Plastome phylogenomics and historical biogeography of aquatic plant genus Hydrocharis (Hydrocharitaceae).

BACKGROUND: Hydrocharis L. and Limnobium Rich. are small aquatic genera, including three and two species, respectively. The taxonomic status, phylogenetic relationships and biogeographical history of these genera have remained unclear, owing to the lack of Central African endemic H. chevalieri from all previous studies. We sequenced and assembled plastomes of all three Hydrocharis species and Limnobium laevigatum to explore the phylogenetic and biogeographical history of these aquatic plants. RESULTS: All four newly generated plastomes were conserved in genome structure, gene content, and gene order. However, they differed in size, the number of repeat sequences, and inverted repeat borders. Our phylogenomic analyses recovered non-monophyletic Hydrocharis. The African species H. chevalieri was fully supported as sister to the rest of the species, and L. laevigatum was nested in Hydrocharis as a sister to H. dubia. Hydrocharis-Limnobium initially diverged from the remaining genera at ca. 53.3 Ma, then began to diversify at ca. 30.9 Ma. The biogeographic analysis suggested that Hydrocharis probably originated in Europe and Central Africa. CONCLUSION: Based on the phylogenetic results, morphological similarity and small size of the genera, the most reasonable taxonomic solution to the non-monophyly of Hydrocharis is to treat Limnobium as its synonym. The African endemic H. chevalieri is fully supported as a sister to the remaining species. Hydrocharis mainly diversified in the Miocene, during which rapid climate change may have contributed to the speciation and extinctions. The American species of former Limnobium probably dispersed to America through the Bering Land Bridge during the Miocene.

Development and utilization of microsatellite markers to assess genetic variation coupled with modelling range shifts of Dodonaea viscosa (L.) Jacq. in isolated Taita Hills and Mount Kenya forests.

BACKGROUND: Understanding genetic variation is critical for the protection and maintenance of fragmented and highly disturbed habitats. The Taita Hills of Kenya are the northernmost part of the Eastern Arc Mountains and have been identified as one of the world's top ten biodiversity hotspots. Over the past century the current forests in the Taita Hills have become highly fragmented. In order to appraise the influence of anthropological disturbance and fragmentation on plant species in these mountains, we studied the genetic variation and population structure of Dodonaea viscosa (L.) Jacq. (Sapindaceae), using newly developed microsatellite (SSR) markers, combined with ecological niche modelling analyses (ENMs). METHODS AND RESULTS: We utilized the Illumina paired-end technology to sequence D. viscosa's genome and developed its microsatellite markers. In total, 646,428 sequences were analyzed, and 49,836 SSRs were identified from 42,638 sequences. A total of 18 out of 25 randomly selected primer pairs were designed to test polymorphism among 92 individuals across eight populations. The average observed heterozygosity and expected heterozygosity ranged from 0.119 to 0.982 and from 0.227 to 0.691, respectively. Analysis of molecular variance (AMOVA) revealed 78% variance within populations and only 20% among the eight populations. According to ENM results, D. viscosa's suitable habitats have been gradually reducing since the last glacial maximum (LGM), and the situation will worsen under the extreme pessimist scenario of (representative concentration pathway) RCP 8.5. Moreover, genetic diversity was significantly greater in larger fragments. CONCLUSIONS: In the present study, we successfully developed and tested SSR markers for D. viscosa. Study results indicate that fragmentation would constitute a severe threat to plant forest species. Therefore, urgent conservation management of smaller fragmented patches is necessary to protect this disturbed region and maintain the genetic resources.

Plastid phylogenomics and insights into the inter-mountain dispersal of the Eastern African giant senecios (Dendrosenecio, Asteraceae).

Giant senecios (Dendrosenecio, Asteraceae), endemic to the tropical mountains of Eastern Africa, are one of the most conspicuous alpine plant groups in the world. Although the group has received substantial attention from researchers, its infrageneric relationships are contentious, and the speciation history remains poorly understood. In this study, whole chloroplast genome sequences of 46 individuals were used to reconstruct the phylogeny of giant senecios using Maximum Likelihood and Bayesian Inference methods. The divergence times of this emblematic group were estimated using fossil-based calibrations. Additionally, the ancestral areas were inferred, and ecological niche modeling was used to predict their suitable habitats. Phylogenetic analyses yielded two robustly supported clades. One clade included taxa sampled from Tanzania, while the other clade included species from other regions. Giant senecios likely originated from the North of Tanzania approximately 2.3 million years ago (highest posterior density 95%; 0.77-4.40), then rapidly radiated into the Kenyan and Ugandan mountains within the last one million years. The potential routes of dispersal have been proposed based on the inferred ancestral areas, estimated time, and predicted past suitable niches. Plio-Pleistocene climate oscillations and orogeny instigated early divergence of the genus. Whereas in situ radiation of giant senecios was chiefly driven by multiple long-distance dispersal events followed by episodes of vicariance, and allopatric speciation (geographic and/or altitudinal).

Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae).

Ailanthus altissima Swingle, is a tree species native to East Asia and has a great potential in decorative, bioenergy and industrial applications in many countries. To date, despite its commercial importance, the genomic and genetic resources available for this species are still insufficient. In this study, we characterized the transcriptome of A. altissima and developed thirteen EST-SSRs (expressed sequence tag-simple sequence repeats) based on Illumina paired-end RNA sequencing (RNA-seq). Besides, we developed ten polymorphic chloroplast microsatellite (cpSSR) markers using the available chloroplast genome of A. altissima. The transcriptome data produced 87,797 unigenes, of which 64,891 (73.91%) unigenes were successfully annotated in at least one protein database. For cpSSR markers the number of detected alleles (N) per marker varied from three at cpSSR12 to twelve at cpSSR8, the unbiased haploid diversity indices (uh) varied from 0.111 to 0.485, and haploid diversity indices (h) ranged from 0.101 to 0.444 with an average unbiased haploid diversity index (uh) of 0.274. Overall, a total of 65 different cpSSR alleles were identified at the ten loci among 165 individuals of A. altissima. The allele number per locus for EST-SSRs varied from 2.143 to 9.357, and the values of observed and expected heterozygosity ranged from 0.312 to 1.000 and 0.505 to 0.826, respectively. The molecular markers developed in this study will facilitate future genetic diversity, population structure, long distance-gene transfer and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China focusing on planted and natural forest stands.

Phylogenomics of the aquatic plant genus Ottelia (Hydrocharitaceae): Implications for historical biogeography.

Ottelia Pers. is the second largest genus of the family Hydrocharitaceae, including approximately 23 extant species. The genus exhibits a diversity of both bisexual and unisexual flowers, and complex reproductive system comprising cross-pollinated to cleistogamous flowers. Ottelia has been regarded as a pivotal group to study the evolution of Hydrocharitaceae, but the phylogenic relationships and evolutionary history of the genus remain unresolved. Here, we reconstructed a robust phylogenetic framework for Ottelia using 40 newly assembled complete plastomes. Our results resolved Ottelia as a monophyletic genus consisting of two major clades, which correspond to the main two centers of diversity in Asia and Africa. According to the divergence time estimation analysis, the crown group Ottelia began to diversify around 13.09 Ma during the middle Miocene. The biogeographical analysis indicated the existence of the most recent common ancestor somewhere in Africa/Australasia/Asia. Basing on further insights from the morphological evolution of Ottelia, we hypothesized that the ancestral center of origin was in Africa, from where the range expanded by transoceanic dispersal to South America and Australasia, and further from Australasia to Asia. We suggested that the climatic change and global cooling since the mid-Miocene, such as the development of East Asian monsoon climate and tectonic movement of the Yunnan-Guizhou Plateau (YGP), might have played a crucial role in the evolution of Ottelia in China.

Cryptic diversity within the African aquatic plant Ottelia ulvifolia (Hydrocharitaceae) revealed by population genetic and phylogenetic analyses.

Revealing cryptic diversity is of great importance for effective conservation and understanding macroevolution and ecology of plants. Ottelia, a typical example of aquatic plants, possesses extremely variable morphology and the presence of cryptic diversity makes its classification problematic. Previous studies have revealed cryptic Ottelia species in Asia, but very little is known about the molecular systematics of this genus in Africa, a center of species diversity of Ottelia. In this study, we sampled Ottelia ulvifolia, an endemic species of tropical Africa, from Zambia and Cameroon. We used six chloroplast DNA regions, nrITS and six polymorphic microsatellite markers to estimate the molecular diversity and population genetic structure in O. ulvifolia. The phylogenetic inference, STACEY and STRUCTURE analyses supported at least three clusters within O. ulvifolia, each representing unique flower types (i.e., bisexual yellow flower, unisexual yellow flower and bisexual white flower types). Although abundant genetic variation (> 50%) was observed within the populations, excessive anthropogenic activities may result in genetic drift and bottlenecks. Here, three cryptic species of O. ulvifolia complex are defined, and insights are provided into the taxonomy of Ottelia using the phylogenetic species concept.

