Chromosome-level genome assembly of a triploid poplar Populus alba ’Berolinensis’

Related studies have provided significant insights into polyploid breeding in recent years, but limited research was focused on trees. The genomic information for the growth and response to abiotic stress in polyploidy trees is still largely unknown. Populus alba ’Berolinensis’, also named “Yinzhong poplar”, is a triploid poplar in the northeast of China. This hybrid triploid poplar is widely used as landscape ornamentals in urban areas because of its fast growth and high tolerance to abiotic stress. As an artificially synthesized male allotriploid hybrid, the three monoploid genomes of P. alba ’Berolinensis’ originated from different poplar species, so it is the desired material for studying polyploidy genomic collaboration mechanisms. Therefore, we intensively studied the allelic genomic collaboration mechanism in P. alba ’Berolinensis’. This study generated a high-quality chromosome-level genome assembly for the P. alba ’Berolinensis’ consisting of 19 allelic chromosomes. Its three monoploid chromosomes are polymorphic with an average of 42.22 variant sites per allelic gene locus. Meanwhile, we found that stress related genes such as RD22 and LEA7 exhibited structure variations. The above information has all been deployed to our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com). These polyploid genomic related resources will provide critical foundations for the molecular breeding of P. alba ’Berolinensis’ and help us uncover the allopolyploidization effects on the resistance and traits of polyploidy species deeper in the future.

Asymmetric Divergence in Transmitted SNPs of DNA Replication/Transcription and Their Impact on Gene Expression in Polyploid Brassica napus

The marked increase in plant genomic data has provided valuable resources for investigating the dynamic evolution of duplicate genes in polyploidy. Brassica napus is an ideal model species for investigating polyploid genome evolution. The present study comprehensively analyzed DNA and RNA variation of two representative B. napus inbredlines, Zhongshuang11 and Zhongyou821, and we investigated gene expression levels of An and Cn subgenomes in multiple tissues of the two lines. The distribution of transmitted single nucleotide polymorphisms (SNPs) was significantly different in two subgenomes of B. napus. Gene expression levels were significantly negatively correlated with number of variations in replication and transcription of the corresponding genes, but were positively correlated with the ratios of transmitted SNPs from DNA to RNA. We found a higher density of SNP variation in An than that in Cn during DNA replication and more SNPs were transmitted to RNA during transcription, which may contribute to An expression dominance. These activities resulted in asymmetrical gene expression in polyploid B. napus. The SNPs transmitted from DNA to RNA could be an important complement feature in comparative genomics, and they may play important roles in asymmetrical genome evolution in polyploidy.

Structural Maintenance of Chromosomes 5/6 Complex Is Necessary for Tetraploid Genome Stability in Arabidopsis thaliana

Polyploidization is a common phenomenon in the evolution of flowering plants. However, only a few genes controlling polyploid genome stability, fitness, and reproductive success are known. Here, we studied the effects of loss-of-function mutations in NSE2 and NSE4A subunits of the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex in autotetraploid Arabidopsis thaliana plants. The diploid nse2 and nse4a plants show partially reduced fertility and produce about 10% triploid offspring with two paternal and one maternal genome copies. In contrast, the autotetraploid nse2 and nse4a plants were almost sterile and produced hexaploid and aneuploid progeny with the extra genome copies or chromosomes coming from both parents. In addition, tetraploid mutants had more severe meiotic defects, possibly due to the presence of four homologous chromosomes instead of two. Overall, our study suggests that the SMC5/6 complex is an important player in the maintenance of tetraploid genome stability and that autotetraploid Arabidopsis plants have a generally higher frequency of but also higher tolerance for aneuploidy compared to diploids.

A super-pangenome framework of the genus Glycine unveils polyploid evolution and life-strategy transition

Polyploidy and life strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and genetic bases of such transitions remain elusive. We assembled plantum genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. The perennials exhibited greater genome stability than the annuals, with few centromere repeats abundant in the latter. Biased subgenome fractionation has occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with preexisting local genomic differentiation. A gene annotated to modulate vegetative to reproductive phase transition was identified to have undergone adaptive evolution underlying the perenniality-annuality transition. Our study provides mechanistic insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.

Discovering subgenomes of octoploid strawberry with repetitive sequences

Although its sequence was recently determined in a genomic tour de force,{Edger 2019} the ancestry of the cultivated octoploid strawberry Fragaria x ananassa remains controversial.{Liston 2020; Edger 2020} Polyploids that arise by hybridization generally have chromosome sets, or subgenomes, of distinct ancestry.{Stebbins 1947; Garsmeur 2014} The conventional method for partitioning a polyploid genome into its constituent subgenomes relies on establishing phylogenetic relationships between protein-coding genes of the polyploid and its extant diploid relatives,{Edger 2018-sub} but this approach has not led to a consensus for cultivated strawberry.{Liston 2020; Edger 2020} Here we resolve this controversy using a complementary strategy that focuses on the chromosomal distribution of transposable elements and depends only on the octoploid sequence itself.{Session 2016; Mitros 2020} Our method independently confirms the consensus that two of the four subgenomes derived from the diploid lineages of F. vesca and F. iinumae.{Tennessen 2014; Edger 2019} For the remaining two subgenomes, however, we find a statistically well-supported partitioning that differs from ref. {Edger 2019} and other work (reviewed in {Hardigan 2020}). We also provide evidence for a shared allohexaploid intermediate and suggest a neutral explanation for the “dominance” of the F. vesca-related subgenome.

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads

BackgroundHaplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads. By the advent of new sequencing technologies, new algorithms are needed to ensure long and accurate haplotypes. While a few linked-read haplotype assembly algorithms are available for diploid genomes, there are no algorithms yet for polyploids.ResultsThe first haplotyping algorithm designed for 10X linked reads generated from a polyploid genome is presented, built on a typical short-read haplotyping method, SDhaP. Using the input aligned reads and called variants, the haplotype-relevant information is extracted. Next, reads with the same barcodes are combined to produce molecule-specific fragments. Then, these fragments are clustered into strongly connected components which are then used as input of a haplotype assembly core in order to estimate accurate and long haplotypes.ConclusionsHap10 is a novel algorithm for haplotype assembly of polyploid genomes using linked reads. The performance of the algorithms is evaluated in a number of simulation scenarios and its applicability is demonstrated on a real dataset of sweet potato.

Flow cytometric characterisation of the complex polyploid genome of Saccharum officinarum and modern sugarcane cultivars

Sugarcane (Saccharum spp.) is a globally important crop for sugar and bioenergy production. Its highly polyploid, complex genome has hindered progress in understanding its molecular structure. Flow cytometric sorting and analysis has been used in other important crops with large genomes to dissect the genome into component chromosomes. Here we present for the first time a method to prepare suspensions of intact sugarcane chromosomes for flow cytometric analysis and sorting. Flow karyotypes were generated for two S. officinarum and three hybrid cultivars. Five main peaks were identified and each genotype had a distinct flow karyotype profile. The flow karyotypes of S. officinarum were sharper and with more discrete peaks than the hybrids, this difference is probably due to the double genome structure of the hybrids. Simple Sequence Repeat (SSR) markers were used to determine that at least one allelic copy of each of the 10 basic chromosomes could be found in each peak for every genotype, except R570, suggesting that the peaks may represent ancestral Saccharum sub genomes. The ability to flow sort Saccharum chromosomes will allow us to isolate and analyse chromosomes of interest and further examine the structure and evolution of the sugarcane genome.

The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio

Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.