Genetic Diversity in Various Accessions of Pineapple [<Emphasis Type="Italic">Ananas comosus</Emphasis> (L.) Merr.] Using ISSR and SSR Markers

Inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers were used to assess the genetic diversity of 36 pineapple accessions that were introduced from 10 countries/regions. Thirteen ISSR primers amplified 96 bands, of which 91 (93.65%) were polymorphic, whereas 20 SSR primers amplified 73 bands, of which 70 (96.50%) were polymorphic. Nei’s gene diversity (h = 0.28), Shannon’s information index (I = 0.43), and polymorphism information content (PIC = 0.29) generated using the SSR primers were higher than that with ISSR primers (h =  0.23, I = 0.37, PIC = 0.24), thereby suggesting that the SSR system is more efficient than the ISSR system in assessing genetic diversity in various pineapple accessions. Mean genetic similarities were 0.74, 0.61, and 0.69, as determined using ISSR, SSR, and combined ISSR/SSR, respectively. These results suggest that the genetic diversity among pineapple accessions is very high. We clustered the 36 pineapple accessions into three or five groups on the basis of the phylogenetic trees constructed based on the results of ISSR, SSR, and combined ISSR/SSR analyses using the unweighted pair-group with arithmetic averaging (UPGMA) method. The results of principal components analysis (PCA) also supported the UPGMA clustering. These results will be useful not only for the scientific conservation and management of pineapple germplasm but also for the improvement of the current pineapple breeding strategies.     

Assessment of genetic diversity and differentiation of <Emphasis Type="Italic">Liposcelis bostrychophila</Emphasis> (Psocoptera: Liposcelidae) in China using inter-simple sequence repeat (ISSR) fingerprinting

Liposcelis bostrychophila (Psocoptera: Liposcelidae) is a widely distributed pest that can cause considerable economic losses and pose human health risks. Rapid development of insecticide resistance has made L. bostrychophila increasingly difficult to control. To obtain information potentially useful for pest management, genetic diversity and differentiation of L. bostrychophila from five geographic locations in China was studied using inter-simple sequence repeat (ISSR). A total of 104 loci were found by ISSR markers and amplified using 9 selected primers. The percentage of polymorphic bands (PPB) was 91.4%. Shannon’s information index (I) and Nei’s gene diversity (He) indicated high genetic diversity at the species level. Population differentiation (Gst = 0.484) was average in these populations. Analysis of molecular variation (AMOVA) indicated that genetic variation was mainly distributed within populations. Gene flow (Nm = 0.534) was moderate. Cluster analysis showed that genotypes isolated from the same locations displayed higher genetic similarity and permitted the grouping of isolates of L. bostrychophila into three distinct clusters. The correlation between genetic distance and geographic distance was not significant.     

Evaluation of genetic diversity amongst <Emphasis Type="Italic">Descurainia sophia</Emphasis> L. genotypes by inter-simple sequence repeat (ISSR) marker

Descurainia sophia is a valuable medicinal plant in family of Brassicaceae. To determine the range of diversity amongst D. sophia in Iran, 32 naturally distributed plants belonging to six natural populations of the Iranian plateau were investigated by inter-simple sequence repeat (ISSR) markers. The average percentage of polymorphism produced by 12 ISSR primers was 86 %. The PIC values for primers ranged from 0.22 to 0.40 and Rp values ranged between 6.5 and 19.9. The relative genetic diversity of the populations was not high (Gst =0.32). However, the value of gene flow revealed by the ISSR marker was high (Nm = 1.03). UPGMA clustering method based on Jaccard similarity coefficient grouped the genotypes into two major clusters. Graph results from Neighbor-Net Network generated after a 1000 bootstrap test using Jaccard coefficient, and STRUCTURE analysis confirmed the UPGMA clustering. The first three PCAs represented 57.31 % of the total variation. The high levels of genetic diversity were observed within populations, which is useful in breeding and conservation programs. ISSR is found to be an eligible marker to study genetic diversity of D. sophia.     

