Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex

The Rhizopus oryzae species complex is a group of zygomycete fungi that are common, cosmopolitan saprotrophs. Some strains are used beneficially for production of Asian fermented foods but they can also act as opportunistic human pathogens. Although R. oryzae reportedly has a heterothallic (+/-) mating system, most strains have not been observed to undergo sexual reproduction and the genetic structure of its mating locus has not been characterized. Here we report on the mating behavior and genetic structure of the mating locus for 54 isolates of the R. oryzae complex. All 54 strains have a mating locus similar in overall organization to Phycomyces blakesleeanus and Mucor circinelloides (Mucoromycotina, Zygomycota). In all of these fungi, the minus (-) allele features the SexM high mobility group (HMG) gene flanked by an RNA helicase gene and a TP transporter gene (TPT). Within the R. oryzae complex, the plus (+) mating allele includes an inserted region that codes for a BTB/POZ domain gene and the SexP HMG gene. Phylogenetic analyses of multiple genes, including the mating loci (HMG, TPT, RNA helicase), ITS1-5.8S-ITS2 rDNA, RPB2, and LDH genes, identified two distinct groups of strains. These correspond to previously described sibling species R. oryzae sensu stricto and R. delemar. Within each species, discordant gene phylogenies among multiple loci suggest an outcrossing population structure. The hypothesis of random-mating is also supported by a 50:50 ratio of plus and minus mating types in both cryptic species. When crossed with tester strains of the opposite mating type, most isolates of R. delemar failed to produce zygospores, while isolates of R. oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species.     

Polymorphic microsatellite DNA markers in the ant Formica exsecta

Highly polymorphic genetic markers provide a useful tool for estimating important genetic parameters in studies of the evolution of sociality in insects. Here we report 14 polymorphic microsatellite markers developed in the ant Formica exsecta. The number of alleles found ranged between 3 and 18 per locus. These markers were developed for studying genetic population structure and mating structure in F. exsecta populations with varying social organizations (monogyne and polygyne types of societies). Cross‐species amplification indicated that some of the markers might be usable even in species belonging to different subfamilies.     

Characterization of microsatellite loci isolated in Mountain Plover (Charadrius montanus)

Primers for 15 microsatellite loci were developed for Mountain Plover, a species whose distribution and abundance have been reduced drastically in the past 30 years. In a screen of 126 individuals collected from four breeding locales across the species’ range, levels of polymorphism ranged from two to 13 alleles per locus. No two loci were found to be linked, although one locus revealed significant departures from Hardy–Weinberg equilibrium. These microsatellite loci can be used in population genetic studies, ultimately aiding in management efforts for Mountain Plover. Additionally, these markers can potentially be used in studies investigating the mating system of Mountain Plover.     

Characterization of 24 microsatellite markers in Primula chungensis(Primulaceae),a distylous-homostylous species,using MiSeq sequencing

Primula chungensis is a species with considerable floral and mating-system variation,including distylous(outcrossing),homostylous(selfing) and mixed populations that contain both outcrossing and selfing forms.We isolated 24 microsatellite markers from P.chungensis using Illumina Mi Seq sequencing.Polymorphism and genetic diversity were then measured based on a sample of 24 individuals from a natural population in southern Tibet.All loci were polymorphic with the number of alleles per locus ranging from 2 to 4.The observed and expected heterozygosity ranged from 0 to 1 and 0.219 to 0.708,respectively.The microsatellite markers we have identified will serve as valuable tools for the investigation of the population genetic structure and phylogeography of P.chungensis and will inform models of the evolutionary history of mating systems in the species.     

Characterization of 24 microsatellite markers in Primula chungensis (Primulaceae), a distylous homostylous species,using MiSeq sequencing

Primula chungensis is a species with considerable floral and mating-system variation, including distylous (outcrossing), homostylous (selfing) and mixed populations that contain both outcrossing and selfing forms. We isolated 24 microsatellite markers from P.chungensis using Illumina MiSeq sequencing. Polymorphism and genetic diversity were then measured based on a sample of 24 individuals from a natural population in southern Tibet. All loci were polymorphic with the number of alleles per locus ranging from 2 to4. The observed and expected heterozygosity ranged from 0 to 1 and 0.219 to 0.708, respectively. The microsatellite markers we have identified will serve as valuable tools for the investigation of the population genetic structure and phylogeography of P.chungensis and will inform models of the evolutionary history of mating systems in the species.     

Microsatellite analysis of Toxoplasma gondii shows considerable polymorphism structured into two main clonal groups.