Population Genetics of Calotropis gigantea, a Medicinal and Fiber Resource Plant, as Inferred from Microsatellite Marker Variation in two Native Countries.

Calotropis gigantea is well known for its aesthetic, medicinal, pharmacological, fodder, fuel, and fiber production potential. Unfortunately, this plant species is still undomesticated, and the genetic information available for crop improvement is limited. For this study, we sampled 21 natural populations of C. gigantea from two key areas of its natural distribution range (Bangladesh and China) and genotyped 379 individuals using nine nuclear microsatellite markers. Population genetic diversity was higher in Bangladesh than that observed in Chinese populations. Overall, a moderate level of genetic diversity was found (Na = 3.73, HE = 0.466), with most of the genetic variation detected within populations (65.49%) and substantial genetic differentiation (FST = 0.345) between the study regions. We observed a significant correlation between genetic and geographic distances (r = 0.287, P = 0.001). The Bayesian clustering, UPGMA tree, and PCoA analyses yielded three distinct genetic pools, but the number of migrants per generation was high (NM = 0.52-2.78) among them. Our analyses also revealed that some populations may have experienced recent demographic bottlenecks. Our study provides a baseline for exploitation of the genetic resources of C. gigantea in domestication and breeding programs as well as some insights into the germplasm conservation of this valuable plant.

The complete chloroplast genome sequence of Dodonaea viscosa: comparative and phylogenetic analyses.

The plant chloroplast (cp) genome is a highly conserved structure which is beneficial for evolution and systematic research. Currently, numerous complete cp genome sequences have been reported due to high throughput sequencing technology. However, there is no complete chloroplast genome of genus Dodonaea that has been reported before. To better understand the molecular basis of Dodonaea viscosa chloroplast, we used Illumina sequencing technology to sequence its complete genome. The whole length of the cp genome is 159,375 base pairs (bp), with a pair of inverted repeats (IRs) of 27,099 bp separated by a large single copy (LSC) 87,204 bp, and small single copy (SSC) 17,972 bp. The annotation analysis revealed a total of 115 unique genes of which 81 were protein coding, 30 tRNA, and four ribosomal RNA genes. Comparative genome analysis with other closely related Sapindaceae members showed conserved gene order in the inverted and single copy regions. Phylogenetic analysis clustered D. viscosa with other species of Sapindaceae with strong bootstrap support. Finally, a total of 249 SSRs were detected. Moreover, a comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates in D. viscosa showed very low values. The availability of cp genome reported here provides a valuable genetic resource for comprehensive further studies in genetic variation, taxonomy and phylogenetic evolution of Sapindaceae family. In addition, SSR markers detected will be used in further phylogeographic and population structure studies of the species in this genus.

The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree.

Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.

Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics.

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.

Comparative Genomics of the Balsaminaceae Sister Genera Hydrocera triflora and Impatiens pinfanensis.

The family Balsaminaceae, which consists of the economically important genus Impatiens and the monotypic genus Hydrocera, lacks a reported or published complete chloroplast genome sequence. Therefore, chloroplast genome sequences of the two sister genera are significant to give insight into the phylogenetic position and understanding the evolution of the Balsaminaceae family among the Ericales. In this study, complete chloroplast (cp) genomes of Impatiens pinfanensis and Hydrocera triflora were characterized and assembled using a high-throughput sequencing method. The complete cp genomes were found to possess the typical quadripartite structure of land plants chloroplast genomes with double-stranded molecules of 154,189 bp (Impatiens pinfanensis) and 152,238 bp (Hydrocera triflora) in length. A total of 115 unique genes were identified in both genomes, of which 80 are protein-coding genes, 31 are distinct transfer RNA (tRNA) and four distinct ribosomal RNA (rRNA). Thirty codons, of which 29 had A/T ending codons, revealed relative synonymous codon usage values of >1, whereas those with G/C ending codons displayed values of <1. The simple sequence repeats comprise mostly the mononucleotide repeats A/T in all examined cp genomes. Phylogenetic analysis based on 51 common protein-coding genes indicated that the Balsaminaceae family formed a lineage with Ebenaceae together with all the other Ericales.

Assembly and comparative analysis of the first complete mitochondrial genome of the invasive water hyacinth, Eichhornia crassipes.

