Background: Trapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time. Results: The Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA—atpF and rps2—rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds. Conclusion: In summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future.

Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa. natans (4x, AABB), i.e., diploid T. natans (2x, AA) and Trapa incisa (2x, BB). In conjunction with four published (sub)genomes of Trapa, we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element (TE) library to develop Trapa genomic resources. The pangenome displayed substantial gene-content variation with dispensable and private gene clusters occupying a large proportion (51.95%) of the total cluster sets in the six (sub)genomes. Genotyping of presence-absence variation (PAVs) identified 40 453 PAVs associated with 2570 genes specific to A- or B-lineages, of which 1428 were differentially expressed, and were enriched in organ development process, organic substance metabolic process and response to stimulus. Comparative genome analyses showed that the allotetraploid T. natans underwent asymmetric subgenome divergence, with the B-subgenome being more dominant than the A-subgenome. Multiple factors, including PAVs, asymmetrical amplification of TEs, homeologous exchanges (HEs), and homeolog expression divergence, together affected genome evolution after polyploidization. Overall, this study sheds lights on the genome architecture and evolution of Trapa, and facilitates its functional genomic studies and breeding program.

Global aquatic habitats are undergoing rapid degradation and fragmentation as a result of climate change and changes in land use. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the genetic diversity and structure of the extant natural populations of Zizania latifolia from five river basins in China based on 46 microsatellite markers. We tested isolation by environment (IBE), isolation by resistance (IBR), and isolation by distance (IBD) patterns using a reciprocal causal model (RCM). Furthermore, we elucidated the impact of the environment on Z. latifolia genetic diversity using generalized linear models (GLMs) and spatially explicit mixed models. Low genetic diversity (H_E = 0.125–0.433) and high genetic differentiation (F_ST = 0.641, Ø_pt = 0.654) were found. Higher historical gene flow (M_H = 0.212–2.354) than contemporary gene flow (M_C = 0.0112–0.0247) and significant bottlenecks in almost all populations were identified, highlighting the negative impact of wetland fragmentation. The IBE model was exclusively supported for all populations and in three river basins. The IBD and IBR models were supported in one river basin each. The maximum temperature of the warmest month and precipitation seasonality were the plausible environmental parameters responsible for the observed pattern of genetic diversity. Local adaptation signatures were found, with nine loci identified as outliers, four of which were gene-linked and associated with environmental variables. Based on these findings, IBE is more important than IBD and IBR in shaping the genetic structure of Z. latifolia.

Magnolia patungensis (Magnoliaceae) is an endangered tree species endemic to China. To facilitate analysis of its genetic variability, we developed novel polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers using transcriptome data. In total, 37 774 SSRs amounting to 91.52 Mb were identified from 131 132 unigenes, with the frequency of 28.81% and the average density of 2.42 kb. Mononucleotide (50.81%) and dinucleotide (34.12%) were the most abundant repeat types. We randomly selected 102 putative loci to test the amplification efficiency and the degree of polymorphism using three populations from which 15 individuals per population were sampled. The successful amplification rate was 36.27% and the polymorphism rate 12.75%. The 13 polymorphic SSR marker primers selected were used to characterize the genetic diversity of M. patungensis. A total of 40 alleles were identified for the species, ranging from 2 to 5 per locus. At the population level, the mean number of alleles per locus ranged from 1.9 to 2.5, and the mean observed and expected heterozygosity values from 0.308 to 0.446 and 0.304 to 0.424, respectively. Significant genetic differentiation (FST = 0.286) and low gene flow (Nm = 0.627) among populations were discovered. Transferability of the markers was tested in five congeneric species. Nine loci were successfully amplified in M. dandyi, eight in M. insignis, M. fordiana and M. hookeri, and seven in M. conifera. These new EST-SSR markers will be an essential tool for the conservation of this endangered species as well as for investigating the evolutionary history for M. patungensis and its congenerics.

Trapa L., an annual floating-leaved herb, is widely distributed in the old world and has important edible and medicinal values. However, the taxonomy and phylogeny of Trapa are unclear. Here, we reported the complete chloroplast genome of a wild species with small nuts, T. incisa. The complete chloroplast genome size of T. incisa was 155, 453 bp, consisting of two inverted repeat (IR) regions (24, 388 bp), one large single copy (LSC) region (88, 398 bp) and one small single copy (SSC) region (18, 279 bp). A total of 129 genes were annotated, including 83 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Among them, 19 genes were duplicated (6 protein-coding genes, 9 tRNA genes and 4 rRNA genes). The phylogenomic analysis suggested a close relationship between T. incisa and T. maximowiczii.

Water chestnut (Trapa L.) is a floating-leaved aquatic plant with high edible and medicinal value. In this study, we presented chromosome-level genome assemblies of cultivated large-seed species Trapa bicornis and its wild small-seed relative Trapa incisa by using PacBio HiFi long reads and Hi-C technology. The T. bicornis and T. incisa assemblies consisted of 479.90 Mb and 463.97 Mb contigs with N50 values of 13.52 Mb and 13.77 Mb, respectively, and repeat contents of 62.88% and 62.49%, respectively. A total of 33,306 and 33,315 protein-coding genes were predicted in T. bicornis and T. incisa assemblies, respectively. There were 159,232 structural variants affecting more than 11 thousand genes detected between the two genomes. The phylogenetic analysis indicated that the lineage leading to Trapa was diverged from the lineage to Sonneratia approximately 23 million years ago. These two assemblies provide valuable resources for future evolutionary and functional genomic research and molecular breeding of water chestnut.