The complete chloroplast genome sequence of Pennisetum flaccidum (Poaceae)

Abstract

Pennisetum flaccidum Grisebach is a typical high-quality forage and adrought-tolerant grass. In this study, we firstly reported the complete chloroplast (cp) genome of P. flaccidum, which was 138,336 bp in length, including a pair of inverted repeats (IR: 22,293 bp), a large single copy (LSC: 81,329 bp), and a small single copy (SSC: 12,421 bp) region. A total of 131 genes were annotated, containing seven rRNA genes, 38 tRNA genes, and 86 protein-coding genes. The GC content of the cp genome was 38.63%. The maximum-likelihood (ML) phylogenetic tree indicated that P. flaccidum was closely related to P. cetaceum in Poaceae.

Keywords:

• Poaceae
• Pennisetum flaccidum
• chloroplast genome
• phylogenetic tree

Pennisetum flaccidum Grisebach is a plant species of the genus of Pennisetum in the family of Poaceae and widely distributes in northern China with high quality and excellent palatability (Joshi and Ludri 1967; Yu et al. 2009). P. flaccidum has strong drought tolerance and can reproduce and grow multiply on sandy land or dunes. It is not only one of the herbaceous species with rich nutrient but also a pioneer species for sand fixation (Editorial Board of Forage flora of China 1987). The analysis of complete chloroplast (cp) genomes has a broad prospect in understanding plant genetic diversity, plant distribution, and phylogenetic evolution (Yang et al. 2019). In this study, we employed Illumina Hiseq to determine and assemble the complete cp genome of P. flaccidum, to provide novelty and information on the understanding of its phylogenetic status.

The fresh leaves of P. flaccidum were collected from Southwestern Mu Us Sandy Land, China (106°24′E, 37°57′N) and dried with silica gel. A specimen (R02) was deposited in the Herbarium of School of Agriculture, Ningxia University (https://nxy.nxu.edu.cn/, Wangsuo Liu [email protected]) under the voucher number 6401812020-LW001. The modified CTAB method was used to extract the whole-genomic DNA (Stefanova et al. 2013). The Illumina Hiseq PE150 sequencing was conducted by Biomarker Technologies Co., Ltd. (Qingdao, China). After removal and filtration of low-quality reads, in total, 5 Gb clean reads (the average Q30 was 92.14%) were obtained. The qualified reads were assembled using SPAdes version 3.11.0 software

Table

Q5 (Bankevich et al. 2012). The genome annotation was performed by GeSeq (Tillich et al. 2017). Draw annotation map was used by OGDRAW (Greiner et al. 2019) in web service (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html). The complete cp genome

Table

Q3 sequence and annotation of P. flaccidum were submitted to GenBank (accession No. MW442087).

The borders of IR, LSC, and SSC regions were identified using an online tool, IRscope (Amiryousefi et al. 2018). The cp genome of P. flaccidum was 138,336 bp in length and with four typical regions, containing two inverted repeats (IRa and IRb: 22,293 bp), a large single copy (LSC: 81,329 bp), and a small single copy (SSC: 12,421 bp) region. A total of 131 genes were annotated, including seven rRNA genes, 38 tRNA genes, and 86 protein-coding genes. The GC content of the cp genome was 38.63%. In these genes, there were 93 unique genes and 19 were duplicated in the IR regions. The 19 duplicates including eight protein-coding genes (rps19, rpl2, rpl23, ycf2, ndhB, rps7, rps12, and rps15), eight tRNA genes (trnH-GUG, trnl-CAU, trnL-CAA, trnV-GAC, trnl-GAU, trnA-UGC, trnR-ACG, and trnN-GUU), and three rRNA genes (rrn4.5, rrn5, and rrn16).

In order to clarify the phylogenetic location of P. flaccidum, the cp genome sequence of 12 Poaceae was downloaded from NCBI and added three whole cp genome sequences of Pennisetum (SY001901, SY001902, and SY001903) at https://lcgdb.wordpress.com/. All cp genomes were aligned by MAFFT version 7.037 (Katoh and Standley 2013). Maximum-likelihood (ML) tree was constructed by PhyML-3.1(GTR) (Guindon et al. 2010) with 1000 bootstrap replications, and the diagram was processed by FigTree version 1.4.4 as shown in the Figure 1. The result showed that P. flaccidum closely clustered with P. cetaceum. Our study provides a reference for the phylogenetic and taxonomic status of Pennisetum in Poaceae.

Figure 1. Maximum-likelihood phylogenetic tree based on 14 complete cp genomes. The plant species targeted by a hollow triangle is Pennisetum flaccidum in our study.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings of this study are openly available in NCBI database at https://www.ncbi.nlm.nih.gov/, reference number MW442087. The associated BioProject, Biosample, and SRA numbers are PRJNA689090, SAMN17199738, and SRS7976986, respectively.

Additional information

Funding

Financial support for this study was provided by the National Key Research and Development Project of China [2016YFC0500505], National Natural Science Foundation of China [42001095], Ningxia Key Research and Development Project[2019BEB04011], Project for High-Level Overseas Talents returning to China [[2019] 160] and Ningxia Natural Science Foundation [2020AAC03273], and Project for High Level Overseas Talents returning to China.