Genetic diversity and structure of <Emphasis Type="Italic">Capparis spinosa</Emphasis> L. in Iran as revealed by ISSR markers

Capparis spinosa L. (caper bush) is an economically and ecologically important perennial shrub that grows across different regions of Iran. In this study, the genetic diversity and population structure of Iranian genepool of C. spinosa is evaluated using Inter Simple Sequence Repeat (ISSR) markers. Using 10 ISSR primers, 387 DNA fragments (bands) were amplified from the genomic DNA of 92 individuals belonging to twenty-one populations of C. spinosa, of which 378 (97.7%) were polymorphic. High level of genetic diversity (percentage of polymorphic loci = 98.2%, h = 0.1382, I = 0.243), high genetic differentiation (G_st = 0.5234) and low gene flow (Nm = 0.4553) among populations were observed. Caper bush populations were divided into 4 groups in the dendrogram, PCoA plot and Bayesian clustering results, mostly corresponded to their geographic regions. The results showed that there are value in sampling Iranian caper bush populations to look for valuable alleles for use in plant breeding programs.     

Evaluation of genetic homogeneity of in vitro-raised plants of <Emphasis Type="Italic">Tecomella undulata</Emphasis> (Sm.) Seem. using molecular markers

Tecomella undulata (Sm.) Seem (family Bignoniaceae) is an economically and pharmaceutically important timber tree of arid regions of India. Overexploitation of natural stands coupled with minimal conservation and reforestation efforts has led to its incorporation in list of endangered species. This monotypic genus can be propagated only through seeds as no methods are available for its vegetative propagation. Therefore, protocol for multiplication of T. undulata via direct regeneration using nodal segments from mature trees has been standardized. Authentication of genetic homogeneity of these in vitro-raised plants is necessary for commercial-scale application of the developed micropropagation protocol. PCR-based molecular markers which have emerged as simple, fast, reliable, and labor-effective tools for testing the genetic homogeneity of in vitro-raised plants were used in the present study. Arbitrary (random amplified polymorphic DNA, RAPD), semi-arbitrary (inter-simple sequence repeat, ISSR; start codon targeted (SCoT) polymorphism), and sequence-based (simple sequence repeat, SSR) markers were used. DNA samples of shoots maintained in vitro for 2 years collected after every 4 subculture cycles (of 3 weeks each) and field-transferred plantlets were compared with the mother tree DNA using 131 primers (25 each of RAPD, ISSR, SCoT and 56 SSR). Scorable unambiguous and reproducible DNA fragments were produced by 77 (21 RAPD, 20 ISSR, 22 SCoT and 14 SSR) primers. A total of 71, 93, 94, and 42 distinct and scorable DNA fragments were produced by RAPD, ISSR, SCoT, and SSR primers respectively with an average of 3.38, 4.65, 4.27, and 3.0 DNA fragments per primer. The true-to-type nature of the in vitro-raised plants of T. undulata undergoing up to 32 subculture passages over a period of approximately 2 years was authenticated by monomorphic DNA fragments amplified with all primer combinations. Therefore, the developed micropropagation protocol can be safely used on a commercial scale for multiplying T. undulata plants.     

Genetic Diversity and Phylogenetic Relationships of Two Closely Related Northeast China <Emphasis Type="Italic">Vicia</Emphasis> Species Revealed with RAPD and ISSR Markers

RAPD and ISSR analyses revealed genetic diversity and relationships among 11 populations of two closely related northeast China Vicia species, Vicia ramuliflora and V. unijuga. Both methods yielded similar and complementary results, showing high genetic diversity. Vicia ramuliflora had 100% polymorphic loci in both RAPD and ISSR, and V. unijuga had 100% polymorphic loci for RAPD and 98.96% for ISSR. Genetic differentiation was moderate among populations of each species. Genetic variation was distributed mainly within populations for the two species. The high level of gene flow was important for the allocation of genetic variation. The UPGMA dendrogram and principal coordinates analysis at the level of individuals and populations showed that V. ramuliflora and V. unijuga were more closely related than either of them was to the outgroup species, V. cracca. The small molecular variance of V. ramuliflora and V. unijuga supports the conclusion that these two species had a common ancestor.     

