Insights into the Differentiation and Adaptation Within Circaeasteraceae from Genome Sequencing and Resequencing

Overview

Journal iScience

Publisher Cell Press

Date 2023 Mar 10

PMID 36895650

Authors

Yanxia Sun

Aidi Zhang

Xu Zhang

Jacob B Landis

Huajie Zhang

XiuJun Zhang

Hang Sun

Hengchang Wang

Affiliations

Soon will be listed here.

Abstract

and are sister species that reproduce sexually and mainly asexually respectively, providing a good system for comparative genome evolution between taxa with different reproductive models. Comparative genome analyses revealed the two species have similar genome size, but encodes many more genes. The gene families specific to show significant enrichment of genes associated with defense response, while those gene families specific to are enriched in genes regulating root system development. Collinearity analyses revealed experienced two rounds of whole-genome duplication. st outlier test across 25 populations uncovered a close inter-relationship between abiotic stress and genetic variability. Genetic feature comparisons showed presents much higher genome heterozygosity, transposable element load, linkage disequilibrium degree, and π/π ratio. This study provides new insights into understanding the genetic differentiation and adaptation within ancient lineages characterized by multiple reproductive models.

References

Otto S . Selective Interference and the Evolution of Sex. J Hered. 2020; 112(1):9-18. DOI: 10.1093/jhered/esaa026. View

Holt C, Yandell M . MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011; 12:491. PMC: 3280279. DOI: 10.1186/1471-2105-12-491. View

Chen J, Glemin S, Lascoux M . Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species. Mol Biol Evol. 2017; 34(6):1417-1428. DOI: 10.1093/molbev/msx088. View

Chen C, Chen H, Zhang Y, Thomas H, Frank M, He Y . TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020; 13(8):1194-1202. DOI: 10.1016/j.molp.2020.06.009. View

Harrang E, Lapegue S, Morga B, Bierne N . A high load of non-neutral amino-acid polymorphisms explains high protein diversity despite moderate effective population size in a marine bivalve with sweepstakes reproduction. G3 (Bethesda). 2013; 3(2):333-41. PMC: 3564993. DOI: 10.1534/g3.112.005181. View

Sun Y, Deng T, Zhang A, Moore M, Landis J, Lin N . Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization. iScience. 2020; 23(5):101124. PMC: 7232092. DOI: 10.1016/j.isci.2020.101124. View

Louwers M, Splinter E, van Driel R, de Laat W, Stam M . Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C). Nat Protoc. 2009; 4(8):1216-29. DOI: 10.1038/nprot.2009.113. View

Ament-Velasquez S, Figuet E, Ballenghien M, Zattara E, Norenburg J, Fernandez-Alvarez F . Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect. Mol Ecol. 2016; 25(14):3356-69. DOI: 10.1111/mec.13717. View

Lohmueller K . The distribution of deleterious genetic variation in human populations. Curr Opin Genet Dev. 2014; 29:139-46. DOI: 10.1016/j.gde.2014.09.005. View

10.

Wright S, Finnegan D . Genome evolution: sex and the transposable element. Curr Biol. 2001; 11(8):R296-9. DOI: 10.1016/s0960-9822(01)00168-3. View

11.

Brandt A, Tran Van P, Bluhm C, Anselmetti Y, Dumas Z, Figuet E . Haplotype divergence supports long-term asexuality in the oribatid mite . Proc Natl Acad Sci U S A. 2021; 118(38). PMC: 8463897. DOI: 10.1073/pnas.2101485118. View

12.

Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A . The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449(7161):463-7. DOI: 10.1038/nature06148. View

13.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

14.

Sun Y, Zhang X, Zhang A, Landis J, Zhang H, Sun H . Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual (Circaeasteraceae, Ranunculales). Int J Mol Sci. 2023; 24(2). PMC: 9866071. DOI: 10.3390/ijms24021451. View

15.

Zhang X, Sun Y, Landis J, Zhang J, Yang L, Lin N . Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales). New Phytol. 2020; 228(1):285-301. DOI: 10.1111/nph.16669. View

16.

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B . AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006; 34(Web Server issue):W435-9. PMC: 1538822. DOI: 10.1093/nar/gkl200. View

17.

Otto S . The evolutionary enigma of sex. Am Nat. 2009; 174 Suppl 1:S1-S14. DOI: 10.1086/599084. View

18.

Strand A, Williams L, Oleksiak M, Sotka E . Can diversifying selection be distinguished from history in geographic clines? A population genomic study of killifish (Fundulus heteroclitus). PLoS One. 2012; 7(9):e45138. PMC: 3458873. DOI: 10.1371/journal.pone.0045138. View

19.

Le Rouzic A, Boutin T, Capy P . Long-term evolution of transposable elements. Proc Natl Acad Sci U S A. 2007; 104(49):19375-80. PMC: 2148297. DOI: 10.1073/pnas.0705238104. View

20.

Zhang X, Zhang S, Zhao Q, Ming R, Tang H . Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nat Plants. 2019; 5(8):833-845. DOI: 10.1038/s41477-019-0487-8. View