Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives

Abstract

Background As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. Results We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. Conclusion In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa.

The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia

“…Genetic analysis is essential for cultivar breeding and utilization, and plastomes can significantly contribute to these efforts, particularly in the fields of pedigree analysis [ 17 , 61 ], evaluation of genetic diversity [ 53 ], and exploration of domestication [ 18 ]. To compare the genetic structure of cultivated and natural Paeonia accessions, we manually clustered 63 accessions into five groups.…”

“…Thus, a more comprehensive plastome-based phylogenetic study is needed to provide new insight into the evolutionary history of Paeonia . Furthermore, some research indicated that domestication can lead to variation in plastomes between wild and cultivated materials, including the positive selection of genes and single nucleotide variants [ 17 , 18 ]. However, comparative studies related to domestication are still lacking in Paeonia .…”

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

“…To add a (pan-)genomic layer, we generated low-pass whole genome shotgun data for all accessions as well as long reads for selected beet genomes. After assessing the phylogenetic placements of these accessions (Sielemann et al, 2022(Sielemann et al, , 2023a, we estimated their repetitive DNA content and finely classified their repetitive DNA sequences in the respective TE and TR hierarchies. This not only allows following repetitive DNA evolution comprehensively across the beet genera, determining repeat gains, losses and replacements, but also linking it back to chromosomal location and karyotypic stability.…”

“…We target all major species across all sections, including higher polyploids. Building onto the plastome-based phylogenetics framework (Sielemann et al, 2022(Sielemann et al, , 2023a, our 17-beet-speciespanel represents a well-characterized sugar beet and CWR panel with regard to tracing genome evolution, chromosome stability, pangenomics, and taxonomy.…”

Current Approaches to Genome Sequencing in Sugar Beet (Beta Vulgaris) and Its Wild Relatives

“…Ayrıca, daha yüksek hizalama uzunluklarının kullanımı ve amino asitler yerine nükleotidlerin kullanımı, iyi desteklenen filogenilerin oluşturulması için tercih edilmektedir. Bu nedenle, kültüre alınmış ve yabani pancarlar arasındaki ilişkileri çözmek için tüm plastom temelli yaklaşımının en güvenilir olduğu sonucuna varılmıştır (Sielemann, 2022).…”