In this study, the chloroplast (cp) genomes of Hemiptelea davidii, Ulmus parvifolia, Ulmus lamellosa, Ulmus castaneifolia, and Ulmus pumila ‘zhonghuajinye’ were spliced, assembled and annotated using the Illumina HiSeq PE150 sequencing platform, and then compared to the cp genomes of other Ulmus and Ulmaceae species. The results indicated that the cp genomes of the five sequenced species showed a typical tetrad structure with full lengths ranging from 159,113 to 160,388 bp. The large single copy (LSC), inverted repeat (IR), and small single copy (SSC) lengths were in the range of 87,736–88,466 bp, 26,317–26,622 bp and 18,485–19,024 bp, respectively. A total of 130–131 genes were annotated, including 85–86 protein-coding genes, 37 tRNA genes and eight rRNA genes. The GC contents of the five species were similar, ranging from 35.30 to 35.62%. Besides, the GC content was different in different region and the GC content in IR region was the highest. A total of 64-133 single sequence repeat (SSR) loci were identified among all 21 Ulmaceae species. The (A)n and (T)n types of mononucleotide were highest in number, and the lengths were primarily distributed in 10–12 bp, with a clear AT preference. A branch-site model and a Bayes Empirical Bayes analysis indicated that the rps15 and rbcL had the positive selection sites. Besides, the analysis of mVISTA and sliding windows got a lot of hotspots such as trnH/psbA, rps16/trnQ, trnS/trnG, trnG/trnR and rpl32/trnL, which could be utilized as potential markers for the species identification and phylogeny reconstruction within Ulmus in the further studies. Moreover, the evolutionary tree of Ulmaceae species based on common protein genes, whole cp genome sequences and common genes in IR region of the 23 Ulmaceae species were constructed using the ML method. The results showed that these Ulmaceae species were divided into two branches, one that included Ulmus, Zelkova and Hemiptelea, among which Hemiptelea was the first to differentiate and one that included Celtis, Trema, Pteroceltis, Gironniera and Aphananthe. Besides, these variations found in this study could be used for the classification, identification and phylogenetic study of Ulmus species. Our study provided important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Ulmus and Ulmaceae species.
Ulmus elongata is a species of Sect. Chaetoptelea (Liemb.) S chneid in Ulmaceae, and it is an endangered wild plant listed in the second class of the Protected Plants in China. The complete chloroplast genome (cp) of U. elongata was reported in this study. The result showed that the cp genome was 159,230 bp in length including a large single-copy (LSC) 87,718 bp and a small single-copy (SSC) 18,690 bp, which were separated by two inverted repeats (IRs) of 26,411 bp with the typical quadripartite structure, respectively. The genome encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The GC content was 35.57%. Chloroplast sequences were used for constructing phylogenetic tree to determine the evolutionary status of U. elongata. The maximum-likelihood phylogenetic analysis showed that U. elongata was clustered with five other Ulmus species, and the relationship between Ulmus and Zelkova was closest. The success of cp genome assembly of U. elongata has laid a foundation for the study of chloroplast molecular biology and can effectively promote the study of genetic breeding and molecular evolution of U. elongata. ARTICLE HISTORY
This study was conducted to sequence, assemble, annotate, and characterize the complete chloroplast (cp) genome sequence of Ulmus lanceaefolia. The result showed that the cp genome was 158,652 bp in length with 35.63% GC content, including a large single-copy (LSC) region of 87,119 bp, a small singlecopy (SSC) region of 18,697 bp and an inverted repeat sequence (IRa/IRb) region of 26,418 bp, which was a typical tetrad structure. We had identified a total of 132 genes, including 87 protein-coding genes, eight rRNA genes, and 37 tRNA genes. The phylogenetic trees were constructed based on the cp genome sequences of U. lanceaefolia and 12 plants in the NCBI database, and the phylogenetic positions of U. lanceaefolia in the Ulmaceae were identified.
In this study, the whole chloroplast genome of Ulmus bergmanniana was sequenced, assembled, annotated and characterized for the first time. The results showed that the total length of U. bergmanniana chloroplast genome was 160,060 bp and the GC content was 35.52%, which had the typical circular double-stranded tetrad structure of angiosperm chloroplast genome. It includes a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRa/IRb), with lengths of 88,161 bp, 19,029 bp, and 26,435 bp, respectively. A total of 131 genes were annotated, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Based on the chloroplast genome sequences of 14 plants in U. bergmanniana and NCBI database, the phylogenetic tree was constructed, and the phylogenetic position of U. bergmanniana in Ulmaceae was determined. The results will provide a theoretical basis for molecular identification and resource development and utilization of U. bergmanniana.
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