Previous studies on Toxoplasma gondii population structure, based essentially on multilocus restriction fragment length polymorphism analysis or on multilocus enzyme electrophoresis, indicated that T. gondii comprises three clonal lineages. These studies showed a weak polymorphism of the markers (2-4 alleles by locus). In this study, we used eight microsatellite markers to type 84 independent isolates from humans and animals. Two microsatellite markers were present in the introns of two genes, one coding for beta-tubulin and the other for myosin A, and six were found in expressed sequence tags. With 3-16 alleles detected, these markers can be considered as the most discriminating multilocus single-copy markers available for typing T. gondii isolates. This high discriminatory power of microsatellites made it possible to detect mixed infections and epidemiologically related isolates. Evolutionary genetic analyses of diversity show that the T. gondii population structure consists of only two clonal lineages that can be equated to discrete typing units, but there is some evidence of occasional genetic exchange that could explain why one of these discrete typing units is less clearly individualised than the other.     

Isolation of compound microsatellite markers for the endangered plant Neolitsea sericea (Lauraceae)

? Premise of the study: The development of compound microsatellite markers was conducted in Neolitsea sericea to investigate genetic diversity and population genetic structure of this endangered insular species. ? Methods and Results: Using the compound microsatellite marker technique, 10 compound microsatellite markers that were successfully amplified showed polymorphism when assessed in 55 individuals from two populations in East China and Japan. Overall, the number of alleles ranged from 3 to 17, with an average of 7.9 alleles per locus. In addition, these primers could be easily amplified in Neolitsea aurata var. paraciculata and N. aurata var. chekiangensis. ? Conclusions: The highly polymorphic markers developed and characterized in this study will be useful for population genetic studies of N. sericea.     

Isolation and characterization of 10 new compound microsatellite markers for a mangrove tree species,Avicennia marina (Forsk.) Vierh. (Avicenniaceae)

Avicennia marina is an ecologically important mangrove tree species. We isolated 10 polymorphic microsatellite loci from this species using an improved technique. Our isolated loci provided compound microsatellite markers with polymorphism of two to six alleles per locus. The observed and expected heterozygosities ranged from 0.025 to 0.625 and from 0.096 to 0.767, respectively. These markers would be the useful tools for researching on the genetic diversity and population genetic structure of A. marina.     

Infra-specific diversity of Colletotrichum truncatum associated with chilli anthracnose in India based on microsatellite marker analysis

Colletotrichum truncatum is a fungal species associated with anthracnose disease in many economically important crops within the plant families Fabaceae and Solanaceae. Understanding the degree of genetic diversity within C. truncatum population will provide insights into the ability of this species to evolve in response to environmental conditions, and thus be helpful in designing effective control strategies for this pathogen. In this study, microsatellite markers from 27 loci were used to investigate the genetic diversity and population structure among 99 isolates of C. truncatum from India. All the loci (100%) were polymorphic and a total of 140 different alleles were amplified. Six distinct groups were obtained based on unweighted pair group method with arithmetical average cluster analysis. The isolates belonging to Group V showed the highest level of genetic diversity and a broad host range. Analysis of molecular variance analysis showed that the variation occurs mostly within groups. Microsatellite markers-based genetic diversity estimation revealed high diversity among C. truncatum isolates from India.     

Isolation and characterization of microsatellite loci from Corydalis ambigua (Papaveraceae)

Primers for seven unlinked and highly polymorphic microsatellite loci were developed for Corydalis ambigua to investigate its mating system and population genetics. This species can be used to explore the impact of an alien bumblebee on plant reproduction. Genetic diversity and other population genetic parameters were estimated in two populations with and without the alien bumblebee. The number of alleles per locus ranged from 4 to 20, and observed heterozygosities ranged from 0.355 to 0.969. These markers can be applied to study mating systems and population genetics in C. ambigua.     

Development, characterization, and transferability of microsatellite markers for Kirengeshoma palmata (Hydrangeaceae)

? Premise of the study: Microsatellite markers were developed for Kirengeshoma palmata to assess the population genetics and mating pattern of this critically endangered species. ? Methods and Results: A total of 24 microsatellite markers were developed for K. palmata using an enrichment protocol. These markers were screened in 37 individuals from four populations in China and Japan, and twelve were found to be polymorphic, with the number of alleles per locus ranging from two to eight. All of these primers also amplified in K. koreana. ? Conclusions: These microsatellite markers provide a useful tool to investigate the mating system, gene flow, parentage, and population dynamics of Kirengeshoma.     

Isolation and characterization of microsatellite loci in Epidendrum puniceoluteum, an endemic orchid from the Atlantic Rainforest

Epidendrum puniceoluteum is an endemic orchid of Atlantic Rainforest, restricted to few populations only due to the destruction and fragmentation of its native habitat. Here, we report on the development of 10 microsatellite markers isolated from this orchid species. Genetic variability was characterized in two distant populations from Brazil coast. The number of alleles observed for each locus ranged from two to 12 and with an average of 6.4 alleles per locus. These microsatellites should be valuable tools for studying both fine-scale genetic structure of scattered E. puniceoluteum population and patterns will be useful genetic markers for other closely related taxa.     

