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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., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

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.

Background: Nelumbo nucifera Gaertn., a perennial aquatic macrophyte species, has been cultivated in several Asian countries for its economic importance, and medicinal uses. Two distinct ecotypes of the species are recognized based on the geographical location where the genotypes are adapted, i.e., tropical lotus and temperate lotus. The genetic diversity levels and differentiation of the tropical lotus from poorly studied geographic regions still remain unclear. Here, the population genetic diversity and structure of 15 tropical lotus populations sampled from the previous understudied natural distribution ranges, including India, Thailand, and Australia, were assessed using nine polymorphic SSR markers. Results: The SSR markers used to genotype the 216 individuals yielded 65 alleles. The highest and lowest genetic diversity estimates were found in Thailand and Indian populations, respectively. STRUCTURE analysis revealed three distinct genetic clusters, with relatively low admixtures, supported by PCoA cluster analysis. Low levels of gene flow (mean N⁠m = 0.346) among the three genetic clusters signified the Mantel test for isolation by distance, revealing the existence of a positive correlation between the genetic and geographic distances (r = 0.448, P = 0.004). Besides, AMOVA analysis revealed a higher variation among populations (59.98%) of the three groups. Overall, the populations used in this study exposed a high level of genetic differentiation (FST = 0.596). Conclusions: The nine polymorphic microsatellite markers used in our study sufficiently differentiated the fifteen tropical N. nucifera populations based on geography. These populations presented different genetic variability, thereby confirming that populations found in each country are unique. The low genetic diversity (HE = 0.245) could be explained by limited gene flow and clonal propagation. Conserving the available diversity using various conservation approaches is essential to enable the continued utilization of this economically important crop species. We, therefore, propose that complementary conservation approaches ought to be introduced to conserve tropical lotus, depending on the genetic variations and threat levels in populations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Podocarpus latifolius [(Thunb.) R.Br. ex Mirb.], also known as real yellow wood, is a large evergreen tree with exceptionally high-quality wood. It is a member of the Podocarpaceae family, which includes many species widely grown for wood pulp as well as timber for construction. Despite its importance, studies focusing on its genetic characterization and molecular biology are limited. Therefore, this study reports the complete plastome of P. latifolius, which is a circular molecule of 134 020 base pairs (bp) in length, lacking a quadripartite structure. The P. latifolius plastome encodes 117 unique genes, consisting of 82 protein-coding genes, 31 transfer RNA genes and four ribosomal RNA genes. The analysis showed that the Podocarpaceae plastomes have experienced some intron and gene losses, inversions, and inverted repeat (IR) loss resulting in a diverse plastome organization at the species and genus levels. Therefore, to understand the extent of these genomic rearrangements, more sampling of the Podocarpaceae plastomes is necessary. A total of 149 editing sites were predicted in 28 genes, all of which were C to U conversions. Moreover, a total of 164 simple sequence repeats (SSRs) were identified in the P. latifolius plastome, the majority being mononucleotide repeat motifs with A/T sequence predominance. Overall, the data obtained in this study will be useful for population genetics, evolutionary history and phylogenetic studies of the species in this genus. [ABSTRACT FROM AUTHOR]

