Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)

Cai, Liming; Arnold, Brian J.; Xi, Zhenxiang; Khost, Danielle E.; Patel, Niki; Hartmann, Claire B.; Sugumaran, Manickam; Sasirat, Sawitree; Nikolov, Lachezar A.; Mathews, Sarah; Sackton, Timothy B.; Davis, Charles C.

doi:10.1016/j.cub.2020.12.045

Cited by 72 publications

(126 citation statements)

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“…However, genomic data regarding non-photosynthetic plants are still insufficient to state this with confidence. A study of the nuclear genome of a non-photosynthetic plant Sapria himalayana indicates expansion of transposons in this species, thus supporting our hypothesis (Cai et al, 2021). Of the five species studied in our work, there are two nuclear genome size estimates that included a genome of greater than 30 Gb for Rhopalocnemis phalloides (Schelkunov, Nuraliev & Logacheva, 2019) and a 221 Mb genome for Santalum album (Mahesh et al, 2018).…”

Section: Nuclear Gene Content As Inferred From the Transcriptome Assembliessupporting

confidence: 85%

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

Schelkunov

Nuraliev

Logacheva

2021

PeerJ

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The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.

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Section: Nuclear Gene Content As Inferred From the Transcriptome Assembliessupporting

confidence: 85%

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

Schelkunov

Nuraliev

Logacheva

2021

PeerJ

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“…Here, the large number of intron-less GhEXO genes suggests that at the early expansion stage, genes containing more introns could be lost during the passage of time ( Roy and Penny, 2007 ; Liu et al, 2021 ), and these genes then formed advanced families with reduced numbers of introns ( Roy and Gilbert, 2005 , 2006 ; Tan et al, 2018 ). Furthermore, insertion/deletion events result in structural differences that permit the estimation of evolutionary timing ( Lecharny et al, 2003 ; Liu et al, 2021 ), and the genes with fewer or no introns evolve more rapidly because introns experience weak selection pressure even though exons/introns focus more on functional roles, whether the sequence is conserved ( Frugoli et al, 1998 ; Cai et al, 2021 ). The exon/intron and motif distribution patterns in most gene families are conserved, and many gene families with fewer or no introns have been identified ( Li et al, 2019 ; Qanmber et al, 2019b ; Quan et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Identification and Analysis of GhEXO Gene Family Indicated That GhEXO7_At Promotes Plant Growth and Development Through Brassinosteroid Signaling in Cotton (Gossypium hirsutum L.)

Liu

Chen

et al. 2021

Front. Plant Sci.

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Brassinosteroids (BRs), an efficient plant endogenous hormone, significantly promotes plant nutrient growth adapting to biological and abiotic adversities. BRs mainly promote plant cell elongation by regulating gene expression patterns. EXORDIUM (EXO) genes have been characterized as the indicators of BR response genes. Cotton, an ancient crop, is of great economic value and its fibers can be made into all kinds of fabrics. However, EXO gene family genes have not been full identified in cotton. 175 EXO genes were identified in nine plant species, of which 39 GhEXO genes in Gossypium hirsutum in our study. A phylogenetic analysis grouped all of the proteins encoded by the EXO genes into five major clades. Sequence identification of conserved amino acid residues among monocotyledonous and dicotyledonous species showed a high level of conservation across the N and C terminal regions. Only 25% the GhEXO genes contain introns besides conserved gene structure and protein motifs distribution. The 39 GhEXO genes were unevenly distributed on the 18 At and Dt sub-genome chromosomes. Most of the GhEXO genes were derived from gene duplication events, while only three genes showed evidence of tandem duplication. Homologous locus relationships showed that 15 GhEXO genes are located on collinear blocks and that all orthologous/paralogous gene pairs had Ka > Ks values, indicating purifying selection pressure. The GhEXO genes showed ubiquitous expression in all eight tested cotton tissues and following exposure to three phytohormones, IAA, GA, and BL. Furthermore, GhEXO7_At was mainly expressed in response to BL treatment, and was predominantly expressed in the fibers. GhEXO7_At was found to be a plasma membrane protein, and its ectopic expression in Arabidopsis mediated BR-regulated plant growth and development with altered expression of DWF4, CPD, KCS1, and EXP5. Additionally, the functions of GhEXO7_At were confirmed by virus-induced gene silencing (VIGS) in cotton. This study will provide important genetic resources for future cotton breeding programs.

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“…A parasite plant would also be a possible vector. Saparia , an endoparasitic flowering plant, showed host-to-parasite horizontal gene transfers with Vitaceae [ 43 ], which satisfies the second condition. To understand the mechanisms of HTs to multiple recipients, further studies on interkingdom or host-parasite HT with these organisms are needed.…”

Section: Discussionmentioning

confidence: 99%

Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis

Park

Sarkhosh

Tsolova

et al. 2021

IJMS

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While horizontally transferred transposable elements (TEs) have been reported in several groups of plants, their importance for genome evolution remains poorly understood. To understand how horizontally transferred TEs contribute to plant genome evolution, we investigated the composition and activity of horizontally transferred TEs in the genomes of four Vitis species. A total of 35 horizontal transfer (HT) events were identified between the four Vitis species and 21 other plant species belonging to 14 different families. We determined the donor and recipient species for 28 of these HTs, with the Vitis species being recipients of 15 of them. As a result of HTs, 8–10 LTR retrotransposon clusters were newly formed in the genomes of the four Vitis species. The activities of the horizontally acquired LTR retrotransposons differed among Vitis species, showing that the consequences of HTs vary during the diversification of the recipient lineage. Our study provides the first evidence that the HT of TEs contributes to the diversification of plant genomes by generating additional TE subfamilies and causing their differential proliferation in host genomes.

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Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)

Cited by 72 publications

References 104 publications

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

Identification and Analysis of GhEXO Gene Family Indicated That GhEXO7_At Promotes Plant Growth and Development Through Brassinosteroid Signaling in Cotton (Gossypium hirsutum L.)

Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis

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