The complete chloroplast genome sequence of Ulmus lanceifolia Roxburgh ex Wallich (Ulmaceae)

Abstract

Ulmus lanceifolia, which plays an important role in ecology and economy, is one of the main evergreen broad leaved arbor species in southern China. In this study, we assembled its complete chloroplast genome. The total genome size of U. lanceifolia was 158,652bp, containing a large single-copy region of 87,119bp, a small single-copy region of 18,697bp, and a pair of inverted repeat regions of 26,418bp. The overall GC content of U. lanceifolia chloroplast genome is 35.63%. We obtained the 132 genes chloroplast genome, including 86 proteincoding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic analysis suggests that U. lanceifolia is a monophyletic taxa and a transitional species between the 2 groups which were combined by Ulmus americana, U. elongate and Zelkova serrate, Z. schneideriana respectively in Ulmaceae.

Keywords:

• Ulmus lanceifolia
• complete chloroplast genome
• Phylogenomics
• Ulmaceae

Ulmus lanceifolia (Roxburgh ex Wallich 1831) is one of the main evergreen broad leaved arbor species in southern China, with fairly good material toughness. It is around 30 meters tall, with a diameter of 40–80 centimeters at breast hight. Bark yellowish gray to chestnut brown, exfoliating in irregular flakes (Fu et al. 2003). The timber of U. lanceifolia is heavy and hard, not only is a good material for furniture, indoor decoration and plywood, but also suitable for vehicles, ships, farm tools, sporting goods and musical instruments (Xiao and Mu 1998). In addition, U. lanceifolia also has great potential in medicinal application. But to date, there is still no complete chloroplast (cp) genome is characterized for U. lanceifolia. The object of this work was to explore the intrinsic distinction in an effort to vindicate its taxonomic status in Ulmaceae. Here we present the cp genome of U. lanceifolia (GeneBank accession number: MZ159247) as an initial approach toward developing genomic tools to better understand U. lanceifolia and its close relatives.

The fresh leaves of U. lanceifolia were sampled from Xishuangbanna Tropical Botanical Garden (**latitude**101.262951, **longitude**21.931604), Yunnan, China. A specimen was deposited at the herbarium of Nanjing Forestry University (contact person: [email protected]) under the voucher number NF2021039. The whole genome sequencing was conducted using the Illumina NovaSeq platform by Nanjing Genepioneer Biotechnology Inc. (Nanjing, China). The raw reading was filtered by software fastp version 0.20.0, and the clean reading was used to assemble the chloroplast genome by SPAdes v3.10.1 (Bankevich et al. 2012). Finally, the gene structure was annotated using CpGAVAS2(Liu et al. 2012). The 20 complete chloroplast sequences were aligned by the MAFFT v7.475 (Katoh et al. 2019). Then we generated a maximum-likelihood (ML) tree through IQ TREE (Nguyen et al. 2015) with 1000 bootstrap alignments.

The complete chloroplast genome of U. lanceifolia was determined to be 158,652bp in length and contained 2 inverted repeat (IRa and IRb) regions of 26,418bp. The repeat regions divided the genome into 2 single-copy regions, SSC and LSC with 18,697bp and 87,119bp. A total of 132 genes are encoded, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Most of genes occurred in a single copy; however, 7 protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7, ycf15 and ycf2), 7 tRNA genes (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG and trnV-GAC) and 4 distinct rRNA gene (23S, 16S, 5S and 4.5S) are duplicated. A total of 18 protein-coding genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps12, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, trnV-UAC) contained 1 intron while the other 2 genes (clpP, ycf3) had 2 intron each. The overall GC content of U. lanceifolia genome was 35.63%, and the corresponding values in LSC, SSC and IR regions were 33.14%, 28.34%, and 42.33%, respectively.

The ML analysis reveals that U. lanceifolia is a monophyletic taxa and a transitional species between the 2 groups which were combined by Ulmus americana, U. elongate and Zelkova serrate, Z. schneideriana respectively in Ulmaceae (Figure 1).

Figure 1. Phylogenetic relationships among 22 complete chloroplast genomes of Ulmaceae. Elaeagnus multiflora, Elaeagnus umbellata, Rhamnus taquetii and Rhamnus heterophylla were used as outgroups. The bootstrap supported the values shown at the branches.

Disclosure statement

No potential conflict of interest was reported by the authors.

The data availability statement

The data that support the findings of this study are openly available in the Genbank database at https://www.ncbi.nlm.nih.gov/, under accession number [MZ159247]. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA753672, SRR15412756, and SAMN20695145 respectively.

Additional information

Funding

This research work was supported by the (The Biodiversity Investigation, Observation and Assessment Program of Ministry of Ecology and Environment of China #1) under Grant [number 20191226]; (The Special Fiscal Funds for Repair and Purchase in National Public Institutions #2) under Grant [number 2010002002]; and (Jiangsu Forestry Science and Technology Innovation and Extension Program #3) under Grant [number LYKJ[2018]13].