Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia

Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity

Background

The mitochondrion is an important cellular component in plants and that functions in producing vital energy for the cell. However, the evolution and structure of mitochondrial genomes (mitogenomes) remain unclear in the Rosaceae family. In this study, we assembled 34 Rosaceae mitogenomes and characterized genome variation, rearrangement rate, and selection signal variation within these mitogenomes.

Results

Comparative analysis of six genera from the Amygdaloideae and five from the Rosoideae subfamilies of Rosaceae revealed that three protein-coding genes were absent from the mitogenomes of five Rosoideae genera. Positive correlations between genome size and repeat content were identified in 38 Rosaceae mitogenomes. Twenty repeats with high recombination frequency (> 50%) provided evidence for predominant substoichiometric conformation of the mitogenomes. Variations in rearrangement rates were identified between eleven genera, and within the Pyrus, Malus, Prunus, and Fragaria genera. Based on population data, phylogenetic inferences from Pyrus mitogenomes supported two distinct maternal lineages of Asian cultivated pears. A Pyrus-specific deletion (DEL-D) in selective sweeps was identified based on the assembled genomes and population data. After the DEL-D sequence fragments originally arose, they may have experienced a subsequent doubling event via homologous recombination and sequence transfer in the Amygdaloideae; afterwards, this variant sequence may have significantly expanded to cultivated groups, thereby improving adaptation during the domestication process.

Conclusions

This study characterizes the variations in gene content, genome size, rearrangement rate, and the impact of domestication in Rosaceae mitogenomes and provides insights into their structural variation patterns and phylogenetic relationships.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01383-3.

High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy

Dormancy-associated MADS-box (DAM) genes serve as crucial regulators of the endodormancy cycle in rosaceous plants. Although pear DAM genes have been identified previously, the lack of a high-quality reference genome and techniques to study gene function have prevented accurate genome-wide analysis and functional verification of such genes. Additionally, the contribution of other genes to the regulation of endodormancy release remains poorly understood. In this study, a high-quality genome assembly for 'Cuiguan' pear (Pyrus pyrifolia), which is a leading cultivar with a low chilling requirement cultivated in China, was constructed using PacBio and Hi-C technologies. Using this genome sequence, we revealed that pear DAM genes were tandemly clustered on Chr8 and Chr15 and were differentially expressed in the buds between 'Cuiguan' and the high-chilling-requirement cultivar 'Suli' during the dormancy cycle. Using a virus-induced gene silencing system, we determined the repressive effects of DAM genes on bud break. Several novel genes potentially involved in the regulation of endodormancy release were identified by RNA sequencing and H3K4me3 chromatin immunoprecipitation sequencing analyses of 'Suli' buds during artificial chilling using the new reference genome. Our findings enrich the knowledge of the regulatory mechanism underlying endodormancy release and chilling requirements and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.

Genetic Diversity and Population Genetic Structure of Ancient Platycladus orientalis L. (Cupressaceae) in the Middle Reaches of the Yellow River by Chloroplast Microsatellite Markers

Ancient trees are famous for their life spans of hundreds or even thousands of years. These trees are rare, a testament to history and are important for scientific research. Platycladus orientalis, with the longest life span and a beautiful trunk, has become the most widely planted tree species and is believed to be sacred in China. Extensive declines in habitat area and quality pose the greatest threats to the loss of genetic diversity of ancient P. orientalis trees in the middle reaches of the Yellow River. Strengthening the protection of P. orientalis genetic resources is of great significance for the long-term development of reasonable conservation and breeding strategies. To better understand the genetic diversity and population structure of P. orientalis, we successfully analyzed four polymorphic chloroplast simple sequence repeat (cpSSR) loci and applied them to diversity and population structure analyses of 202 individuals from 13 populations in the middle reaches of the Yellow River. Based on the cpSSR data, 16 alleles were detected across 202 individuals, and a moderate level of genetic diversity was inferred from the genetic diversity parameters (H = 0.367 and AR = 1.964). The mean pairwise genetic differentiation coefficient (Fst) between populations was 0.153, indicating relatively high genetic population differentiations. Analysis of molecular variance (AMOVA) showed that only 8% of the variation occurred among populations. Structure analysis divided the 13 P. orientalis populations into two groups with no significant geographic population structure, which was consistent with the unweighted pair group method with arithmetic mean (UPGMA) and Mantel test results. These results may indicate that transplanting and cultivation by ancient human activities are the main factors responsible for the revealed pattern of genetic differentiation of ancient P. orientalis populations. Our research is of great significance for the future establishment of protection schemes and scientific breeding of P. orientalis.

Complete chloroplast genome of Myracrodruon urundeuva and its phylogenetics relationships in Anacardiaceae family

Continuous exploratory use of tree species is threatening the existence of several plants in South America. One of these threatened species is Myracroduron urundeuva, highly exploited due to the high quality and durability of its wood. The chloroplast (cp) has been used for several evolutionary studies as well traceability of timber origin, based on its gene sequences and simple sequence repeats (SSR) variability. Cp genome organization is usually consisting of a large single copy and a small single copy region separated by two inverted repeats regions. We sequenced the complete cp genome from M. urundeuva based on Illumina next-generation sequencing. Our results show that the cp genome is 159,883 bp in size. The 36 SSR identified ranging from mono- to hexanucleotides. Positive selection analysis revealed nine genes related to photosystem, protein synthesis, and DNA replication, and protease are under positive selection. Genome comparison a other Anacardiaceae chloroplast genomes showed great variability in the family. The phylogenetic analysis using complete chloroplast genome sequences of other Anacardiaceae family members showed a close relationship with two other economically important genera, Pistacia and Rhus. These results will help future investigations of timber monitoring and population and evolutionary studies.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00989-1.

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.