Genetic diversity and population structure of Chinese <Emphasis Type="Italic">Lentinula edodes</Emphasis> revealed by InDel and SSR markers

Genetic diversity and population structure of 88 Chinese Lentinula edodes strains belonging to four geographic populations were inferred from 68 Insertion-Deletion (InDel) and two simple sequence repeat (SSR) markers. The overall values of Shannon’s information index and gene diversity were 0.836 and 0.435, respectively, demonstrating a high genetic diversity in Chinese L. edodes strains. Among the four geographic populations, the Central China population displayed a lower genetic diversity. Multiple analyses resolved two unambiguous genetic groups that corresponded to two regions from which the samples were collected—one was a high-altitude region (region 1) and the other was a low-altitude region (region 2). Results from analysis of molecular variance suggested that the majority of genetic variation was contained within populations (74.8 %). Although there was a strong genetic differentiation between populations (F _ST ?=?0.252), the variability of ITS sequences from representative strains of the two regions (<3 %) could not support the existence of cryptic species. Pairwise F _ST values and Nei’s genetic distances showed that there were relatively lower genetic differentiations and genetic distances between populations from the same region. Geographic distribution could play a vital role in the formation of the observed population structure. Mycelium growth rate and precocity of L. edodes strains displayed significant differences between the two regions. Strains from region 2 grew faster and fructified earlier, which could be a result of adaptation to local environmental factors. To the best of our knowledge, this was the first study on the genetic structure and differentiation between populations, as well as the relationship between genetic structure and phenotypic traits in L. edodes.     

Patterns of subspecies genetic diversity among oilseed <Emphasis Type="Italic">Brassica rapa</Emphasis> as revealed by agro-morphological traits and SSR markers

Brassica rapa (2n = 20, AA genome) is an important oil yielding species of the family Brassicaceae and characterized by wide range of genetic and morphological subtypes suitable for cultivation under diverse agro-climatic regions of India. In this study, genetic diversity among three subspecies of B. rapa including yellow sarson, toria and outlier brown sarson was estimated using various agro-morphological traits and simple sequence repeat (SSR) markers. Maximum variability was recorded for siliqua angle (Coefficient of variation = 30.9%), followed by seeds/siliqua (CV = 18.8%), leaf length (CV = 10%) and plant height (CV = 16.8%). Principal component analysis explained more than 50% of the total observed morphological variability for first two components. Of the 107 SSR markers tested, 80 generated reproducible, clear and distinct amplicons of which, 65 (81.25%) were found polymorphic. The number of alleles at each locus ranged from 2 to 7, with an average of 3.03 alleles per marker. A total of 197 alleles were detected at 65 SSR loci with average PIC value of 0.457 and a mean resolving power of 3.04. Neighbor-Joining cluster analysis based on morphological traits and SSR markers separately classified all the 28 genotypes into five major groups. The population structure analysis resulted into three sub-populations with certain extent of admixture among the earlier established taxonomic sub-groups. Twenty-three unique alleles were detected in thirteen B. rapa varieties. The clustering analysis and principal coordinate analysis outlined the genetic relationships among different varieties belonging to the three subspecies of B. rapa. Genetically diverse genotypes as illustrated by score plots and from the clustering patterns brought out the wide range of diversity present among B. rapa genotypes and the underlying options available for selecting parental genotypes for hybridization and developing high yielding cultivars suitable for Indian conditions.     