Development of microsatellite markers in a mangrove tree species Aegiceras corniculatum (Myrsinaceae)

Aegiceras corniculatum is an ecologically important mangrove tree species. We isolated 18 polymorphic microsatellite loci from this species. These loci provided microsatellite markers with polymorphism of two to eight alleles per locus. The observed and expected heterozygosities ranged from 0.050 to 0.550, and from 0.097 to 0.736, respectively. These markers will contribute to research on the conservation, genetic diversity and mating patterns of A. corniculatum.     

Isolation and characterization of microsatellite markers in black muntjac (Muntiacus crinifrons)

The black muntjac (Muntiacus crinifrons) is a vulnerable species found in the mountains of eastern China, about which little is known. Here we develop 11 polymorphic microsatellite loci from a (CA)(n) -enrichment library for the animal. In the analyses of 25 individuals sampled, unbiased expected heterozygosity levels varied from 0.686 to 0.876 and the number of alleles per locus varied from five to nine. Results that 11 microsatellite loci were highly polymorphic indicated that these markers are sufficiently powerful to address such questions as parentage, mating system and population genetic structure of M. crinifrons.     

Development and characterization of microsatellite markers for the Brazil nut tree Bertholletia excelsa Humb. & Bonpl. (Lecythidaceae)

Twelve polymorphic microsatellite markers were developed for the Brazil nut (Bertholletia excelsa), one of the most valuable non‐timber forest products from the Amazon, based on enrichment protocol. Six to 18 (mean 10.4) alleles per locus were identified and the expected heterozygosity ranged from 0.663 to 0.923 based on a screen of 40 individuals from one population of B. excelsa. The combined probabilities of genetic identity (8.39 × 10^?17) and paternity exclusion (0.999999) indicated that multilocus genotypes are likely to be unique allowing precise analyses of genetic structure, gene flow, and mating system of this economically important species.     

A set of microsatellite markers for use in the endangered sea urchin <Emphasis Type="Italic">Strongylocentrotus nudus</Emphasis> developed from <Emphasis Type="Italic">S. purpuratus</Emphasis> ESTs

The first set of nine microsatellite markers for the endangered sea urchin Strongylocentrotus nudus was developed from EST databases of S. purpuratus. Number of alleles per locus ranged from two to thirteen. The observed and expected heterozygosities ranged from 0.000 to 0.645 and from 0.063 to 0.912, respectively. These informative microsatellite markers will be useful in studies of population genetic structure for this species.     

Isolation and characterization of fifteen polymorphic microsatellite loci from Primula merrilliana (Primulaceae), an endemic from China

Primula merrilliana (Primulaceae) is an endangered plant endemic to south Anhui Province in China. In this study, we isolated fifteen polymorphic microsatellite loci from a population of 22 individuals using a modified biotin-capture method. Our isolated loci provided microsatellite markers with polymorphism of 3–11 alleles per locus. The expected and observed heterozygosities ranged from 0.392 to 0.855 and from 0.136 to 1.000, respectively. These markers would be the useful tools for analyzing questions concerning population genetic structure and mating system of Primula merrilliana.     

Isolation and characterization of eight compound microsatellite markers in a mangrove tree Kandelia candel (L.) Druce

Kandelia candel is an important mangrove tree species of family Rhizophoraceae. Here we isolated eight codominant compound microsatellite simple sequence repeat (SSR) loci from K. candel. Our isolated loci provided compound SSR markers with polymorphism of three to 11 alleles per locus. The expected and observed heterozygosities ranged from 0.230 to 0.887 and from 0.083 to 1.00, respectively. These markers would be the useful tools for analysing questions concerning population genetic structure and mating system of K. candel.     

Microsatellite markers for Ceiba pentandra (Bombacaceae), an endangered tree species of the Amazon forest

From a genomic library enriched for AG/TC repeats, eight polymorphic microsatellite markers were developed for Ceiba pentandra, a pan‐tropical forest tree. Polymorphism was evaluated using a panel of 74 adult trees. Using automated fluorescence detection, a total of 112 alleles was detected with an average of 14 alleles per locus. All microsatellite loci showed very high levels of genetic information content, with expected heterozygosity ranging from 0.814 to 0.895. These microsatellite markers represent a powerful tool to investigate refined questions of mating systems, gene flow, family structure and population dynamics in natural populations of C. pentandra.     

PERMANENT GENETIC RESOURCES: Development of microsatellite markers in the Japanese common squid Todarodes pacificus (Ommastrephidae)

Todarodes pacificus is an important species for commercial fisheries, but its reproductive biology has been little understood. We isolated 11 polymorphic microsatellite loci from this species. These loci provided highly polymorphic microsatellite markers with four to 26 alleles per locus. The observed and expected heterozygosities ranged from 0.150 to 1.000, and from 0.660 to 0.974, respectively. These markers will be useful for research about the mating systems and genetic diversity of T. pacificus.