In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
Clematis is an important horticultural and medicinal genus in Ranunculaceae. Here, we report three complete chloroplast genome sequences of C. acerifolia, C. smilacifolia, and C. uncinata. The chloroplast genomes were found to be 159,552 bp, 159,624 bp, and 159,524 bp in length, and GC contents were 37.9, 37.9, and 38.0%, respectively. The sequence of each species contained 112 unique genes, including 29 tRNA, 4 rRNA, and 79 protein-coding genes. These chloroplast genome sequences provide knowledge to the genetic variations and evolution of Clematis and Ranunculaceae.
Aesculus chinensis Bunge was widely cultivated as a street tree. The complete chloroplast genome of A. chinensis, a plant species with edible seeds in family Sapindaceae, was generated in this study. The length of the complete chloroplast genomes was 155,706 bp and the total GC contents were 38.0%, 85,506 bp of large single copy (LSC) and 18,714 bp of small single copy (SSC) regions were separated by 25,743 bp of inverted repeat (IR) regions. One hundred thirty genes were predicted, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of A. chinensis and related species revealed that A. chinensis was most closely related to A. wangii.
Allium ovalifolium var. leuconeurum is an endemic plant in Southwest China. The complete chloroplast genome sequence of A. ovalifolium var. leuconeurum was generated by de novo assembly using highthroughput sequencing. The length of chloroplast genome was 153,635 bp in length, containing a large-single copy region (LSC) of 82,693 bp, a small-single copy region (SSC) of 17,932 bp, and a pair of inverted repeats (IRa and IRb) regions of 26,505 bp. The genome contains 132 genes, including 86 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. Phylogenetic analysis with the reported chloroplast sequences shows that A. ovalifolium var. leuconeurum is more closely related to Allium prattii, both of which belong to the Sect. Anguinum.
Pyrus phaeocarpa Rehd. belongs to the Pyrus genus (Rosaceae) with high commercial value in China. Many trees in the wild have been destroyed affected by human activities and needed to be protection urgently. In this study, we reported the complete chloroplast genome sequence of P. phaeocarpa using Illumina sequencing technology. The complete chloroplast genome of P. phaeocarpa was 160,203 bp in length, containing a large single copy (LSC, 88,200 bp), a small single copy (SSC, 19,231 bp), and a pair of inverted repeats (IRs, 26,385 bp). The chloroplast genome GC content was 36.54%, contained 113 unique genes, including 30 tRNA, four rRNA, and 79 protein-coding genes. Phylogenetic analysis revealed that P. phaeocarpa was close to P. pashia, P. pyrifolia, and P. ussuriensis, provided strong support for the relationship of Pyrus.
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