Population genetic diversity and geographical differentiation of MHC class II DAB genes in the vulnerable Chinese egret (<Emphasis Type="Italic">Egretta eulophotes</Emphasis>)

Major histocompatibility complex (MHC) genes are excellent markers for the study of adaptive genetic variation occurring over different geographical scales. The Chinese egret (Egretta eulophotes) is a vulnerable ardeid species with an estimated global population of 2600–3400 individuals. In this study, we sampled 172 individuals of this egret (approximately 6 % of the global population) from five natural populations that span the entire distribution range of this species in China. We examined their population genetic diversity and geographical differentiation at three MHC class II DAB genes by identifying eight exon 2 alleles at Egeu-DAB1, eight at Egeu-DAB2 and four at Egeu-DAB3. Allelic distributions at each of these three Egeu-DAB loci varied substantially within the five populations, while levels of genetic diversity varied slightly among the populations. Analysis of molecular variance showed low but significant genetic differentiation among five populations at all three Egeu-DAB loci (haplotype-based ?_ST: 0.029, 0.020 and 0.042; and distance-based ?_ST: 0.036, 0.027 and 0.043, respectively; all P < 0.01). The Mantel test suggested that this significant population genetic differentiation was likely due to an isolation-by-distance pattern of MHC evolution. However, the phylogenetic analyses and the Bayesian clustering analysis based on the three Egeu-DAB loci indicated that there was little geographical structuring of the genetic differentiation among five populations. These results provide fundamental population information for the conservation genetics of the vulnerable Chinese egret.     

Molecular variation and population structure in endangered <Emphasis Type="BoldItalic">Limonium</Emphasis><Emphasis Type="BoldItalic">bicolor</Emphasis>: genetic diversity of microsatellite markers and amplified fragment length polymorphism analysis

Knowledge and analysis of the genetic structure of an endangered species is important for its conservation and evolutionary process. Simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs) were used in evaluation of the genetic diversity and population differentiation in Limonium bicolor (Plumbaginaceae), an endangered herb with high medicinal and horticulture value. A total of 117 alleles were detected with an average 5.85 alleles per locus using SSR and 222 bands from AFLP were amplified in six populations. It was found that L. bicolor was characterized by high levels of genetic polymorphism (100 and 83.78%), low levels of total genetic diversity (\(H_{\mathrm{t}}=\) 0.2824 and 0.2424), and moderate degrees of genetic differentiation among populations (\(\Phi _{\mathrm{ST}} =\) 0.284 and 0.251). Analysis of molecular variance (AMOVA) revealed that the main variation component existed within populations (71.56%; 74.93%) rather than among populations (28.44%; 25.07%). Four main clusters were displayed in the UPGMA using TFPGA, which was consistent with the result of principal coordinate analysis (PCA) using NTSYS. Mutations or infrequent gene flow among populations can increase the plant slowly, thus in situ conservation policies should be implemented first for effective and sustainable development. At the same time, ex situ measures, such as those individuals with rare alleles, to maintain the relationships between individuals and populations are also proposed.     

Genetic diversity of Indian jujube cultivars using SCoT,ISSR, and rDNA markers

Genetic variation and relationships among 37 cultivars of Ziziphus mauritiana (Lamk.) native of India were analyzed using start codon targeted (SCoT), inter-simple sequence repeats (ISSR), and ribosomal DNA (rDNA) markers. High level of polymorphism among SCoT (61.6%) and ISSR (61%) primers with higher PIC values ranging from 63.1 to 90.4% of SCoT and 47.3 to 88.8% of ISSR primers was recorded. SCoT and ISSR dendrograms revealed similarity coefficients ranging from 0.80 to 0.92 and 0.79 to 0.96, respectively, and clearly delineated all the cultivars of Z. mauritiana into well-supported distinct clusters. Greater Gst signifies higher amount of differentiation observed over multiple loci among seven Z. mauritiana populations. On the other hand, higher gene flow demonstrating a very high migration rate between Z. mauritiana populations indicated higher rates of transfer of alleles or genes from one population to another. The genetic diversity of population 1 (Rajasthan) was the richest among all the seven populations. The largest genetic distance was measured between Maharashtra and West Bengal and the least between Rajasthan and Punjab cultivars. Most of the genetic diversity exists within population rather than among populations. Substantial variation in the ITS-1 region signifies its phylogenetic utility specifically in assessing genetic diversity in Z. mauritiana. The clustering patterns using three molecular marker systems vis-à-vis place of origin exhibited no consistency in grouping of Z. mauritiana cultivars as cultivars from the same place of origin were genetically cataloged into different SCoT, ISSR, and ITS phylogram clusters indicating wide genetic diversity and distribution across agro-climatic zones validating the robustness of marker systems tested.     

