Analysis Of Molecular Variance Research Articles

Analysis of the Mitochondrial COI Gene and Genetic Diversity of Endangered Goose Breeds

The mitochondrial cytochrome c oxidase subunit I (COI) genes of six endangered goose breeds (Xupu, Yangjiang, Yan, Wuzong, Baizi, and Lingxian) were sequenced and compared to assess the genetic diversity of endangered goose breeds. By constructing phylogenetic trees and evolutionary maps of genetic relationships, the affinities and degrees of genetic variations among the six different breeds were revealed. A total of 92 polymorphic sites were detected in the 741 bp sequence of the mtDNA COI gene after shear correction, and the GC content of the processed sequence (51.11%) was higher than that of the AT content (48.89%). The polymorphic loci within the populations of five of the six breeds (Xupu, Yangjiang, Yan, Baizi, and Lingxian) were more than 10, the haplotype diversity > 0.5, and the nucleotide diversity (Pi) > 0.005, with the Baizi geese being the exception. A total of 35 haplotypes were detected based on nucleotide variation among sequences, and the goose breed haplotypes showed a central star-shaped dispersion; the FST values were −0.03781 to 0.02645, The greatest genetic differentiation (FST = 0.02645) was observed in Yan and Wuzong breeds. The most frequent genetic exchange (Nm > 15.00) was between the Wuzong and Yangjiang geese. An analysis of molecular variance showed that the population genetic variation mainly came from within the population; the base mismatch differential distribution analysis of the goose breeds and the Tajima’s D and Fu’s Fs neutral detection of the historical occurrence dynamics of their populations were negative (p > 0.10). The distribution curve of the base mismatches showed a multimodal peak, which indicated that the population tended to be stabilised. These results provide important genetic information for the conservation and management of endangered goose breeds and a scientific basis for the development of effective conservation strategies.

Comparison of population genetic structure of Pinus mugo Turra forest stands in the Giant Mountains by analysis of nSSR molecular marker data

Abstract Pinus mugo (dwarf mountain pine) communities in the protected area of Krkonoše National Park are extremely valuable. After extensive deforestation during the sixteenth to nineteenth centuries, P. mugo recovered naturally in some parts of the Giant Mountains, and in some places imported seeds were likely used for reforestation. To distinguish between native and possibly introduced local P. mugo populations, genetic variations between 12 populations from the Czech Sudeten part of the Giant Mountains and between the two populations from the Tatra Mountains were analysed using 12 nuclear microsatellite markers (nuclear simple sequence repeats). Based on the simple sequence repeat data, 146 alleles were found, and Shannon’s information index, number of private alleles, and expected heterozygosity (HE) of populations averaged 1.12, 0.16, and 0.53, respectively. Analysis of molecular variance indicated that most of the variation was detected within populations. Low levels of genetic differentiation were also observed (average FST = 0.023). The population structure was examined by Bayesian clustering. The results of STRUCTURE analysis confirmed that the introduced populations were different from the autochthonous populations. Some of the introduced Czech Sudeten populations had similar genetic structure as the more distant native populations from the Tatra Mountains. Our results provide important genetic information for the reconstruction of natural communities in the Giant Mountains.

Panmixia and local endemism: a revision of the Eubranchus rupium species complex with a description of new species.

Species of the genus Eubranchus Forbes, 1838 (Mollusca: Gastropoda: Nudibranchia) are common faunistic elements of boreal benthic ecosystems, associated with hydroid communities. Recent studies have suggested that the widely distributed trans-Arctic E. rupium (Møller, 1842) constitutes a complex of at least three candidate species, but the detailed taxonomy of the complex remains unresolved. The purpose of the present paper is to conduct an integrative taxonomic study including molecular genetic methods (a phylogenetic analysis using COI , 16S rRNA and histone H3 with application of species delimitation methods) and morphological study (light and scanning electron microscopy) of E. rupium and closely related species. The specific aims of this study were to establish the species boundaries, morphological variability, and the phylogeographic structure within this group. The phylogeographic analysis included a TCS -based network analysis, an analysis of molecular variance (AMOVA), divergence time estimations, and ancestral area reconstructions. We demonstrate that specimens initially identified as E. rupium included three distinctive species: the nominal E. rupium with an amphiboreal range, the new species Eubranchus novik sp. nov. from the Sea of Japan, for which a taxonomic description is provided in this paper, and Eubranchus sp. from the northern Kuril Islands, which requires the collection and study of additional material for formal description. Our results confirm the amphiboreal distribution of E. rupium , as no geographic structure was found across Pacific, Arctic and Atlantic populations, and the results of the AMOVA analysis showed no differences between groups of samples from different geographic regions. The divergence of the 'Eubrancus rupium species complex' is estimated from the late Miocene or the Miocene-Pliocene boundary to the late Pliocene. It is hypothesised that the most probable ancestral region for the Eubranchus rupium species complex is the north-western Pacific, and the subsequent speciation likely occurred due to dispersal followed by allopatric speciation. ZooBank: urn:lsid:zoobank.org:pub:228E0C46-0BF7-4DDD-9C00-67B50E298D65.

