Summary
Speciation via hybridization and polyploidization is a major evolutionary force in plant evolution but is still poorly understood for neopolyploid groups. Challenges are attributed to high ...heterozygosity, low genetic divergence, and missing information on progenitors, ploidy, and reproduction. We study the large Eurasian Ranunculus auricomus species complex and use a comprehensive workflow integrating reduced‐representation sequencing (RRS) genomic data to unravel reticulate evolution, genome diversity and composition of polyploids.
We rely on 97 312 restriction site‐associated DNA sequencing (RAD‐Seq) loci, 576 targeted nuclear genes (48 phased), and 71 plastid regions derived from 78 polyploid apomictic taxa and four diploid and one tetraploid putative sexual progenitor species. We applied (phylo)genomic structure, network, and single nucleotide polymorphism (SNP)‐origin analyses.
Results consistently showed only 3–5 supported and geographically structured polyploid genetic groups, each containing extant sexual and one unknown progenitor species. Combined analyses demonstrated predominantly allopolyploid origins, each involving 2–3 different diploid sexual progenitor species. Young allotetraploids were characterized by subgenome dominance and nonhybrid SNPs, suggesting substantial post‐origin but little lineage‐specific evolution.
The biodiversity of neopolyploid complexes can result from multiple hybrid origins involving different progenitors and substantial post‐origin evolution (e.g. homoeologous exchanges, hybrid segregation, gene flow). Reduced‐representation sequencing genomic data including multi‐approach information is efficient to delimit shallow reticulate relationships.
•cDNA and genomic DNA sequences of the novel S59 allele were determined.•S59-specific and S10-specific PCR detection methods were developed for rapid identification from genomic ...DNA.•Self-incompatibility genotypes of over twenty accessions were characterized.
Apples (Malus × domestica Borkh.) are an economically important crop in many temperate growing regions around the world. Apple being characterized by gametophytic self-incompatibility (GSI) requires cross-pollination with compatible apple pollen during bloom to achieve sufficient fruit set for commercial production. For this reason, in commercial orchards it is common practice to plant pollinizer trees, which can be either crabapples or different apple cultivars, at a density of 5–10%. Crabapple trees, in addition to their ornamental traits, are valued as a source of genetic diversity for pollinating apple orchards. The genetics underlying cross-compatible responses among crabapples and domesticated apples, especially recently released cultivars, have been largely understudied. In this study, we characterized one novel S-RNase allele from the crabapple Malus ‘Doubloons’, named S59, and report an allele-specific PCR method for detection of this allele from genomic DNA. Further, we characterized the self-incompatibility genotypes (S-genotypes) of over twenty previously unreported Malus accessions, including some recent releases from the breeding programs of the University of Minnesota and Washington State University. The results of this work aim to provide new information about cross-compatibility of cultivars and pollinizers and may be used to aid parent selection in apple breeding programs, as well as pollinizer selection for the commercial orchard.
Summary
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. One‐hundred‐seed weight is one of the most important domesticated traits determining soybean yield; however, its ...underlying genetic basis remains elusive.
We characterized a soybean seed size 1 (sss1) mutant featuring large seeds compared to its wild‐type background. Positional cloning revealed that the candidate gene GmSSS1 encoded a SPINDLY homolog and was co‐located in a well‐identified quantitative trait locus (QTL)‐rich region on chromosome 19. Knocking out GmSSS1 resulted in small seeds, while overexpressing GmSSS1/Gmsss1 induced large seeds. Modulating GmSSS1/Gmsss1 in transgenic plants can positively influence cell expansion and cell division. Relative to GmSSS1, one mutation leading to an E to Q substitution at the 182nd residue in Gmsss1 conferred an enhancing effect on seed weight.
GmSSS1 underwent diversification in wild‐type and cultivated soybean, and the alleles encoding the Gmsss1‐type substitution of 182nd‐Q, which originated along the central and downstream parts of the Yellow River, were selected and expanded during soybean domestication and improvement.
We cloned the causative gene for the sss1 mutant, which is linked with a seed weight QTL, identified an elite allele of this gene for increasing seed weight, and provided new insights into soybean domestication and breeding.
Summary
Global warming has reduced the productivity of many field‐grown crops, as the effects of high temperatures can lead to male sterility in such plants. Genetic regulation of the high ...temperature (HT) response in the major crop cotton is poorly understood.
We determined the functionality and transcriptomes of the anthers of 218 cotton accessions grown under HT stress. By analyzing transcriptome divergence and implementing a genome‐wide association study (GWAS), we identified three thermal tolerance associated loci which contained 75 protein coding genes and 27 long noncoding RNAs, and provided expression quantitative trait loci (eQTLs) for 13 132 transcripts.
A transcriptome‐wide association study (TWAS) confirmed six causal elements for the HT response (three genes overlapped with the GWAS results) which are involved in protein kinase activity. The most susceptible gene, GhHRK1, was confirmed to be a previously uncharacterized negative regulator of the HT response in both cotton and Arabidopsis.
These functional variants provide a new understanding of the genetic basis for HT tolerance in male reproductive organs.
Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple ...Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences. Each sequence is translated into a vector in Euclidean space. Distances between the vectors can reflect the relationships between sequences. The mapping between the spectra and moment vector is one-to-one, which means that no information is lost in the power spectra during the calculation. We cluster and classify several datasets including Influenza A, primates, and human rhinovirus (HRV) datasets to build up the phylogenetic trees. Results show that the new proposed cumulative Fourier power spectrum is much faster and more accurately than MSA and another alignment-free method known as k-mer. The research provides us new insights in the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes. The computer programs of the cumulative Fourier power spectrum are available at GitHub (https://github.com/YaulabTsinghua/cumulative-Fourier-power-spectrum).
