Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world’s southernmost poplar (<i>Populus ilicifolia</i>)

Chen, Zeyuan; Ai, Fandi; Zhang, Junlin; Ma, Xinyu; Yang, Wenbo; Wang, Weiwei; Su, Yutao; Wang, Mingcheng; Yang, Yongzhi; Mao, Kangshan; Wang, Qingfeng; Lascoux, Martin; Liu, Jianquan; Ma, Tao

doi:10.1111/tpj.14744

Cited by 31 publications

(25 citation statements)

References 112 publications

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“…The copyright holder for this preprint this version posted January 6, 2022. ; https://doi.org/10.1101/2022.01.06.475294 doi: bioRxiv preprint 14 bottlenecks (Marsden et al 2016;Yang et al 2018;Chen et al 2020). Our results from the analyses of sunflower genomes are broadly consistent with this earlier work and further support the use of π 0 /π 4 for measuring the load of deleterious mutations.…”

Section: Discussionsupporting

confidence: 87%

High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

Huang

Ostevik

Elphinstone

et al. 2022

Preprint

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Recombination is critical both for accelerating adaptation and for the purging of deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination and, thus, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Moreover, there was little evidence of phenotypic overdominance in inversion heterozygotes, consistent with observations of minimal deleterious load. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the geographic structuring and consequent excess homozygosity of inversions in wild sunflowers. Inversions contributing to local adaptation often exhibit geographic structure; such inversions represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely averting the accumulation of deleterious mutations due to recombination suppression.

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Section: Discussionsupporting

confidence: 87%

High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

Huang

Ostevik

Elphinstone

et al. 2022

Preprint

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“…To construct the phylogenetic relationships among the allelic genes on the X/Y or Z/W contigs, we further identified their orthologous genes in P. pruinosa (Yang et al , 2017), P. ilicifolia (Chen et al , 2020) and S. suchowensis (Dai et al , 2014) genomes by combining reciprocal blast results and their syntenic relationships. The sequences were aligned using ClustalW with default parameters provided in MEGA5 (Tamura et al , 2011) and the resulting alignments were adjusted manually.…”

Section: Methodsmentioning

confidence: 99%

A general model to explain repeated turnovers of sex determination in the Salicaceae

Yang

Zhang

Wang

et al. 2020

Preprint

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0Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly 3 1 in multiple plant lineages. However, the specific mechanisms through which sex 3 2 systems evolve and their commonalities among plant species remain poorly 3 3 understood. With both XY and ZW sex systems, the family Salicaceae provides a 3 4 system to uncover the evolutionary forces driving sex chromosome turnovers. In this 3 5 study, we performed a genome-wide association study to characterize sex 3 6 determination in two Populus species, P. euphratica and P. alba. Our results reveal an 3 7XY system of sex determination on chromosome 14 of P. euphratica, and a ZW 3 8 system on chromosome 19 of P. alba. We further assembled the corresponding sex 3 9 determination regions, and found that their sex chromosome turnovers may be driven 4 0 by the repeated translocations of a Helitron-like transposon. During the translocation, 4 1 this factor may have captured partial or intact sequences that are orthologous to a 4 2 type-A cytokinin response regulator gene. Based on results from this and other 4 3recently published studies, we hypothesize that this gene may act as a master regulator 4 4 of sex determination for the entire family. We propose a general model to explain how 4 5 the XY and ZW sex systems in this family can be determined by the same RR gene. 6Our study provides new insights into the diversification of incipient sex chromosome 4 7 in flowering plants by showing how transposition and rearrangement of a single gene 4 8 can control sex in both XY and ZW systems. 4 9 5 0

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“…The genetic burden has been examined in many annual crops such as rice, maize, and rapeseed, revealing accumulation of deleterious alleles due to "domestication cost" [21][22][23][24]. However, very few studies have investigated the change in genetic burden during the adaptation and improvement of perennial trees [25]. To evaluate the individual mutation burden for J. sigillata and J. regia samples, we used J. nigra as an outgroup to polarize the allele frequency.…”

Section: Characterization Of Deleterious Mutations In Walnut Genomesmentioning

confidence: 99%

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

Zhang

et al. 2021

Genome Biol

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Background Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored. Results We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively. Conclusions The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.

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Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world’s southernmost poplar (Populus ilicifolia)

Cited by 31 publications

References 112 publications

High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

A general model to explain repeated turnovers of sex determination in the Salicaceae

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

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