Assessment of Genetic Diversity and Relatedness of Local Banana (Musa spp.) Cultivars in Malaysia Using Simple Sequence Repeat (SSR) Markers

Banana (Musa spp.) is an economically important crop widely consumed all over the world. Understanding the genetic diversity and relatedness between various banana cultivars is important to continuously improve its fruit characteristics, nutritional value, and disease resistance. This study aimed to develop a DNA fingerprinting panel using polymorphic simple sequence repeat (SSR) markers for the genetic characterisation of 11 banana cultivars in Malaysia. A total of 10 polymorphic SSR markers were developed into a multiplex PCR reaction and capillary electrophoresis to uniquely profile our collection of banana cultivars. The developed fingerprinting panel successfully amplified a total of 95 alleles, with 6 to 13 alleles per SSR marker. The average SSR marker polymorphic information content (PIC) value is 0.812, indicating the informativeness of the panel. Analysis of molecular variance (AMOVA) shows that 97% of the molecular variance from our banana collection is due to inter-variety genetic diversity, while the remaining 3% is due to intra-variety genetic diversity. A population structure analysis groups our collection of banana varieties according to the presence of at least one M. balbisiana (B) genome in their genetic makeup. The Cavendish variety, however, showed a distinct structure compared to the other cultivars. This SSR fingerprinting panel provides valuable insights into the genetic diversity and relatedness between banana cultivars in Malaysia. It has the potential to assist future banana breeding initiatives and serve as an effective quality control measure for verifying varieties in a tissue culture facility involved in banana planting materials production.

Genetic diversity and population structure in banana (Musa spp.) breeding germplasm.

Bananas (Musa spp.) are one of the most highly consumed fruits globally, grown in the tropical and sub-tropical regions. We evaluated 856 Musa accessions from the breeding programs of the International Institute of Tropical Agriculture of Nigeria, Tanzania, and Uganda; the National Agricultural Research Organization of Uganda; the Brazilian Agricultural Research Corporation (Embrapa); and the National Research Centre for Banana of India. Accessions from the in vitro gene bank at the International Transit Centre in Belgium were included to provide a baseline of available global diversity. A total of 16,903 informative single nucleotide polymorphism markers were used to estimate and characterize the genetic diversity and population structure and identify overlaps and unique material among the breeding programs. Analysis of molecular variance displayed low genetic variation among accessions and diploids and a higher variation among tetraploids (p<0.001). Structure analysis revealed two major clusters corresponding to genomic composition. The results indicate that there is potential for the banana breeding programs to increase the diversity in their breeding materials and should exploit this potential for parental improvement and to enhance genetic gains in future breeding efforts.

Integrating wing morphometrics and mitochondrial DNA analysis to assess the filaria vector Mansonia uniformis (Diptera: Culicidae) populations in Thailand.