Eichhornia crassipes is an aquatic plant in tropical and subtropical regions, renowned for its notorious invasive tendencies. In this study, we assembled the complete mitogenome of E. crassipes into a single circle molecule of 397,361 bp. The mitogenome has 58 unique genes, including 37 protein-coding genes (PCGs), 18 tRNA genes, three rRNA genes, and 47 % GC content. Sixteen (6.93 %) homologous fragments, ranging from 31 bp to 8548 bp, were identified, indicating the transfer of genetic material from chloroplasts to mitochondria. In addition, we detected positive selection in six PCGs (ccmB, ccmC, ccmFC, nad3, nad4 and sdh4), along with the identification of 782 RNA editing sites across 37 mt-PCGs. These findings suggest a potential contribution to the robust adaptation of this invasive plant to the stressful environment. Lastly, we inferred that phylogenetic conflicts of E. crassipes between the plastome and mitogenome may be attributed to the difference in nucleotide substitution rates between the two organelle genomes. In conclusion, our study provided vital genomic resources for further understanding the invasive mechanism of this species and exploring the dynamic evolution of mitogenomes within the monocot clade.

Deep evaluation of the evolutionary history of the Heat Shock Factor (HSF) gene family and its expansion pattern in seed plants.

Heat shock factor (HSF) genes are essential in some of the basic developmental pathways in plants. Despite extensive studies on the structure, functional diversification, and evolution of HSF genes, their divergence history and gene duplication pattern remain unknown. To further illustrate the probable divergence patterns in these subfamilies, we analyzed the evolutionary history of HSF genes using phylogenetic reconstruction and genomic syntenic analyses, taking advantage of the increased sampling of genomic data from pteridophytes, gymnosperms and basal angiosperms. We identified a novel clade that includes HSFA2, HSFA6, HSFA7, and HSFA9 with a complex relationship, which is very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We hypothesized that HSFA9 derives from HSFA2 through gene duplication in eudicots at the ancestral state, and then expanded in a lineage-specific way. Our findings indicate that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in the most recent common ancestors of monocots. We also presumed that HSFC2 derives from HSFC1 in ancestral monocots. This work proposes that during the radiation of flowering plants, an era during which there was a differentiation of angiosperms, the size of the HSF gene family was also being adjusted with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication, gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying the evolutionary history of this multigene family.

Systematics of Lobelioideae (Campanulaceae): review, phylogenetic and biogeographic analyses.

Lobelioideae, the largest subfamily within Campanulaceae, includes 33 genera and approximately1200 species. It is characterized by resupinate flowers with zygomorphic corollas and connate anthers and is widely distributed across the world. The systematics of Lobelioideae has been quite challenging over the years, with different scholars postulating varying theories. To outline major progress and highlight the existing systematic problems in Lobelioideae, we conducted a literature review on this subfamily. Additionally, we conducted phylogenetic and biogeographic analyses for Lobelioideae using plastids and internal transcribed spacer regions. We found that former studies have reached agreement on the southern African origin of Lobelioideae, herbaceous habit and Asian origin of giant lobelioids, the convergent evolution of giant rosette lobelioids, and lastly, the multiple cosmopolitan and independent radiation of lobelioids in Africa, Pacific Basin, and the Hawaiian Islands. Also, Apetahia Baill., Sclerotheca A.DC., and Cyanea Gaudich. are paraphyletic, while Lobelia L., Pratia Gaudich., Centropogon C.Presl, Siphocampylus Pohl, and Isotoma Lindl. are polyphyletic. The taxonomy of these genera, especially Lobelia, is particularly quite frustrating. This calls for further reappraisals using both morphological and molecular data.

Distribution pattern and habitat preference for Lobelia species (Campanulaceae) in five countries of East Africa.

East Africa is one of the centres of distribution and diversity for Lobelia L. (Campanulaceae, sub-family Lobelioideae). Lobelia habitats in East Africa have been facing habitat fragmentation and loss, which are recognised as a major threat to biodiversity. However, previous plant conservation studies in East Africa only focused on protected areas and ignored unprotected areas. Future conservation strategies of plants, such as Lobelia, will depend on knowledge of their distribution patterns and habitat preference in East Africa. To understand the distribution pattern and the habitat preference of Lobelia in five countries (Kenya, Uganda, Tanzania, Rwanda and Burundi) of East Africa, we conducted a literature review in the seven major vegetation regions (afro-alpine, afro-montane forest, drier savannah, grasslands, wetter savannah, Zambezian woodland and semi-desert and desert). We also employed meander and patterned searches, which allowed greater opportunities for recording Lobelia species. Our results showed that the genus is distributed in all of the seven regions of the five countries with 54 taxa. The afro-montane forest region, with 41 taxa, is the richest in species diversity, followed by the Zambezian woodland region with 18 taxa. The semi-desert and desert region has the lowest number with only four taxa. The afro-alpine region has 15 taxa, although the region is the smallest by area. The herbaceous type was found in all regions, while the giant type has a clear preference for the afro-alpine and afro-montane forest regions. Future conservation for Lobelia should consider its habitat preference by, for example, focusing on the afro-alpine and afro-montane forest regions. This study will facilitate the setting of future conservation strategies for Lobelia.

