknown whether medicinal landraces are genetically differentiated from other landraces. Here, we characterize the genetic diversity of medicinal enset landraces to support effective conservation and utilization of their diversity ResultsWe evaluated the genetic diversity of 51 enset landraces of which 38 have reported medicinal value. A total of 38 alleles were detected across the 15 SSR loci. AMOVA revealed that 97.6% of the total genetic variation is among individual with an FST of 0.024 between medicinal and non-medicinal landraces. A neighbor-joining tree showed four separate clusters with no correlation to the use values of the landraces. Principal coordinate analysis also confirmed the absence of distinct clustering between the groups, showing low differentiation among landraces used in traditional medicine and those having other use values. ConclusionWe found that enset landraces were clustered irrespective of their use value, showing no evidence for genetic differentiation between enset grown for medicinal uses and non-medicinal landraces. This suggests that enset medicinal properties may be restricted to a more limited number of genotypes, a product of interaction with the environment or management practice, or partly misreported. The study provide baseline information that promotes further investigations in exploiting the medicinal value of these specific landraces

genetics↗