Mansonia uniformis (Diptera: Culicidae) is recognized as a vector of Brugia malayi and has been reported to transmit Wuchereria bancrofti, both causing lymphatic filariasis in humans. This study employed geometric morphometrics (GM) to investigate wing shape variation and analyzed genetic diversity through cytochrome c oxidase subunit 1 (COI) gene analyses in Ma. uniformis populations across Thailand. Wing GM analyses indicated significant differences in wing shape based on Mahalanobis distances among nearly all population pairs (p < 0.05), with no significant correlation between wing shape and geographic distance (r = 0.210, p > 0.05). Genetic analyses identified 63 haplotypes and 49 polymorphic sites, with the overall population exhibiting a nucleotide diversity of 0.006 (± 0.001) and a haplotype diversity of 0.912 (± 0.017). Deviations from neutrality, as indicated by Tajima's D and Fu's FS tests for the overall Ma. uniformis populations in Thailand, were statistically significant and negative, suggesting population expansion (both p < 0.05). Analysis of molecular variance revealed no significant genetic structure when all populations were categorized based on collection sites and geographic regions. However, significant differences in FST values were observed between some populations. These findings enhance our understanding of the geographical and genetic factors influencing Ma. uniformis populations, which are crucial for developing effective control strategies in Thailand.

Disparities in Genetic Diversity Drive the Population Displacement of Two Invasive Cryptic Species of the Bemisia tabaci Complex in China.

Within the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) complex, two cryptic species, namely Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), are important invasive pests affecting global agriculture and horticulture. They were introduced into China sequentially in the mid-1990s and around 2003, respectively. Subsequently, the latter invader MED has outcompeted the earlier invader MEAM1, becoming the dominant population in the field. Although extensive studies have explored the underlying mechanisms driving this shift, the contribution of population genetics remains notably underexplored. In this study, we analyzed the genetic diversity and structure of 22 MED and 8 MEAM1 populations from various regions of China using mitochondrial DNA sequencing and microsatellite genotyping. Our results indicate low and moderate levels of genetic differentiation among geographically separate populations of MED and MEAM1, respectively. Median-joining network analysis of mtCOI gene haplotypes revealed no clear geographic structuring for either, with common haplotypes observed across provinces, although MED had more haplotypes. Comparative analyses revealed that MED presented greater genetic diversity than MEAM1 on the basis of two markers. Furthermore, analysis of molecular variance supported these findings, suggesting that while some genetic variation exists between populations, a significant amount is also present within populations. These findings reveal the population genetics of the two invasive cryptic species of the B. tabaci complex in China and suggest that the disparities in genetic diversity drive the displacement of their populations in the field. This work also provides valuable information on the genetic factors influencing the population dynamics and dominance of these invasive whitefly species.

Genetic diversity and population structure of Uganda cassava germplasm.

Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.

Genetic diversity and population genetics of Schistosoma haematobium isolated from children in Lusaka and Siavonga districts, Zambia.

Urogenital schistosomiasis remains a pervasive health challenge in rural Zambian communities. This study explores the molecular epidemiology and genetic diversity of Schistosoma haematobium using mitochondrial genes (cox1 and nadh1). Urine samples from 421 children in Siavonga and Lusaka districts, Zambia, were collected between December 2020 and February 2022. Microscopy and DNA extraction facilitated the identification of S. haematobium, followed by amplification, sequencing, and phylogenetic analysis of cox1 and nadh1 genes. Phylogenetic analysis revealed clustering with samples from mainland African countries, emphasizing shared haplotypes. Both mitochondrial genes exhibited substantial diversity, with 5 haplotypes from 37 cox1 sequences and 12 haplotypes from 23 nadh1 sequences. High haplotype diversity (0.621-0.808) and low nucleotide diversity (0.00181-0.03288) were observed. Siavonga and Lusaka districts shared the majority of S. haematobium haplotypes. Molecular variance and genetic differentiation analysis indicated variations within populations rather than between populations (cox1: -0.025, nadh1: 0.01646). These findings suggest a limited differentiation between S. haematobium populations in Siavonga and Lusaka, potentially indicating gene flow. Tajima's test revealed negative values, indicating a departure from neutrality, introduction of rare alleles, and recent population expansion. This study contributes essential insights into S. haematobium population genetics, crucial for effective urogenital schistosomiasis control in Zambia.

