Comparative chloroplast genome analyses of cultivated spinach and two wild progenitors shed light on the phylogenetic relationships and variation

Hongbing She,Feng Cheng,Xiaowu Wang,Helong Zhang,Zhaosheng Xu,Wei Qian,Zhiyuan Liu,Jian Wu

doi:10.1038/s41598-022-04918-4

Hongbing She, Feng Cheng + Show 6 more

Open Access

https://doi.org/10.1038/s41598-022-04918-4

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Abstract

Spinacia is a genus of important leafy vegetable crops worldwide and includes cultivated Spinacia oleracea and two wild progenitors, Spinacia turkestanica and Spinacia tetrandra. However, the chloroplast genomes of the two wild progenitors remain unpublished, limiting our knowledge of chloroplast genome evolution among these three Spinacia species. Here, we reported the complete chloroplast genomes of S. oleracea, S. turkestanica, and S. tetrandra obtained via Illumina sequencing. The three chloroplast genomes exhibited a typical quadripartite structure and were 150,739, 150,747, and 150,680 bp in size, respectively. Only three variants were identified between S. oleracea and S. turkestanica, whereas 690 variants were obtained between S. oleracea and S. tetrandra, strongly demonstrating the close relationship between S. turkestanica and S. oleracea. This was further supported by phylogenetic analysis. We reported a comprehensive variant dataset including 503 SNPs and 83 Indels using 85 Spinacia accessions containing 61 S. oleracea, 16 S. turkestanica, and eight S. tetrandra accessions. Thirteen S. oleracea accessions were derived through introgression from S. turkestanica that acts as the maternal parent. Together, these results provide a valuable resource for spinach breeding programs and improve our understanding of the phylogenetic relationships within Amaranthaceae.

Highlights

Spinacia is a genus of important leafy vegetable crops worldwide and includes cultivated Spinacia oleracea and two wild progenitors, Spinacia turkestanica and Spinacia tetrandra
0.93% (3,763,621), 1.24% (4,712,787), and 1.51% (5,078,425) of the clean reads mapped on the reference chloroplast genome sequence of S. oleracea (GenBank Accession Number: NC_002202.1) were used for the de novo assembly of S. oleracea, S. turkestanica, and S. tetrandra, respectively
We constructed phylogenetic trees of 14 Amaranthaceae species based on complete chloroplast genome sequences, large single copy (LSC) regions, inverted repeats (IRs) regions, SSC regions, and protein sequences (Fig. 2 and Table S2)

Summary

Introduction

Spinacia is a genus of important leafy vegetable crops worldwide and includes cultivated Spinacia oleracea and two wild progenitors, Spinacia turkestanica and Spinacia tetrandra. We reported the complete chloroplast genomes of S. oleracea, S. turkestanica, and S. tetrandra obtained via Illumina sequencing. Thirteen S. oleracea accessions were derived through introgression from S. turkestanica that acts as the maternal parent Together, these results provide a valuable resource for spinach breeding programs and improve our understanding of the phylogenetic relationships within Amaranthaceae. Previous investigations demonstrated that S. turkestanica was more closely related to the cultivated S. oleracea than S. tetrandra[13,16,18]. These wild species have been proven to be a valuable genetic resource for improving the quality of spinach varieties, including regarding disease and pest r esistance[19,20]. Chloroplast genome sequences in Spinacia have remained limited to date, as only the S. oleracea chloroplast genome has been reported[21]

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