Investigating the genetic diversity and differentiation patterns in the <Emphasis Type="Italic">Penstemon scariosus</Emphasis> species complex under different sample sizes using AFLPs and SSRs

Habitat fragmentation due to anthropogenic activities is the major cause of biodiversity loss. Endemic and narrowly distributed species are the most susceptible to habitat degradation. Penstemon scariosus is one of many species whose natural habitat is vulnerable to industrialization. All varieties of P. scariosus (P. scariosus var. albifluvis, P. scariosus var. cyanomontanus, P. scariosus var. garrettii, P. scariosus var. scariosus) have small distribution ranges, but only P. scariosus var. albifluvis is being considered for listing under the Endangered Species Act. We used eight microsatellites or simple sequence repeats (SSRs) loci and two amplified fragment length polymorphism (AFLP) primer combinations to investigate the population genetic structure and diversity of P. scariosus varieties. Moreover, we compared the utility of the two marker systems in conservation genetics and estimated an appropriate sample size in population genetic studies. Genetic differentiation among populations based on F_st ranged from low to moderate (F_st?=?0.056–0.157) and from moderate to high when estimated with D_es (D_es?=?0.15–0.32). Also, AMOVA analysis shows that most of the genetic variation is within populations. Inbreeding coefficients (F_is) were high in all varieties (0.20–0.56). The Bayesian analysis, STRUCTURE, identified three clusters from SSR data and four clusters from AFLPs. Clusters were not consistent between marker systems and did not represent the current taxonomy. MEMGENE revealed that a high proportion of the genetic variation is due to geographic distance (R²?=?0.38, P?=?0.001). Comparing the genetic measurements from AFLPs and SSRs, we found that AFLP results were more accurate than SSR results across sample size when populations were larger than 25 individuals. As sample size decreases, the estimates become less stable in both AFLP and SSR datasets. Finally, this study provides insight into the population genetic structure of these varieties, which could be used in conservation efforts.     

Genetic analysis of forest species <Emphasis Type="Italic">Eugenia uniflora</Emphasis> L. through of newly developed SSR markers

Nine microsatellite loci for genetic analysis of three populations of the tropical tree Eugenia uniflora L. (pitanga or Brazilian cherry) from fragments of semideciduous forest were developed. We used the technique of building a (GA) _n and (CA) _n microsatellite-enriched library by capture with streptavidin-coated magnetic beads. We assessed the polymorphism of seven microsatellites in 84 mature trees found in three areas (Ribeirão Preto, Tambaú and São José do Rio Pardo), highly impacted by the agricultural practices, in a large region among Pardo river and Mogi-Guaçu river basins, in state of São Paulo, Brazil. All loci were polymorphic, and the number of alleles was high, ranging from 6 to 24, with a mean of 14.4. All stands showed the same high level of genetic diversity (mean H _E  = 0.83) and a low genetic differentiation (mean F _ST = 0.031), indicating that genetic diversity was higher within rather than among populations. Seven of the nine loci were highly variable, and sufficiently informative for E. uniflora. It was concluded that these new SSR markers can be efficiently used for gene flow studies.     

Genetic diversity and genetic structure of black alder (<Emphasis Type="Italic">Alnus glutinosa</Emphasis> [L.] Gaertn) in the Belgium-Luxembourg-France cross-border area