Population Genetics of the Endemic Hemiculterella wui (Wang, 1935) in the Poyang Lake Basin (China)

The Yangtze River floodplain is an area with an extremely rich diversity of fish species. Poyang Lake, as an important part of this river–floodplain system, is a crucial habitat for the survival of fish. However, prolonged human activities, such as environmental pollution and hydroelectric development, have degraded the habitat in the Poyang Lake Basin, posing threats to fish populations. Understanding genetic diversity is crucial for maintaining fish populations and understanding their dynamics. The genetic diversity of Hemiculterella wui, an economically endemic species in China of subfamily Cultrinae (Cypriniformes: Cyprinidae), has been understudied. This study investigated the genetic diversity and structure of H. wui populations from the Ganjiang, Xinjiang, Fuhe, and Raohe rivers in the Poyang Lake Basin using mitochondrial Cytb gene analysis. Results showed high haplotype diversity but low nucleotide diversity in H. wui’s Cytb sequences. Analysis of molecular variance (AMOVA) showed no significant geographic genetic structure among populations. Haplotype network analysis revealed no clear geographical clustering. Neutrality tests and haplotype nucleotide mismatch distribution indicated that all populations had experienced expansion events. These findings suggest that H. wui in Poyang Lake does not show a distinct geographic structure. However, it is still necessary to monitor the genetic characteristics of H. wui to maintain the genetic diversity of fishes in Poyang Basin, considering the threat of habitat loss and fragmentation to the population.

Exploring genetic diversity and population structure in Cinnamomum cassia (L.) J.Presl germplasm in China through phenotypic, chemical component, and molecular marker analyses.

Cinnamomum cassia (L.) J.Presl, a tropical aromatic evergreen tree belonging to the Lauraceae family, is commonly used in traditional Chinese medicine. It is also a traditional spice used worldwide. However, little is currently known about the extent of the genetic variability and population structure of C. cassia. In this study, 71 individuals were collected from seven populations across two geographical provinces in China. Nine morphological features, three chemical components, and single nucleotide polymorphism (SNP) markers were used in an integrated study of C. cassia germplasm variations. Remarkable genetic variation exists in both phenotypic and chemical compositions, and certain traits, such as leaf length, leaf width, volatile oil content, and geographic distribution, are correlated with each other. One-year-old C. cassia seedling leaf length, leaf width, elevation, and volatile oil content were found to be the main contributors to diversity, according to principal component analysis (PCA). Three major groupings were identified by cluster analysis based on the phenotypic and volatile oil data. This was in line with the findings of related research using 1,387,213 SNP markers; crucially, they all demonstrated a substantial link with geographic origin. However, there was little similarity between the results of the two clusters. Analysis of molecular variance (AMOVA) revealed that the genetic diversity of C. Cassia populations was low, primarily among individuals within populations, accounting for 95.87% of the total. Shannon's information index (I) varied from 0.418 to 0.513, with a mean of 0.478 (Na=1.860, Ne =1.584, Ho =0.481, He =0.325, and PPB =86.04%). Genetic differentiation across populations was not significant because natural adaptation or extensive exchange of seeds among farmers between environments, thus maintaining the relationship. Following a population structure analysis using the ADMIXTURE software, 71 accessions were found to be clustered into three groups, with 38% of them being of the pure type, a finding that was further supported by PCA. Future breeding strategies and our understanding of the evolutionary relationships within the C. cassia population would benefit greatly from a thorough investigation of phenotypic, chemical, and molecular markers.

Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China

BackgroundWheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms.ResultsTo understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation.ConclusionsA core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.

Genetic structure and gene flow among populations of willow (Salix species)

The newly developed Salix hybrids were assessed for genetic diversity using ISSR (Inter Simple Sequence Repeats) molecular markers. The results revealed 88.08 polymorphism, 0.53 polymorphism information content, 4.70 effective multiplex ratio, 2.54 marker index, and 7.18 resolving power from the amplified primers. Clones of the Salix matsudana (MAT) population recorded a maximum mean number of effective alleles (1.42), Shannon information index (0.38), gene diversity (0.25), and percentage of polymorphic loci (82.24 %). The AMOVA (Analysis of molecular variance) results revealed a moderate genetic divergence with a genetic variation of 88 per cent within populations and 12 per cent among the populations. The highest value of total diversity (0.28) and gene diversity (0.24) was recorded between S. matsudana (MAT) and S. tetrasperma (TETRA) populations, while there was more gene flow between S. matsudana (MAT) and S. tetrasperma (TETRA) populations (5.86). The clustering pattern obtained through STRUCTURE software showed two main gene pools and a mixture of 6–7 gene pools to confirm the hybrids based on ISSR marker data. S. matsudana and S. tetrasperma clones showed the highest gene diversity due to their proximity from their original locations, resulting in the least amount of gene exchange among populations. Molecular characterization using ISSR markers was extremely useful for studying the genetic diversity among the willow hybrids and high genetic variability should be utilized for breeding purposes in the future.

