Unprecedented Parallel Photosynthetic Losses in a Heterotrophic Orchid Genus

AbstractHeterotrophic plants are evolutionary experiments in genomic, morphological, and physiological change. Yet, genomic sampling gaps exist among independently derived heterotrophic lineages, leaving unanswered questions about the process of genome modification. Here, we have sequenced complete plastid genomes for all species of the leafless orchid genus Hexalectris, including multiple individuals for most, and leafy relatives Basiphyllaea and Bletia. Our objectives are to determine the number of independent losses of photosynthesis and to test hypotheses on the process of genome degradation as a result of relaxed selection. We demonstrate four to five independent losses of photosynthesis in Hexalectris based on degradation of the photosynthetic apparatus, with all but two species displaying evidence of losses, and variation in gene loss extending below the species level. Degradation in the atp complex is advanced in Hexalectris warnockii, whereas only minimal degradation (i.e., physical loss) has occurred among some “housekeeping” genes. We find genomic rearrangements, shifts in Inverted Repeat boundaries including complete loss in one accession of H. arizonica, and correlations among substitutional and genomic attributes. Our unprecedented finding of multiple, independent transitions to a fully mycoheterotrophic lifestyle in a single genus reveals that the number of such transitions among land plants is likely underestimated. This study underscores the importance of dense taxon sampling, which is highly informative for advancing models of genome evolution in heterotrophs. Mycoheterotrophs such as Hexalectris provide forward-genetic opportunities to study the consequences of radical genome evolution beyond what is possible with mutational studies in model organisms alone.

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Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat

Genome Biology and Evolution ◽

10.1093/gbe/evz187 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2789-2796 ◽

Cited By ~ 6

Author(s):

Xiao-Jian Qu ