Phlox pilosa ssp. sangamonensis is a state-endangered and narrowly endemic taxon only found in Champaign and Piatt counties, Illinois. Here, we present evidence of natural hybridization between Phlox ...divaricata ssp. laphamii and P. pilosa ssp. sangamonensis. In May 2018, we collected a putative F1 hybrid of the two taxa in a sympatric population. We screened six microsatellites developed for North American Phlox species and measured eight morphological traits to test the specimen's hybrid status. The microsatellite data were analyzed using a Bayesian clustering technique to infer genetic groupings. The eight morphological characteristics were analyzed using principal components analysis. We also measured the flowering phenology of P. divaricata ssp. laphamii and P. pilosa ssp. sangamonensis to assess the possibility of cross pollination. Bayesian clustering and the principal components analysis indicated that the sample was a Phlox divaricata ssp. laphamii × Phlox pilosa ssp. sangamonensis. There was modest phenological overlap between the two taxa, suggesting that gene flow is possible—though likely uncommon—in sympatric populations. We then discuss the effects of this hybridization on P. pilosa ssp. sangamonensis conservation and genetic composition.
Pepper blight, caused by the oomycete pathogen Phytophthora capsici (P. capsici), is one of the most destructive soilborne diseases worldwide. Between 2019 and 2020, 235 single spore isolates of P. ...capsici were collected from 36 commercial pepper planting areas in Sichuan, Chongqing, and Guizhou provinces in China. A novel full set of 323 high-quality polymorphic microsatellites was obtained by resequencing 10 isolates. In total, 163 isolates with two alleles per microsatellite locus were used for population analysis and resulted in 156 genotypes on 10 microsatellite loci. The genetic diversity, population differentiation, principal component, genetic structure, and genetic relationships analyses showed an extensive variety of the P. capsici in Sichuan and Guizhou with clonal lineages, two shared genotypes, and no geographic differentiation. The population from Chongqing was differentiated from that of Sichuan and Guizhou and had the highest genetic diversity. There was no significant distinction between the populations of the two sampling years, but there was a small differentiation between the populations from bell peppers and hot peppers. The isolates from Southwest China were largely distant from the two reference isolates from the USA. The analysis of molecular variance showed that the major variance of the populations was within populations. The linkage equilibrium test, mating type composition, and oospore detection indicated that only P. capsici from the Jiulongpo district of Chongqing had appeared in sexual recombination. Overall, this study revealed that the high and complex genetic diversity population of P. capsici in Sichuan, Chongqing, and Guizhou with uneven geographic variation and limited sexual reproductive behavior in Chongqing, potentially driven by differences in the geographical environment, reproductive patterns, different cultivars, and artificial long-distance transfers.
Phytophthora capsici, a notorious soilborne and rapidly evolving pathogen with a wide range of hosts, is a huge threat to pepper production worldwide. However, the detailed genetic structure and dynamics of P. capsici in most Chinese provinces are still unclear, even though China is the world's largest producer and consumer of peppers. Here, a novel full set of high-quality polymorphic microsatellites, obtained by genome resequencing data of 10 isolates from Southwest China, was provided for future population analyses. In this study, we further investigated and established the genetic structure, sexual recombination, geographic subdivisions, interannual stability, differentiation in different types of host peppers, and member relationships of P. capsici from three provinces in Southwest China. These results reveal the genetic structure and dynamics of P. capsici in three provinces of Southwest China and help us to execute more effective management strategies in the future.
Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the underlying cause of many genetic diseases. There ...are challenges associated with accurately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NGS). In particular, accurate detection of pathological STR expansion is limited by the sequence read length during whole-genome analysis. We developed TREDPARSE, a software package that incorporates various cues from read alignment and paired-end distance distribution, as well as a sequence stutter model, in a probabilistic framework to infer repeat sizes for genetic loci, and we used this software to infer repeat sizes for 30 known disease loci. Using simulated data, we show that TREDPARSE outperforms other available software. We sampled the full genome sequences of 12,632 individuals to an average read depth of approximately 30× to 40× with Illumina HiSeq X. We identified 138 individuals with risk alleles at 15 STR disease loci. We validated a representative subset of the samples (n = 19) by Sanger and by Oxford Nanopore sequencing. Additionally, we validated the STR calls against known allele sizes in a set of GeT-RM reference cell-line materials (n = 6). Several STR loci that are entirely guanine or cytosines (G or C) have insufficient read evidence for inference and therefore could not be assayed precisely by TREDPARSE. TREDPARSE extends the limit of STR size detection beyond the physical sequence read length. This extension is critical because many of the disease risk cutoffs are close to or beyond the short sequence read length of 100 to 150 bases.
Aedes albopictus is an indigenous primary vector for dengue and Zika viruses in China. Compared with its insecticide resistance, biology and vector competence, little is known about its genetic ...variation, which corresponds to environmental variations. Thus, the present study examines how Ae. albopictus varies among different climatic regions in China and deciphers its potential dispersal patterns.
The genetic variation and population structure of 17 Ae. albopictus populations collected from three climatic regions of China were investigated with 11 microsatellite loci and the mitochondrial coxI gene.
Of 44 isolated microsatellite markers, 11 pairs were chosen for genotyping analysis and had an average PIC value of 0.713, representing high polymorphism. The number of alleles was high in each population, with the n
value increasing from the temperate region (3.876) to the tropical region (4.144). Twenty-five coxI haplotypes were detected, and the highest diversity was observed in the tropical region. The mean Ho value (ca. 0.557) of all the regions was significantly lower than the mean He value (ca. 0.684), with nearly all populations significantly departing from HWE and displaying significant population expansion (p value < 0.05). Two genetically isolated groups and three haplotype clades were evaluated via STRUCTURE and haplotype phylogenetic analyses, and the tropical populations were significantly isolated from those in the other regions. Most genetic variation in Ae. albopictus was detected within populations and individuals at 31.40 and 63.04%, respectively, via the AMOVA test, and a relatively significant positive correlation was observed among only the temperate populations via IBD analysis (R
= 0.6614, p = 0.048). Recent dispersions were observed among different Ae. albopictus populations, and four major migration trends with high gene flow (Nm > 0.4) were reconstructed between the tropical region and the other two regions. Environmental factors, especially temperature and rainfall, may be the leading causes of genetic diversity in different climatic regions.
Continuous dispersion contributes to the genetic communication of Ae. albopictus populations across different climatic regions, and environmental factors, especially temperature and rainfall, may be the leading causes of genetic variation.
In countries where farming is largely subsistence, no pedigree records of farm animals are maintained at farmers' herd and scientific mating plans are not observed which leads to the accumulation of ...inbreeding and loss of production potential. Microsatellites have been widely used as reliable molecular markers to measure inbreeding. We attempted to correlate autozygosity estimated from microsatellite data with the inbreeding coefficient (F) calculated from pedigree data in Vrindavani crossbred cattle developed in India. The inbreeding coefficient was calculated from the pedigree of ninety-six Vrindavani cattle. Animals were further grouped into three groups viz. acceptable/low (F: 0-5%), moderate (F: 5-10%) and high (F: ≥10%), based on their inbreeding coefficients. The overall mean of the inbreeding coefficient was found to be 0.070 ± 0.007. A panel of twenty-five bovine-specific loci were chosen for the study according to ISAG/FAO. The mean F
IS,
F
ST,
and F
IT
values were 0.0548 ± 0.025, 0.012 ± 0.001 and 0.0417 ± 0.025, respectively. There was no significant correlation between the F
IS
values obtained and the pedigree F values. The locus-wise individual autozygosity was estimated using the method-of-moments estimator (MME) formula for locus-specific autozygosity. The autozygosities ascribing to CSSM66 and TGLA53 were found to be significantly (p < .01 and p < .05, respectively) correlated with pedigree F values.
The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration ...of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome.
Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (F
) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis.