The complete plastome sequences of five Aponogeton species (Aponogetonaceae): Insights into the structural organization and mutational hotspots.

Members of the aquatic plant genus Aponogeton are widely used commercially in aquariums because of their variable leaf shape and unique inflorescences. However, due to extensive similarity between species in this genus, morphological characters are generally inadequate for taxonomic classification. Currently, molecular makers available for taxonomic and phylogenetic studies of Aponogeton are limited. One approach to clarifying relationships between species in these complex groups is to use divergence hotspot regions within the genome. Here, we sequenced and analyzed the plastomes of five Aponogeton species collected from China, Zambia, and Kenya, and subsequently screened these plastomes for divergent DNA hotspots. The five plastomes are circular structures with sizes ranging from 154,167 bp to 154,860 bp. The Large and the Small Single Copies are separated by two Inverted Repeats. One hundred and thirteen unique genes were identified including 79 protein-coding, 30 tRNA, and four rRNA genes. We found that the most abundant repeats in all but one species were mononucleotide repeats (A/T) and that there were 23 potential RNA ending sites. Interestingly, a ~3 kb inversion, which includes the accD gene, was detected within the Asian species of Aponogeton. The inversion may be related to more frequent exchanges between this region and the nuclear genome. Furthermore, we detected mutational hotspot sites among the five Aponogeton species. Three of these hotspots are intergenic spacer regions (accD-psaI, rbcL-accD and trnH-GUG-psbA) that might be suitable for use as barcodes to resolve intra-generic relationships. We also identified four highly variable protein-coding genes (ccsA, rpl22, rps16 and ycf1) may be used as barcodes to resolve the higher-level phylogenies. Our study will provide valuable molecular resources for the taxonomic and phylogenomic study of the complex genus Aponogeton.

Genetic diversity and population structure of the endangered basal angiosperm Brasenia schreberi (Cabombaceae) in China.

Brasenia schreberi J.F. Gmelin (Cabombaceae), an aquatic herb that occurs in fragmented locations in China, is rare and endangered. Understanding its genetic diversity and structure is crucial for its conservation and management. In this study, 12 microsatellite markers were used to estimate the genetic diversity and variation in 21 populations of B. schreberi in China. A total of 61 alleles were found; assessment of allelic richness (Ar = 1.92) and observed and expected heterozygosity (HO = 0.200, HE = 0.256) suggest lower genetic diversity compared to some endangered species, and higher variation was observed within populations (58.68%) rather than among populations (41.32%). No significant correlation between geographical and genetic distance among populations was detected (Mantel test, r = 0.0694; P = 0.7985), which may have likely resulted from barriers to gene flow (Nm = 0.361) that were produced by habitat fragmentation. However, Bayesian and neighbor-joining cluster analyses suggest a population genetic structure consisting of two clusters (I and II) or four subclusters (I-1, 2 and II-1, 2). The genetic structure and distribution of B. schreberi in China may have involved glacial refugia that underwent range expansions, introgression, and habitat fragmentation. The findings of the present study emphasize the importance for both in situ and ex situ conservation efforts.

Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae).

Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively. The chloroplast genome was observed to contain 116 unique genes, of which 80 are protein-coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. The phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciflorus and Dorcoceras hygrometricum.

Development and characterization of EST-SSR markers for Ottelia acuminata var. jingxiensis (Hydrocharitaceae).

PREMISE OF THE STUDY: Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. METHODS AND RESULTS: Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis. One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively. Interestingly, in cross-varietal amplification, 13 out of the 16 loci were successfully amplified in O. acuminata var. acuminata, and 12 amplified in each of the other three varieties of O. acuminata. CONCLUSIONS: These newly developed SSR markers will facilitate further study of genetic variation and provide important genetic data needed for appropriate conservation of natural populations of all varieties of O. acuminata.

The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica's chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.