Apocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measure the genome size of A. venetum, and bioinformatics methods were employed for the evaluation of the genome size, heterozygosity ratio, repeated sequences, and GC content in order to provide a foundation for subsequent whole-genome sequencing. The sequencing analysis results indicated that the preliminary estimated genome size of A. venetum was 254.40 Mbp, and its heterozygosity ratio and percentage of repeated sequences were 0.63 and 40.87%, respectively, indicating that it has a complex genome. We used k-mer = 41 to carry out a preliminary assembly and obtained contig N50, which was 3841 bp with a total length of 223949699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227322054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous. We recommend the use of the ‘2+3’ (Illumina+PacBio) sequencing combination to supplement the Hi-C technique and resequencing technique in future whole-genome research in A. venetum.
Plants generally adopt different reproductive strategies to adapt to their environments and increase their fitness. Here, we studied the effects of enclosure cultivation on the reproductive allocation of a wheatgrass species Agropyron mongolicum in the Desert steppes of Northern China. The results showed that: (a) after enclosure cultivation, the height, clump width, coverage, and clump biomass of A. mongolicum significantly increased by 78.96% (p = .040), 63.50% (p = .013), 50.89% (p = .032), and 205.38% (p = .022), respectively, whereas density did not show a significant change (p = .330). (b) Enclosure cultivation significantly affected the biomass of A. mongolicum. Compared with cultivation outside the fence, root, leaf, and spike biomass of A. mongolicum inside the fence significantly increased by 183.52% (p = .020), 334.09% (p = .011), and 381.25% (p = .005), respectively. In addition, root biomass was the highest among the components (38.53 and 13.59 g inside and outside the fence, respectively) and spike biomass was the lowest (6.16 and 1.28 g inside and outside the fence, respectively). (c) Enclosure cultivation affected elemental nutrient allocation and the caloric values of various components of A. mongolicum, and the caloric values are positively correlated with carbon, nitrogen, and phosphorus contents. Enclosure cultivation significantly reduced carbon, nitrogen, and phosphorus in the roots, as well as nitrogen and phosphorus in the spikes, but significantly increased nitrogen in the spikes by 9.78%. The caloric values of A. mongolicum inside and outside the fence in decreasing order were as follows: spikes > leaves > stems > roots. Comparison of cultivation effects between inside and outside the fence showed that the caloric values of the spikes and roots significantly increased by 0.92% and 1.60%, respectively, whereas those of the leaves significantly decreased by 0.70%. Our results demonstrate that the reproductive allocation of elemental nutrients and caloric values in nonreproductive and reproductive organs are plastic to arid environments.
Backgroud Apocynum cannabinum is an important plant resource from the Apocynaceae family. However, the lack of complete genome information has severely impeded research progress of molecular biology research in this plant. Whole-genome sequencing can provide an in-depth understanding of species growth, development, and evolutionary origin, and is the most effective method for scientifically exploring the ecological and economic value of a plant. Methods and results In this study, we employed Illumina HiSeq, single-molecule real-time sequencing, 10X genomics linked reads, and chromatin interaction (Hi-C), a new assembly technique, to successfully assemble the whole draft genome for A.cannabinum (260 Mb). The super-scaffold N50 genome size from the Hi-C assisted assembly was 21.16 Mb and was anchored to 11 chromosome, resulting in a high-quality reference genome at the chromosome level (2n = 2x = 22). We further annotated, analyzed, and predicted 22,793 protein-coding genes, of which the functions of 95.6% were already annotated, 92.3% contained conserved protein domains, and 78.7% were aligned to known metabolic pathways. Colclushions This high-quality A.cannabinum genome can be used to analyze growth and development and evaluate gene evolution at the genome level, as well as assist in the comparative genomics and genetic modification of other important medicinal plants in Apocynaceae. Comparative analysis of the gene families showed that A. cannabinum speciated around 35.8 (27.0–46.9) million years ago.
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