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.

Madagascar shelters over 14,000 plant species, of which 90% are endemic. Some of the plants are very important for the socio-cultural and economic potential. Tampolo forest, located in the northeastern part of Madagascar, is one of the remnant littoral forests hinged on by the adjacent local communities for their daily livelihood. However, it has considerably shrunk due to anthropogenic activities forming forest patches. Thus, documenting the useful plants in and around the forest is important for understanding the ethnobotany in this area. Methods: In this study we (1) collected and identified useful plants utilized by local communities. Voucher specimens were collected following the information given by interviewees, (2) recorded the collection activities and the consumption methods through semi-structured interviews of the local inhabitants, and (3) performed a phytochemical screening to identify the active compounds and the potential healing metabolites of the medicinal plants. Results: A total of 65 people between 25 and 75 years old were interviewed. Surveys recorded 123 species used as timber, food, or medicine. Among them, 92 were forest species and 31 were ruderal species. Medicinal plants were mostly used to cure stomach ailments (71%), fever (33.3%), and fatigue (25%) with leaves (68%) being the most used plant part. Phytochemical analyses of 20 endemic medicinal species showed the presence of compounds that could be responsible for the therapeutic effects of the plants. Conclusions: Tampolo forest proves to be an important littoral forest highly utilized by the adjacent local communities due to the presence of a high number of useful plants which are mostly endemic to the region. Hence, our investigation assessed the importance of these species in the locality and this can be used for further study on ecology, conservation, and valorization of these species.

Climate change is predicted to affect species in aquatic ecosystems. In Africa, factors that may influence the responses of aquatic species are poorly studied and challenging to predict. In this study, we examined the potential distribution of three aquatic fern species in the genus Azolla in Africa under projected climate change scenarios. MaxEnt was used to create ecological niche models of the three species using occurrence data and environmental variables. All models had satisfactory AUC and TSS values, indicating high prediction precision (AUC and TSS > 0.801). Results showed that elevation and precipitation were the most important variables limiting the species' expansion in the future. In addition, we observed significant variations in the climatic niches of the three species and their distinct climatically appropriate regions. The current potential distribution ranges for the species varied between 2,328,726 km² and 4,026,363 km². According to the model predictions for the current period, the potential range of Azolla species extended outside the known and recorded locations; however, under future climate conditions, the species were projected to lose between 8.1% and 48% of their suitable habitats due to climate change. Our findings can be used to develop sustainable conservation measures for aquatic species and raise awareness about the effects of climate change.

High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing six gastropod mitogenomes ( Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata ) from a graduate level biodiversity course. The students were able to produce mitochondrial genomes from sampling to annotation using existing protocols and programs. Approximately 4Gb of sequence was produced from 15 Flongle and two R9.4 Flowcells, averaging 235Mb and N50=4.4kb per Flowcell. Five of the six 14.1-18kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing reveal that the ONT assemblies were able to span over highly AT rich sequence in the control region that was otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7bp with the majority occurring at homopolymer regions. Our findings suggest that ONT are portable and can be used to rapidly produce mitogenomes at low cost and tailored to genomics-based training in biodiversity research.

PCR‐based high‐throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR‐based approaches. Marine drifting animals—zooplankton—play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others. In the present study, we collected 48 size‐fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients. To investigate the spatiotemporal dynamics of zooplankton diversity patterns and the effect of PCR amplification biases across these complex communities, we first took metatranscriptomics approach. Comprehensive computational analyses revealed a clear pattern of higher/lower homogeneity in smaller/larger zooplankton compositions across samples respectively. Our study thus suggests changes in the role of dispersal across the sizes. Next, we applied in silico PCR to the metatranscriptomics datasets, in order to estimate the extent of PCR amplification bias. Irrespective of stringency criteria, we observed clear separations of size fraction sample clusters in both metatranscriptomics and in silico datasets. In contrast, the pattern—smaller‐fractioned communities had higher compositional homogeneity than larger ones—was observed in the metatranscriptomics data but not in the in silico datasets. To investigate this discrepancy further, we analysed the mismatches of widely used mitochondrial CO1 primers and identified priming site mismatches likely driving PCR‐based biases. Our results suggest the use of metatranscriptomics or, although less ideal, redesigning the CO1 primers is necessary to circumvent these issues.