Due to its beneficial effects on river ecosystems, black alder (Alnus glutinosa) is one of the tree species selected for planting on riverbanks in the cross-border area encompassing Wallonia in Belgium, Lorraine in France, and Luxembourg. The preservation of this species, however, is threatened by an invasive pathogen that particularly targets and kills young alder individuals. The objectives of this study were to characterize the genetic diversity and the genetic structure of A. glutinosa at this local level with the aim of assisting the conservation and replanting strategies and to determine if a germplasm collection comprising individuals from the same cross-border area captures the diversity present in the region. Nuclear simple sequence repeat (SSR) and chloroplastic DNA (cpDNA) markers were used to analyze four local wild populations and the germplasm collection which is representative of two river catchments and six legal provenance regions. Three populations distant from the studied area were also included. A panel of 14 nuclear SSR loci revealed high allelic diversity and very low differentiation among wild populations (mean F _ST?=?0.014). The germplasm collection displayed a range of alleles that were representative of the different populations, and no significant differentiation between the germplasm collection and the local wild populations was observed, making this collection, as far as allelic diversity is concerned, suitable for providing trees for riverbank replanting programs. Using SSR markers, various statistical approaches consistently indicated the lack of a significant geographical structure at the level of the river catchments or provenance regions. In contrast, two cpDNA haplotypes were detected and displayed a cross-border geographically structured distribution that could be taken into account in defining new cross-border provenance regions.     

Genetic consequences of anthropogenic disturbances and population fragmentation in <Emphasis Type="Italic">Acacia senegal</Emphasis>

Acacia senegal is endemic to dry forest and woodland ecosystems of Sub-Saharan Africa and provides both ecological and socio-economic benefits. However, these ecosystems are threatened by escalating human disturbances and fragmentation. To investigate the human impacts on genetic diversity and structure of A. senegal, we studied genetic variability and differentiation of 330 individual trees from 11 natural A. senegal populations, grouped into lightly and heavily disturbed, using 12 polymorphic nuclear microsatellite markers. Gene diversity (H _E ) ranged from H _E = 0.570 to H _E = 0.632. Significant differences (P < 0.05) between the levels of disturbances are reported for mean gene diversity, number of alleles and allelic richness with lightly disturbed populations showing higher values. Overall, the indirect estimates of average outcrossing rates ranged from 0.794 (Kiserian) to 0.999 (Kampi ya Moto) with a mean of 0.997 suggesting a predominantly outcrossing species. There was no significant relationship (P > 0.05) detected between genetic and geographic distances, showing lack of isolation by distance. Analysis of population structure using unweighted pair group method with arithmetic mean and Bayesian model suggests presence of three gene pools as most probable, although most individuals showed mixed ancestry. The diversity and genetic structure reported in this study revealed negative impacts of human disturbance on A. senegal within this ecosystem. We recommend in-situ conservation strategies to safeguard the woodland ecosystem from further deforestation.     

Genetic diversity and population structure of a drought-tolerant species of <Emphasis Type="Italic">Eucalyptus</Emphasis>, using microsatellite markers

Given the impact of climate change on the availability of water resources, it becomes necessary the use of plant species well suited to planting on dryland sites. Eucalyptus cladocalyx, a native tree of South Australia, is capable of growing under relatively dry environments and saline soils. Two hundred twenty simple sequence repeat (microsatellites) markers, from a consensus linkage map of Eucalyptus, were selected to examine genetic diversity and population structure in a collection of E. cladocalyx introduced to southern Atacama Desert, Chile. A total of 130 microsatellites were successfully amplified, some of which are associated with quantitative traits of interest in Eucalyptus. Genetic analysis revealed a total of 457 alleles, ranging from 2 to 8 alleles per locus. A moderate level of genetic diversity (He = 0.492) and differentiation (FST = 0.086) was found among the populations. Mount Remarkable and Marble Range showed the highest and lowest level of genetic diversity, respectively. The Bayesian clustering analysis revealed three homogeneous genetic groups confirming that the individuals of E. cladocalyx from natural forest are highly and significantly structured. These results provide a novel information for the development of breeding strategies in E. cladocalyx by using marker-assisted selection in regions with low rainfall patterns.     