This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.
Perennial kale is a rare leafy vegetable and forage crop that is mainly vegetatively propagated and therefore expensive to conserve ex situ. A genebank collection of 47 perennial kales and 34 ...reference samples from the main Brassica oleracea crop types were characterized with seven microsatellite markers in order to verify potential redundancies and to obtain more insight in the position of perennial kales within B. oleracea. Based on the obtained results and on data from previous studies, the collection was reduced with 49% to 24 perennial kales. Considering this level of reduction, it was estimated that the investments made for the final verification by microsatellite analysis are returned after only 4-year time. A principal coordinate plot clearly separated the perennial kales from the other crop types of B. oleracea, except in one case. This deviating accession of vegetatively preserved perennial kale clustered closely together with the single seed-preserved accession of perennial kale included in the study. These two accessions occupied an intermediate position between the group of vegetatively propagated perennial kales and the group of seed-propagated Brassica accessions, suggesting a hybridization background with another B. oleracea crop type. The microsatellite study demonstrated a close genetic relationship among the investigated perennial kales and their unique position within B. oleracea.
Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., ...microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted.
Here we used microsatellite and SNP data generated from Gunnison sage-grouse (Centrocercus minimus) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (H
, H
, F
, A
) and differentiation (F
, G
, D
). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for H
, F
, A
, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data.
We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.
Microsatellites are repeats of 1- to 6-bp units, and approximately 10 million microsatellites have been identified across the human genome. Microsatellites are vulnerable to DNA mismatch errors and ...have thus been used to detect cancers with mismatch repair deficiency. To reveal the mutational landscape of microsatellite repeat regions at the genome level, we analyzed approximately 20.1 billion microsatellites in 2717 whole genomes of pan-cancer samples across 21 tissue types. First, we developed a new insertion and deletion caller (MIMcall) that takes into consideration the error patterns of different types of microsatellites. Among the 2717 pan-cancer samples, our analysis identified 31 samples, including colorectal, uterus, and stomach cancers, with a higher proportion of mutated microsatellite (≥0.03), which we defined as microsatellite instability (MSI) cancers of genome-wide level. Next, we found 20 highly mutated microsatellites that can be used to detect MSI cancers with high sensitivity. Third, we found that replication timing and DNA shape were significantly associated with mutation rates of microsatellites. Last, analysis of mutations in mismatch repair genes showed that somatic SNVs and short indels had larger functional impacts than germline mutations and structural variations. Our analysis provides a comprehensive picture of mutations in the microsatellite regions and reveals possible causes of mutations, as well as provides a useful marker set for MSI detection.
Simple sequence repeats (SSR), also called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects. At present, the genomes of more than 100 ...insect species are available. However, the features of SSRs in most insect genomes remain largely unknown.
We identified 15.01 million SSRs across 136 insect genomes. The number of identified SSRs was positively associated with genome size in insects, but the frequency and density per megabase of genomes were not. Most insect SSRs (56.2-93.1%) were perfect (no mismatch). Imperfect (at least one mismatch) SSRs (average length 22-73 bp) were longer than perfect SSRs (16-30 bp). The most abundant insect SSRs were the di- and trinucleotide types, which accounted for 27.2% and 22.0% of all SSRs, respectively. On average, 59.1%, 36.8%, and 3.7% of insect SSRs were located in intergenic, intronic, and exonic regions, respectively. The percentages of various types of SSRs were similar among insects from the same family. However, they were dissimilar among insects from different families within orders. We carried out a phylogenetic analysis using the SSR frequencies. Species from the same family were generally clustered together in the evolutionary tree. However, insects from the same order but not in the same family did not cluster together. These results indicated that although SSRs undergo rapid expansions and contractions in different populations of the same species, the general genomic features of insect SSRs remain conserved at the family level.
Millions of insect SSRs were identified and their genome features were analyzed. Most insect SSRs were perfect and were located in intergenic regions. We presented evidence that the variance of insect SSRs accumulated after the differentiation of insect families.
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