• We firstly report the complete chloroplast genome of Menyanthaceae. • The rpl 2 gene was missing in all Nymphoides. • The divergence hotspots (gene ccsA and intergeneric region trnK-UUU-rps16) were determined. • The monophyletic position of Nymphoides as well as Menyanthes was confirmed. The Menyanthaceae is a family of aquatic flowering plants with diverse leaf and floral traits, leading to uncertainty about taxonomic, phylogenetic and evolutionary relationships within this family. In order to study the molecular evolution and phylogeny within Menyanthaceae, we sequenced the complete chloroplast (cp) genomes of six representative species from Nymphoides and the monotypic genus Menyanthes. In our study, the chloroplast genomes sizes ranged from 151,985 bp for Nymphoides coronata to 154,313 bp for Menyanthes trifoliata in length. Large Single-Copy (LSC), Small Single-Copy (SSC) and Inverted Repeat regions (IRs) portrayed normal length similar to most reported angiosperms. Menyanthaceae family chloroplast genomes possess a typical quadripartite structure, conserved in genomic structure and gene order. The size of the cp genome for the seven Menyanthaceae species consistently encoded 112–113 unique genes, including 79–80 protein-coding genes, 29 transfer RNA (tRNAs), and four ribosomal RNAs (rRNAs), 17 genes were duplicated in the inverted repeat region (IR) in both Nymphoides to 18 genes in Menyanthes respectively. Comparative analysis of the chloroplast genomes showed that Nymphoides species have lost the rpl2 intron which could be a derived feature in Nymphoides species. Phylogenetic analyses were conducted using 70 protein-coding genes in other families in order Asterales. Menyanthaceae divided into two clades with robust support. The genus Nymphoides was closely related to Menyanthes. In all studied chloroplast genomes, 30 codons had relative synonymous codon usage RSCU > 1 (higher preference), 29 codons had RSCU < 1 (low preference). The largest nucleotide diversity was found in gene ccsA in CDS region and trnK-UUU-rps16 in the IGS region. Most simple sequence repeats like in other reported angiosperms were mononucleotides ending with A/T in all cp genomes. [ABSTRACT FROM AUTHOR]

Highlights • Almost the entire geographical distribution of O. acuminata var. jingxiensis in China was sampled. • Phylogenetic analyses revealed a remarkable genetic structure among populations. • The two major genetic clusters were consistent with geographical regions. Abstract O. acuminata var. jingxiensis , an endangered endemic species, is only distributed in rivers or streams in karst areas of southwest China. In this study, the genetic variation of 10 natural populations sampled from karst rivers was detected using 12 SSR markers. The results revealed a moderate level of genetic diversity within the populations (mean H E = 0.441, I = 0.781) and population structure which significantly correlated with geographic distance (r = 0.825, P < 0.01). This pattern could be attributed to either restricted gene flow (Nm = 0.341) between the long-isolated populations or the occurrence of biparental inbreeding in closely distributed individuals (F IS = 0.362). The analysis of molecular variance (AMOVA) revealed a high level of genetic variation among the populations (F ST = 0.423) of O. acuminata var. jingxiensis and accounted for over 55% of the total genetic differentiation. Compared to gene flow, genetic drift is more likely to promote the current genetic structure because of low gene exchange among isolated habitats. Complete geographical isolation offers an opportunity for allopatric speciation at relatively small spatial scales that promotes high endemism. Our result indicated that it is likely that cryptic varieties exist in O. acuminata , such as Baishou (BS) and Luzhai (LZ) populations. Based on the available results, both in situ and ex situ efforts should be used to conserve this species. [ABSTRACT FROM AUTHOR]

Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships. [ABSTRACT FROM AUTHOR]

• Most of the natural geographical distribution of Nulembo lutea was sampled. • Low level of genetic diversity was revealed in American lotus populations. • High genetic differentiation and strong population structure was observed. • Low level of gene flow among the genetic pools was revealed. American lotus (Nelumbo lutea Willd.) is a popular plant with ornamental, medicinal, and culinary value. Studies related to the genetic diversity and population structure of N. lutea are limited. We sampled 326 individuals from 19 populations of wild N. lutea across its distribution range in the USA and genotyped them using 12 microsatellite markers. A total of 274 alleles were amplified by 12 microsatellites with a mean of 22.83. We observed a low level of genetic diversity for American lotus (A e = 2.40 and H E = 0.459) in the USA. The analysis of molecular variance (AMOVA) exhibited closer variation among populations (42.00%) than within populations (58.00%) of N. lutea, with strong genetic differentiation observed (F ST = 0.419). There was no significant correlation between genetic and geographic distances. The Bayesian analysis and neighbor-joining dendrogram displayed strong population structure. A very low level of historical gene flow (N M = 0.073) was observed among the populations. Fourteen of the 19 populations showed a demographic bottleneck, indicating the vulnerability of the American lotus populations. We thus proposed priority population sites for the conservation of N. lutea via both ex-situ and in-situ techniques. [ABSTRACT FROM AUTHOR]