Development of SSR markers related to agarwood production and genetic diversity of Aquilaria sinensis (Lour.) Spreng wild populations

Aquilaria sinensis (Lour.) Spreng is an economically important tree that produces agarwood when it is subjected to mechanical wounding. However, the information regarding its heredity is limited. The breeding of A. sinensis has been hindered due to ambiguity in the sources of germplasm, genetic background, and varietal information. Simple sequence repeat (SSR) markers are ideal for studying genetic diversity and germplasm identification in plants. They offer the advantages of high polymorphism, good reproducibility, and co–dominance. Here, we mined SSR markers within agarwood–inducing genes and used them to explore the genetic diversity among A. sinensis natural germplasm. A total of 407 SSR loci were identified within 92 genes. We designed 96 primer pairs, among which 16 showed polymorphism and were subsequently used to analyze the genetic diversity and population structure of 179A. sinensis individuals. A total of 107 alleles were identified, with an average of 7 alleles per locus, and their polymorphism information content ranged between 0.424 to 0.769, with an average of 0.569. The analysis of molecular variance revealed that genetic variation within the individuals accounted for 94% of the total variation, indicating that the variation of A. sinensis is derived from individual variation. Furthermore, the structure analysis indicated that the natural populations of A. sinensis could be theoretically divided into 16 subgroups. The 16 polymorphic SSRs had strong cross–species transferability and distinguished individuals of A. agallochum (Lour.) Roxb. ex Finl. and A. malaccensis Lam. Taken together, these findings provide a useful resource for germplasm identification and molecular marker–assisted breeding of A. sinensis.

Synthetic cultivar development in cumin: Enhancing yield and drought tolerance

Cumin (Cuminum cyminum L.) is a valuable spice crop with medicinal properties belonging to the Apiaceae family. While farmers often favor the cultivation of cumin, low seed yield, particularly under drought stress, poses challenges to its commercial production. Due to cumin small flowers, self-incompatibility, and cross-pollination attributes, the production of synthetic varieties through polycross breeding can be an effective method for improving seed performance and enhancing drought tolerance in cumin. This study, for the first time, investigates the breeding progress of cumin in three populations over two generations. The first generation resulting from polycross breeding (SYN2 population), along with parental genotypes, was evaluated for agro-morphological traits under normal and low-water irrigation conditions in two locations and compared with the SYN1 population. Additionally, genetic diversity among parental genotypes, SYN1, and SYN2 populations was examined using Start Codon Targeted Polymorphism (SCoT) markers. Low water stress negatively affected all studied traits, except for essential oil content. Improved seed yield, increased drought tolerance, and higher cuminaldehyde content were observed in the SYN2 population compared to parental genotypes. Estimation of genetic parameters indicated a higher heritability and heterosis for traits in the SYN1 population compared to SYN2. Furthermore, trait heritability in the SYN2 population was higher under normal irrigation condition than under water stress. The highest narrow-sense heritability in both SYN1 and SYN2 populations was associated with the thousand-seed weight. Positive and significant phenotypic and genotypic correlations between thousand-seed weight and seed yield were observed in the SYN1 population, while the SYN2 population exhibited the least negative impact of drought stress on this trait. Grouping populations through cluster analysis and principal coordinate analysis based on both molecular and agro-morphological data showed complete concordance, effectively distinguishing cumin populations from one another. The SCoT molecular marker confirmed the homogeneity of the improved populations, demonstrating high efficiency in assessing intra- and inter-population diversity. Molecular variance analysis revealed lower within-population diversity (29 %) compared to between-population diversity (71 %). Among populations, SYN1, equivalent to F2 generation, exhibited the highest level of molecular diversity based on diversity indices.

Genetic Analysis and Construction of a Fingerprint for Licensed Triadica sebifera Cultivars Using SSR Markers.

