The complete chloroplast genome of Secale sylvestre (Poaceae: Triticeae)

Secale sylvestre is a wild species of rye, morphologically distinct from domestic species. To draw comparisons between species based on molecular features, it is important to have high-quality sequences, especially in the case of organellar genomes. For such reason, the complete chloroplast genome of Secale sylvestre Host introd. no. 6047 will provide useful data for ecological, agricultural, and phylogenetic purposes. Here we present the complete, annotated chloroplast genome sequence of Secale sylvestre Host introd. no. 6047. The genome is 137116 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number (MW557517).


Introduction
Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae). It includes annual, perennial, selfpollinating, and open-pollinating, cultivated, weedy, and wild species of various morphologies. The genus Secale includes for now four species whose phylogenetic relationships have not been fully determined (GRIN, http:// www. arsgr in. gov). This causes a significantly reduction of progress in rye breeding that can be enriched with functional traits derived from wild rye species. In the genus, the wild species Secale sylvestre Host (1809) is singularized by several genetic peculiarities (Bennett and Smith 1976;Singh and Röbbelen 1977;Shang et al. 2006;Zhou et al. 2010;Skuza et al. 2019a).
Among the 8 chloroplast genome of Secale spp. available on GenBank, none is complete strictly speaking, with the second copy of the inverted repeat (IR) missing all the time, and with the exception of Secale cereale KC912691, they all display several ambiguous and non-attributed bases, rending it difficult to perform accurate SNPs comparisons. Thus, we presume that analysis of the complete chloroplast genome sequences of Secale spp., starting with S. sylvestre, will be useful and cost-effective for evolutionary and phylogenetic studies, as was suggested by our previous studies (Doyle and Doyle 1990;Skuza et al. 2019b).

Material and methods
Seeds of Secale sylvestre Host introd. no. 6047 were obtained from the Botanical Garden of the Polish Academy of Sciences in Warsaw. Total DNA was extracted from young sprouts following Doyle and Doyle (Bankevich et al. 2012). Sequencing took place in BGI Shenzhen's facilities on a. An amount of ca. 40 million clean 100 bp paired-end reads was obtained and assembled using SPAdes 3.14.0 (Gordon and Green 2013) with a k-mer of 85. The contigs corresponding to the chloroplast genome were joined together using Consed (Tillich et al. 2017). Annotations were performed with the help of GeSeq (Katoh and Standley 2013) and manually curated.

Results and discussion
The genome is 137116 bp long (Table 1). The large single copy (LSC) is 81132 bp long, the short single copy (SSC) is 12820 bp long, and the IR is 21582 bp long. No ambiguous bases were found in the genome. As stated above, SNP calling type of analysis was rendered difficult by the presence among 7 out of 8 of the other available genomes of numerous non-attributed bases. Instead, analyses focused on the presence of indels, which were found to be common and often phylogenetically informative (e.g., Chen et al. 2016). To do so, chloroplast genomes were partitioned by sub-units, aligned using MAFFT 7 (Kumar et al. 2018), and then visualized using MEGAX (Mo et al. 2020).

Limitations
The protocol itself showed no limitation, as it allowed to obtain complete and non-ambiguous genome sequence. However, far more clean genome sequences are needed in order to describe the most reliable molecular markers for species identification and phylogeny, especially for what concerns SNPs.
Author contribution LS initiated the project, and LS, RG, and AS conducted experiments and drafted the manuscript. Bioinformatic analyses were performed by RG.
Funding RG thanks the Horizon 2020 Research and Innovation Programme GHaNA (The Genus Haslea, New marine resources for blue biotechnology and Aquaculture) under Grant Agreement No 734708/ GHANA/ H2020-MSCA-RISE-2016, and the 2017-2021 research funds granted for the implementation of a co-financed international research project from Polish Ministry of Science and Higher Education.

Data availability
The genome has been deposited on GenBank with the accession number MW557517. It is also available on Zenodo with the following link: http:// doi. org/ 10. 5281/ zenodo. 45372 81.

Declarations
Ethics approval Not applicable.

Competing interests The authors declare no competing interests.
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/.