De novo genome assembly of Cercospora beticola for microsatellite marker development and validation

Cercospora leaf spot caused by Cercospora beticola is a significant threat to the production of sugar and table beet worldwide. A de novo genome assembly of C. beticola was used to develop eight polymorphic and reproducible microsatellite markers for population genetic analyses. These markers were used, along with five previously described microsatellite loci to genotype two C. beticola populations from table beet fields in New York, USA. High allelic and genotypic diversity and low population differentiation were found between fields. Linkage disequilibrium of loci after clone-correction of datasets was attributed to the presence of two distinct clonal lineages within the populations. Linkage equilibrium of loci in one of the clusters supported the presence of sexual reproduction. The draft de novo genome assembly will help elucidate the reproductive system of C. beticola through investigating evidence of recombination in the C. beticola genome.     

Genetic structure of natural populations of the California black abalone (Haliotis cracherodii Leach, 1814), a candidate for endangered species status

The black abalone (Haliotis cracherodii) has been severely depleted across much of its historic range by a combination of overexploitation and disease. Natural recovery of extirpated populations along the southern California coast will depend on the extent to which remnant populations can serve as larval sources to geographic locations formerly supporting abalone populations. Population genetic analyses of mitochondrial cytochrome oxidase subunit one (COI) DNA sequences, four nuclear microsatellites, and 142 amplified fragment length polymorphisms (AFLPs) were used to evaluate connectivity among populations of H. cracherodii sampled from the central California coast and four islands in the Southern California Bight. Global divergence among populations was significant at COI and the AFLP loci. The Hka28 microsatellite locus and AFLP data showed significant divergence in multiple pairwise population comparisons and exhibited a signal of isolation by distance. Although estimates of gene flow based on genetic analyses must be interpreted with caution, the observed level of interpopulation genetic divergence suggests that larval dispersal is restricted, and natural recovery of decimated H. cracherodii populations along the coast of California is unlikely to occur in the near future.     

Development of EST-derived SSR markers using next-generation sequencing to reveal the genetic diversity of 50 chrysanthemum cultivars

Chrysanthemum plants are popular worldwide as cut flowers, potted, and in gardens. Several hundred cultivars have been commercialized, indicating that there is substantial genetic variations that can be manipulated under cultivations to produce a wide array of phenotypic variation. To study the genetic diversity of chrysanthemum cultivars in Korea, we first identified simple sequence repeats from chrysanthemum expressed sequence tags generated by FLX 454 sequencing. A total of 1109 ESTs out of 18,226 chrysanthemum ESTs were identified to carry SSRs. A total of 16 out of 46 primer pairs exhibited several polymorphisms among 50 chrysanthemum cultivars. The number of alleles per locus varied from 1 to 15, with an average of 6.25 alleles. The expected heterozygosity ranged from 0 to 0.8958, whereas polymorphism information content ranged from 0 to 0.8872. Based on polymorphisms using 16 SSR markers, a phylogenetic tree was generated revealing four groups within the 50 cultivars showing various levels of genetic diversity. The 16 polymorphic chrysanthemum SSR markers generated in this study would be useful for studies of the genetic conservation, diversity, and population structure of commercial chrysanthemum cultivars as well as closely related species.     

Characterization of 15 microsatellite loci and genetic analysis of Heterodera schachtii (Nematoda: Heteroderidae) in South Korea

Heterodera schachtii, the sugar beet cyst nematode, is a major pest of agricultural crops worldwide. We report the development of fifteen polymorphic microsatellite markers and assess the genetic diversity and structure of three populations following a recent invasion of a previously unaffected region. Populations had low levels of heterozygosity, likely indicative of population structure, history, and inbreeding. Genetic diversity analysis suggested that the current infestation in South Korea may have come either from a single source population of mixed ancestry, or from multiple sources, indicating that implementing adequate prevention measures is still an unmet challenge. Much more work is needed on this species to identify global patterns of spread, and the microsatellite loci we develop here should be useful in many regions for modeling range expansion, studying the evolution of resistance, and increasing the effectiveness of pest management strategies.     