•A novel method using moments of cumulative Fourier power spectrum (CPS) in clustering the DNA sequences.•Each sequence is translated into a vector and the distances between vectors represent the relationships between sequences.•The mapping between the spectra and moment vector is one-to-one, thus much information is kept in this way.•CPS outperforms the traditional MSA and another alignment-free method on both the accuracy and the calculation speed.•We upload the code for CPS on GitHub to help people apply and analyze our method in practice.
Schistosomiasis remains a public health concern across sub-Saharan Africa; current control programmes rely on accurate mapping and high mass drug administration (MDA) coverage to attempt disease ...elimination. Inter-species hybridisation can occur between certain species, changing epidemiological dynamics within endemic regions, which has the potential to confound control interventions. The impact of hybridisation on disease dynamics is well illustrated in areas of Cameroon where urogenital schistosomiasis, primarily due to Schistosoma haematobium and hybrid infections, now predominate over intestinal schistosomiasis caused by Schistosoma guineensis. Genetic markers have shown the ability to identify hybrids, however the underlying genomic architecture of divergence and introgression between these species has yet to be established. In this study, restriction site associated DNA sequencing (RADseq) was used on archived adult worms initially identified as; Schistosoma bovis (n = 4), S. haematobium (n = 9), S. guineensis (n = 3) and S. guineensis x S. haematobium hybrids (n = 4) from Mali, Senegal, Niger, São Tomé and Cameroon. Genome-wide evidence supports the existence of S. guineensis and S. haematobium hybrid populations across Cameroon. The hybridisation of S. guineensis x S. haematobium has not been demonstrated on the island of São Tomé, where all samples showed no introgression with S. haematobium. Additionally, all S. haematobium isolates from Nigeria, Mali and Cameroon indicated signatures of genomic introgression from S. bovis. Adaptive loci across the S. haematobium group showed that voltage-gated calcium ion channels (Cav) could play a key role in the ability to increase the survivability of species, particularly in host systems. Where admixture has occurred between S. guineensis and S. haematobium, the excess introgressive influx of tegumental (outer helminth body) and antigenic genes from S. haematobium has increased the adaptive response in hybrids, leading to increased hybrid population fitness and viability.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Anaplasmosis is a rickettsial infection with significant effects on human and animal health, and the discovery of new species or genotypes with zoonotic potential in recent years has increased this ...importance. The aim of this study was to provide the first assessment of the molecular etiology and prevalence of bovine anaplasmosis in Kyrgyzstan (specifically in the Chuy, Talas, Djalal-Abad, Naryn, and Issyk-Kul regions). The prevalence of bovine anaplasmosis was determined as 1.7% (6/358). PCR and partial DNA sequencing results of the 16S ribosomal RNA (rRNA) gene revealed that Anaplasma centrale, A. phagocytophilum like-1, and the human pathogenic novel genotype A. capra are circulating in cattle herds in Kyrgyzstan. Six DNA nucleotide sequences obtained in this study were deposited in GenBank under the following accession numbers: A. centrale (MW672117, MW672118, MW672119, MW672120), A. phagocytophilum (MW672121), and A. capra (MW672115).
Here, to facilitate the solid-phase purification of synthetic DNA sequences, a riboside phosphoramidite, carrying a 5-O-capture linker and a 2-O-silyl ether protecting group, is incorporated into a ...DNA sequence during its last solid-phase synthesis cycle. After deprotection and release of the DNA sequence from the synthesis support, the sequence is then covalently linked to a capture support to enable the removal of shorter unbound DNA sequences by simply washing these off the support. The solid-phase purified DNA sequence is then released from the capture support, through an innovative intramolecular cyclodeesterification of its terminal riboside ethyl phosphate triester entity and is isolated in a yield of 94% while displaying an exquisite purity of 97%.
Summary
Soybean is a major crop that produces valuable seed oil and protein for global consumption. Seed oil and protein are regulated by complex quantitative trait loci (QTLs) and have undergone ...intensive selections during the domestication of soybean. It is essential to identify the major genetic components and understand their mechanism behind seed oil and protein in soybean.
We report that MOTHER‐OF‐FT‐AND‐TFL1 (GmMFT) is the gene of a classical QTL that has been reported to regulate seed oil and protein content in many studies.
Mutation of MFT decreased seeds oil content and weight in both Arabidopsis and soybean, whereas increased expression of GmMFT enhanced seeds oil content and weight. Haplotype analysis showed that GmMFT has undergone selection, which resulted in the extended haplotype homozygosity in the cultivated soybean and the enriching of the oil‐favorable allele in modern soybean cultivars.
This work unraveled the GmMFT‐mediated mechanism regulating seed oil and protein content and seed weight, and revealed a previously unknown function of MFT that provides new insights into targeted soybean improvement and breeding.
See also the Commentary on this article by Mukherjee et al., 239: 815–817.
The recent publication of an alternative nomenclatural code that targets prokaryotes, the Code of Nomenclature of Prokaryotes Described from DNA Sequence Data (SeqCode), raises questions about how to ...treat names 'validly published' under that code in the
(IJSEM). Here, it is reiterated that the IJSEM must function in accordance with the International Code of Nomenclature of Prokaryotes (ICNP). It is also reiterated that the ICNP covers all prokaryotes and that it accordingly assigns a nomenclatural status to all names of prokaryotic taxa. This implies that the ICNP also assigns a status to names that are only 'validly published' under the SeqCode. It follows that the IJSEM must treat such names as not validly published, since 'validly published under the SeqCode' is not a nomenclatural status, under the ICNP. Such names should be marked accordingly as
names or printed in quotation marks. The same measures would need to be taken by other journals which intend to adhere to the ICNP.
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