The chloroplast genome of Elytrigia repens (L.) Nevski (Poaceae: Triticeae), a widespread perennial grass from Qinghai-Tibetan Plateau, China

Abstract

Elytrigia repens (L.) Nevski, belonging to Triticeae of Poaceae, is a wild-growing perennial grass, widely distributed in Qinghai-Tibetan Plateau of China. In this study, the complete chloroplast genome of E. repens was sequenced and analyzed. The complete chloroplast genome size is 134,749 bp with 38.3% GC content. It includes 136 genes, including 89 protein-coding genes, 39 tRNAs genes, and 8 rRNAs genes. Based on chloroplast genome sequences, further phylogenetic analyses between E. repens and other Triticeae species revealed that E. repens, Connorochloa tenuis and three Elymus species formed a distinct clade, showing closer relationships.

Elytrigia repens (L.) Nevski belongs to Triticeae of Poaceae. In Qinghai-Tibetan Plateau of China, E. repens is a widespread wild-growing perennial grass. Previous cultivation and physiological studies of E. repens demonstrated its tolerance to various abiotic stresses, and adaptability for soil and water conservation and rangeland improvement (Mahelka 2006; Gift et al. 2008; Pätsch et al. 2019). Additionally, E. repens was proved to be suitable for phytoremediation of soils contaminated with the metal ion. Its roots could accumulate significant amounts of zinc (Laidinen et al. 2018). Furthermore, the intergeneric hybrids between Triticum aestivum and E. repens could survive and produce seeds (Franke et al. 2008), which would generate well genetic resources for wheat breeding.

E. repens is an allopolyploid grass. The nuclear genome of E. repens is assumed to inherit from Pseudoroegneria (St), Hordeum (H), and distant genetic sources (Pastova et al. 2019). Whereas, few nuclear and even organelle genomic sequences of E. repens are currently available. Compared to its complicated nuclear genome (Mahelka et al. 2005; Meng et al. 2012), the sequencing of E. repens chloroplast genome is simple, which could provide sequence resources for comparative genomics and evolutionary studies between E. repens and other Triticeae species.

The samples of E. repens were collected in Xining at an altitude of 2,324 m (36°73′79″ N, 101°74′86″ E), Qinghai Province, China. The voucher specimen (Accession number: FFK2012631141) was deposited in the National duplicate genebank for crops in Xining (Contact person: Dr. Liling Jiang). Total genomic DNA was extracted from fresh leaves using the improved CTAB method (Yu et al. 2019). According to the manufacturer’s protocol, 350 bp paired-end DNA library was constructed, and subsequently sequenced in Illumina NovaSeq PE150 Platform (Modi et al. 2021). Through filtering of adapter and low-quality bases, 8.8 Gb clean raw reads were generated, with 93% bases’ quality score meeting Q30. Using chloroplast genome sequences of Triticum aestivum (NC_002762) (Ogihara et al. 2002) and Hordeum vulgare (NC_008590) as references, our high-quality clean reads were assembled into circular scaffolds through SOAPdenovo V2.04 (Luo et al. 2012). The detailed parameters for genome assembling are as follows: avg_ins = 150, reverse_seq = 0, asm_flags = 3, pair_num_cutoff = 3, and map_len = 32.

The E. repens chloroplast genome is 134,749 bp in length with the overall GC content of 38.3%, which includes a large single-copy region (LSC) of 80,426 bp, a small single-copy region (SSC) of 12,769 bp, and independently inverted repeat region a and b (IRa and IRb) of 20,777 bp. In the chloroplast genome, a total of 136 genes were annotated through PGA software (Qu et al. 2019), including 89 protein-coding genes, 39 tRNAs genes, and 8 rRNAs genes. Twenty-two genes have two copies, including thirteen protein-coding genes and nine tRNAs genes. Additionally, nine protein-coding genes and six tRNAs genes contain an intron, respectively. Ycf3 even comprises two introns. Interestingly, the genomic sequences revealed RNA editing occurs in the start codon of rpl2. The chloroplast genome sequence and detailed genome annotation of E. repens had been submitted to GenBank under accession number MZ169384.

Furthermore, using Oryza sativa (NC_008155) as the outgroup, a Maximum-Likelihood phylogenetic tree was constructed (Figure 1), based on the chloroplast genome sequences of E. repens and other 15 Triticeae species by IQ-TREE 1.6.12 (Nguyen et al. 2015). The best suitable model for tree construction was calculated by ModelFinder (Kalyaanamoorthy et al. 2017). Phylogenetic analyses revealed that the 16 Triticeae species clustered into three main groups with 100% bootstrap value support. Furthermore, E. repens, Connorochloa tenuis and three Elymus species, including Elymus kamoji, Elymus trachycaulus and Elymus dahuricus, formed a distinct clade, representing closer relationships (Figure 1). In this study, the chloroplast genome of E. repens is completely sequenced and annotated, facilitating the elucidation of phylogenetic relationships between E. repens and its closely related species in Triticeae at the chloroplast-genome level.

Figure 1.

The phylogenetic tree of sixteen Triticeae species. The phylogenetic tree was constructed with 1,000 bootstrap replicates. Bootstrap values are given besides the nodes. GenBank accession number is labeled besides each species in the tree.

Funding Statement

This study was supported by grants from National Natural Science Foundation of China [31760383], Environmental Protection on Agricultural Resources from Ministry of Agricultural and Rural Affairs of China [125A0605], and West Light Talent Program of the Chinese Academy of Sciences.

Disclosure statement

All the authors declared no potential conflicts of interest.

Data availability statement

The chloroplast genome sequence of E. repens sequenced in this study is deposited in NCBI GenBank database, accession number MZ169384. The associated accession number in SRA, BioSample and BioProject database is SRR14535700, SAMN19184023 and PRJNA729858, respectively (www.ncbi.nlm.nih.gov/bioproject/PRJNA729858).