Triadica sebifera is an important landscaping tree species because of its colorful autumn leaves. In recent years, some cultivars have been bred and licensed, but it can be difficult to identify them from their morphological traits due to their similar phenotypes. To explore the genetic relationships and construct a fingerprint of the cultivars, the licensed T. sebifera cultivars were analyzed using SSR markers. A total of 179 alleles were identified among the 21 cultivars at 16 SSR loci, and these alleles exhibited a high level of genetic diversity (He = 0.86). The genetic variations mainly occurred among cultivars based on an analysis of molecular variance (AMOVA). According to phylogenetic analysis, principal coordinate analysis (PCoA), and Bayesian clustering analysis, the genetic relationships were independent of geographic distances, which may be mainly due to transplantations between regions. Some cultivars with different leaf colors showed obvious genetic differentiation and may be preliminary candidates for cross-breeding. Finally, the fingerprint for the licensed cultivars was constructed with two SSR markers. The results of this study can provide technical support for the application and legal protection of licensed Triadica sebifera cultivars.

Genetic diversity and population structure of Bellamya purificata in Guangxi.

Bellamya purificata is an important medicinal value and economically farmed species in China. However, because little is known about the genetic characteristics of this species, the utilization of high-quality germplasm resources is hindered. The study examined the genetic differentiation between, and the structure of 12 B. purificata populations in Guangxi using 7 microsatellite DNA markers. High genetic diversity occurred in each population, with mean observed heterozygosity 0.655 and a mean expected heterozygosity 0.832. Analysis of molecular variance reveals genetic diversity to be greater within (95.2%) than among populations (4.8%). Genetic differentiation between populations is weak (Fst = 0.048, P < 0.001), with mixing of genetic clusters prevalent at the level of the individual. Genetic flow exists between populations (Nm = 3.084-11.778), with Longshui and Guilin populations exchanging frequently. A Mantel test reveals a low correlation between geographic and genetic distances (r = 0.2482, P < 0.071), suggesting that dispersal between neighboring populations facilitates population exchange. No significant heterozygosity excess was observed for any population (P > 0.05), indicating a lack of recent genetic bottlenecks. The results provide important genetic information for B. purificata, and data for potential germplasm discovery and aquaculture development.

Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China

Background Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense.

Characterisation of the Cinnamomumparthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics.

Cinnamomumparthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C.parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C.parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C.parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C.parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C.parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C.parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C.parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C.parthenoxylon.

Phylogenetic Diversity, Host Specificity, and Distribution of the Wood-Decaying Fungus Phellinotus teixeirae in Western Colombia’s Seasonally Dry Tropical Forest

Phellinotus (Polyporales) is a common genus of wood-decay fungi in tropical and subtropical areas, endemic to the Seasonally Dry Tropical Forest (SDTF) biome. However, Phellinotus diversity remains unexplored, despite being a major threat to living trees. Therefore, this study is aimed at confirming and characterizing through morphological and molecular data the first isolates of Phellinotus teixeirae in Pithecellobium dulce (Fabaceae) trees (locally referred to as ‘Chiminango’) from the endangered Colombian SDTF biome. Fifteen fungal specimens were recovered from living P. dulce trees, in the urban area and at the Universidad del Valle campus, and classified as P. teixeirae based on taxonomical descriptors. Phylogenetic relationships were inferred from a four-loci dataset (ribosomal and gene-coding regions), including 82 taxa covering 3991 nucleotide positions. The analysis recovered seven highly supported (&gt;90% bootstrapping) monophyletic taxa of the ‘Phellinotus Clade’, and confirmed the new distribution range of P. teixeirae (100% bootstrap support), which extends approx. 1000 km north in the Neotropics. Hierarchical stratified Analysis of MOlecular VAriance (AMOVA) provided a clear genetic distinction between species (70% of variation, p-value = 0.001) and low differentiation among country of origin within species (11%, p-value = 0.044). Discriminant Analysis for Principal Components (DAPC) indicated complex clustering including closely related species, probably a signal of recent radiation and weak species boundaries. Median-joining haplotype network analysis identified unique haplotypes, which may correlate with new host colonization and population expansion (Tajima’s D ≤ −0.5). In conclusion, this study provides the first assessment of the genetic diversity of P. teixeirae in a novel geography (SDTP) and host tree (P. dulce). However, increasing the number of isolates remains critical to understand further the genus’ distribution patterns and drivers of genetic diversity.