Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub

Abstract

Background Ammopiptanthus nanus is a rare broad-leaved shrub that is found in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the tertiary period, A. nanus is of great significance to plant biogeographic research in the ancient Mediterranean region. Here, we report a draft genome assembly using the Pacific Biosciences (PacBio) platform and gene annotation for A. nanus.FindingsA total of 64.72 Gb of raw PacBio sequel reads were generated from four 20-kb libraries. After filtering, 64.53 Gb of clean reads were obtained, giving 72.59× coverage depth. Assembly using Canu gave an assembly length of 823.74 Mb, with a contig N50 of 2.76 Mb. The final size of the assembled A. nanus genome was close to the 889 Mb estimated by k-mer analysis. The gene annotation completeness was evaluated using Benchmarking Universal Single-Copy Orthologs; 1,327 of the 1,440 conserved genes (92.15%) could be found in the A. nanus assembly. Genome annotation revealed that 74.08% of the A. nanus genome is composed of repetitive elements and 53.44% is composed of long terminal repeat elements. We predicted 37,188 protein-coding genes, of which 96.53% were functionally annotated.ConclusionsThe genomic sequences of A. nanus could be a valuable source for comparative genomic analysis in the legume family and will be useful for understanding the phylogenetic relationships of the Thermopsideae and the evolutionary response of plant species to the Qinghai Tibetan Plateau uplift.

Genome-Wide Identification and Expression Analyses of the Chitinases under Cold and Osmotic Stress in Ammopiptanthus nanus

“…To identify the chitinase genes in A. nanus, the genome sequence and annotation data were obtained from the A. nanus genome project [33]. The Hidden Markov Model (HMM) seed profile of the Glyco_hydro_18 (PF00704) and Glyco_hydro_19 (PF00182) was downloaded from the Pfam database [34], and chitinase genes in A. nanus were identified using HMMER3 (v. 3.0) software [35].…”

“…In recent years, high-throughput sequencing technology has provided a great deal of nucleic acid data for A. nanus [32], especially recently, the whole genome sequencing was completed using single-molecule sequencing [33], which makes it possible to identify chitinase family at the genome level. In the present study, the genome-wide identification of chitinase in A. nanus was conducted and expression profiling of the chitinase family under cold and osmotic stress was performed using quantitative real-time PCR (qRT-PCR).…”

Characterization of the AP2/ERF Transcription Factor Family and Expression Profiling of DREB Subfamily under Cold and Osmotic Stresses in Ammopiptanthus nanus

“…Genome sequence data were obtained from the A. nanus genome project [32]. The hidden Markov model (HMM) model of the Apetala 2 (AP2) (PF00847) was downloaded from the Pfam database [49], and the AP2/ERF family TFs in A. nanus were identified using HMMER3 (v. 3.0) software [50] with a defined threshold of E < 1e −5 .…”

Advances in legume research in the genomics era

“…These studies have enabled the cloning, characterisation and validation of candidate genes shown as beneficial in other model study systems, conferring salinity and heat tolerance to Escherichia coli by the A. nanus betaine aldehyde dehydrogenase gene (Yu et al 2014), or cold tolerance by the A. nanus antifreeze gene AnAFP to both E. coli and tobacco (Deng et al 2014), among many others. Recently, the A. nanus genome was sequenced on the PacBio platform (Table 1; Gao et al 2018), providing an essential resource for functional genomics and improvement studies, with Ammopiptanthus fast becoming a model for understanding drought and cold tolerance.…”