Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2022.06.07.495209

Genomic analyses provide new insights into the evolutionary history and reproduction of the Paleogene relictual Kingdonia (Circaeasteraceae, Ranunculales)

Sun, Y.·Zhang, X.·Zhang, A.·Landis, J. B.·Zhang, H.·Sun, H.·Xiang, J.·Wang, H.
View original source ↗Export metadata ↓

Abstract

Asexual lineages are perceived to be short-lived on evolutionary timescales due to accumulation of deleterious mutations. Hence reports for exceptional cases of putative ancient asexual species usually raise doubts about whether such species are recently derived or engage in some undocumented sexual reproduction. However, there have been few studies to solve the mystery. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having closely related congeneric sexual species, seeming to have persisted under strict asexuality for long periods of time. In this study, we use population genomic analyses to test for reproduction mode and infer the evolutionary process and mechanisms facilitating the survival of the species. Our results indicate the presence of three differentiating genetic lineages within the species and support that asexual reproduction in K. uniflora indicated by high allelic heterozygosity had occurred prior to the lineage differentiation ([~]0.5 mya). We also detected DNA recombination events in some populations, in line with occurrence of unseen and unevenly distributed sexual reproduction among populations. However the observation of high linkage disequilibrium, relatively high ratio of{pi} N/{pi}S (nonsynonymous versus synonymous nucleotide diversity), together with high allelic heterozygosity suggest the sexual reproduction is infrequent. Furthermore, we found that genes containing SNPs with elevated Fst values are significantly enriched in functions associated with seed development, suggesting differentiation in genes regulating seed development is likely to be the key reason of the uneven distribution of sexual reproduction in K. uniflora. Evidence from our study supports predominate asexual reproduction in K. uniflora, but unseen sexual reproduction must have played a key role to ensure the long-term survival of the lineage in general. Uneven distribution of sexual reproduction in the species may be a key factor underlying the observed genetic differentiation between populations. This study provides novel insights into the reproduction and evolution of Kingdonia, a relict lineage evolved in the Paleogene and known for asexual reproduction, and demonstrate the power of data from population genome sequencing in resolving long-standing evolutionary questions.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sun, Y., Zhang, X., Zhang, A., Landis, J. B., Zhang, H., Sun, H., Xiang, J., Wang, H.. 2022-06-12. Genomic analyses provide new insights into the evolutionary history and reproduction of the Paleogene relictual Kingdonia (Circaeasteraceae, Ranunculales). https://doi.org/10.1101/2022.06.07.495209

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