High genetic diversity and differentiation of an extremely narrowly distributed and critically endangered decaploid rose (<Emphasis Type="Italic">Rosa praelucens</Emphasis>): implications for its conservation

Rosa praelucens is a critically endangered decaploid alpine rose with an extremely narrow geographic distribution in Northwestern Yunnan, China. We sampled almost all the extant individuals (527 individuals in 31 natural locations and 56 individuals preserved in three local living collections) to assess the genetic variation and to probe the genetic connectivity among the individuals and populations based on three cpDNA intergenic spacers and six fluorescent amplified fragment length polymorphism (AFLP) markers. The morphological traits from seven populations were also measured. R. praelucens exhibited high levels of morphological variation, genetic diversity, and differentiation. The extant individuals were clustered into eight groups in neighbor-net networks, and subsequent Bayesian analysis assigned them into three larger gene pools, both in accordance with their morphological traits, especially flower color. The living collections embraced two private cpDNA haplotypes and included three out of the species’ total eight AFLP genotypes. Rhizome clonal growth, decaploid, and mixed breeding system may largely contribute to high genetic diversity and differentiation in R. praelucens. We concluded that the endangered status of R. praelucens may mainly be due to habitat fragmentation and loss and inherent reproductive difficulties, rather than low genetic diversity. The populations contributing higher cpDNA genetic diversity, representing more AFLP genotypes, and encompassing private cpDNA haplotypes should be given conservation priority by creating plant-micro reserves. The living collections should also be targeted for further ex situ conservation, population recovery, and reintroduction of R. praelucens plants.     

Complete chloroplast genome sequence of <Emphasis Type="Italic">Capsicum</Emphasis><Emphasis Type="Italic">baccatum</Emphasis> var. <Emphasis Type="Italic">baccatum</Emphasis>

Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Complete chloroplast (cp) genome sequences of Capsicum species have been reported. We herein report the complete chloroplast genome sequence of Capsicum baccatum var. baccatum, a wild Capsicum species. The total length of the chloroplast genome is 157,145 bp with 37.7 % overall GC content. One pair of inverted repeats, 25,910 bp in length, was separated by a small single-copy region (17,974 bp) and large single-copy region (87,351 bp). This region contains 86 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 11 genes contain one or two introns. Pair-wise alignments of chloroplast genome were performed for genome-wide comparison. Analysis revealed a total of 134 simple sequence repeat (SSR) motifs and 282 insertions or deletions variants in the C. baccatum var. baccatum cp genome. The types and abundances of repeat units in Capsicum species were relatively conserved, and these loci could be used in future studies to investigate and conserve the genetic diversity of the Capsicum species.     

Molecular phylogeography and population evolution analysis of <Emphasis Type="Italic">Citrus ichangensis</Emphasis> (Rutaceae)

Ichang papeda (Citrus ichangensis), a wild and endemic perennial plant in Rutaceae, is characterized by the existence of wild and natural populations in southwestern and middle-west China. We analyzed a total of 231 individuals across 16 natural populations using chloroplast SSR markers, nuclear SSR markers, and single-copy nuclear genes. Standard population genetic analyses as well as Bayesian and maximum likelihood models were used to clarify the genetic diversity, population differentiation, barriers to gene flow, bottleneck events, isolation by distance, history migration, demographic history among populations, and phylogeny evolution. The chloroplast and nuclear genome analyses revealed a low level of genetic diversity in C. ichangensis. Clear signals of recent bottlenecks and strong patterns of isolation by distance were detected among different subpopulations, indicating a low extent of historical gene flow for this species and that genetic drift would occur after population differentiation. Bayesian clustering analyses revealed a clear pattern of genetic structure, with one cluster spanning the potential refugia in Wuling Mountains and Ta-pa Mountains, and other two clusters covering a more limited distribution range. The demographic history also supported the scenario that two isolated clusters originated in parallel from the genetic diversity center. Taxonomically, Ichang papeda may be a member of subgenus Citrus. Owing to the complicated topography, the mountainous regions and the Yangtze River have provided long-term stable habitats for C. ichangensis and acted as main barriers for its expansion, which might facilitate the process of speciation. Statistical population models and genetic data indicated strong genetic structure in C. ichangensis, which might result from the restricted gene flow, genetic drift, and population bottlenecks.