De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China

Abstract

Background Acer yangbiense is a newly described critically endangered endemic maple tree confined to Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on “plant species with extremely small populations (PSESP)”. Findings We generated 64, 94, and 110 Gb of raw DNA sequences and obtained a chromosome-level genome assembly of A. yangbiense through a combination of Pacific Biosciences Single-molecule Real-time, Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is ∼666 Mb, with 13 chromosomes covering ∼97% of the genome and scaffold N50 sizes of 45 Mb. Further, BUSCO analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the A. yangbiense genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, a nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolutionary history between A. yangbiense and grape, indicating that the genome has not undergone a whole-genome duplication event after the core eudicot common hexaploidization. Conclusion Here, we report a high-quality de novo genome assembly of A. yangbiense, the first genome for the genus Acer and the family Aceraceae. This will provide fundamental conservation genomics resources, as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.

SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango,Mangifera indica

“…Augustus 33 and SNAP 34 were used to perform the de novo prediction, with two rounds of iterative training. The protein sequences from Arabidopsis thaliana (TAIR10) 35 , Anacardium occidentalie (phytozome v12), Acer yangbiense 36 and Citrus sinensis 37 , were mapped to the genome by Exonerate 38 , using the Protein2Genome model. For RNA-seq aided gene annotation, the transcriptomic reads of five tissues, including seeds, mesocarps, leaves, flowers, and exocarps, were downloaded from NCBI SRA database under accession number SRR2163402- SRR2163406.…”

An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome

“…wtd produces highly fragmented assemblies in comparison to all other assemblers when shorter read lengths are included, with enhanced N50 and reduced number of contigs occurring when only longer read lengths are provided (Figure 2 ). This result is due to its underlying algorithm having only a single consensus step and is reiterated by a significant improvement of contiguity, gene completeness and N50 after racon and pilon polishing, which has been identified as an issue in other plant species assemblies such as Acer yangbiense (Yang et al, 2019 ).…”

An exploration of assembly strategies and quality metrics on the accuracy of theKnightia excelsa(rewarewa) genome

“…WTDBG2 produces highly fragmented assemblies in comparison to all other assemblers when shorter read lengths are included, with enhanced N50 and reduced number of contigs occurring when only longer read lengths are provided (Figure 2). This result is due to its underlying algorithm having only a single consensus step and is reiterated by a significant improvement of contiguity, gene completeness and N50 after Racon and Pilon polishing, which has been identified as an issue in other plant species assemblies such as Acer yangbiense (Yang et al, 2019).…”