Microsatellite and Mitochondrial Diversity Analysis of Native Pigs of Indo-Burma Biodiversity Hotspot

Assessment of genetic diversity in indigenous animals is an important and essential task for animal genetic improvement studies as well as conservation decision-making. The genetic diversity and evolutionary relationships among geographically and phenotypically distinct three pig breeds/types native to Indo-Burma and Eastern Himalayan global biodiversity hotspots were determined by genotyping with a panel of 22 ISAG recommended microsatellite loci as well as sequencing partial MTRNR1gene. The mean number of alleles per locus, effective number of alleles and observed heterozygosity were found to be 11.27 ± 0.85, 5.29 ± 0.34, and 0.795 ± 0.01, respectively. The moderate F_ST value (0.115 ± 0.01) indicated a fair degree of genetic differentiation among the native breeds. The Nei’s unbiased genetic identity estimates indicated less genetic distance (0.2909) between Niang Megha and Tenyi Vo pigs than the both individually with Ghoongroo breed. The divergence time was also estimated from the microsatellite analysis. Analysis of MTRNR1gene revealed distinct clustering of native Indian pigs with Chinese pigs over European pigs. The study revealed the abundance of genetic variation within native Indian pigs and their relationships as well as genetic distances.     

Geographic structure with no evidence for host-associated lineages in European populations of Lysiphlebus testaceipes,an introduced biological control agent

Lysiphlebus testaceipes (Cress.) is an aphidiine parasitoid originally introduced to Europe as a biological control agent of citrus aphids in the Mediterranean. It has rapidly become widespread in coastal areas continuing gradually to expand inland. L. testaceipes exploited a large number of aphids in Europe, including new hosts and significantly changed the relative abundance of the native parasitoids. This behavior may reflect a broad oligophagy of the introduced parasitoid or it may require the evolution of host specialization that results in genetically differentiated subpopulations on different hosts. To address this issue we used the mitochondrial cytochrome oxidase subunit I and seven microsatellite loci to analyze the structure of genetic variation for L. testaceipes samples collected from 12 different aphid hosts across seven European countries, as well as some samples from Benin, Costa Rica, USA, Algeria and Libya for comparison. Only five COI haplotypes with moderate divergence were identified overall. There was no evidence for the association of haplotypes with different aphid hosts in the European samples, but there was geographic structuring in this variation. Haplotype diversity was highest in France, where L. testaceipes was introduced, but only a single haplotype was detected in areas of south-eastern Europe that were invaded subsequently. The analysis of microsatellite variation confirmed the lack of host-associated genetic structure, as well as differentiation between populations from south-western and south-eastern Europe. The parasitoid L. testaceipes in Europe is thus an opportunistic oligophagous species with a population structure shaped by the processes of introduction and expansion rather than by host exploitation.     

Complete chloroplast genome of Myracrodruon urundeuva and its phylogenetics relationships in Anacardiaceae family

Continuous exploratory use of tree species is threatening the existence of several plants in South America. One of these threatened species is Myracroduron urundeuva, highly exploited due to the high quality and durability of its wood. The chloroplast (cp) has been used for several evolutionary studies as well traceability of timber origin, based on its gene sequences and simple sequence repeats (SSR) variability. Cp genome organization is usually consisting of a large single copy and a small single copy region separated by two inverted repeats regions. We sequenced the complete cp genome from M. urundeuva based on Illumina next-generation sequencing. Our results show that the cp genome is 159,883 bp in size. The 36 SSR identified ranging from mono- to hexanucleotides. Positive selection analysis revealed nine genes related to photosystem, protein synthesis, and DNA replication, and protease are under positive selection. Genome comparison a other Anacardiaceae chloroplast genomes showed great variability in the family. The phylogenetic analysis using complete chloroplast genome sequences of other Anacardiaceae family members showed a close relationship with two other economically important genera, Pistacia and Rhus. These results will help future investigations of timber monitoring and population and evolutionary studies. Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-00989-1.     

A methodological approach for non-invasive sampling for population size estimates in wild boars (Sus scrofa)

Composite microsatellite genotypes were determined at five loci from 35 tissue-sampled wild boars and used as reference genotypes to estimate both allelic drop-out rate and false allele rate in comparison to genotypes from scats and hair strands of the same animals. These rates allow to assess the genotyping reliability when only non-invasively collected material is available. Polymerase chain reaction (PCR) amplification from scats was often corrupted by inhibitors and worked poorly, whereas genotyping success in hair samples was high. Body region of hair origin had no influence on PCR suitability, whereas the type of hair had. We recommend the use of bristles. PCR conditions were optimized for single-hair (bristle) genotyping.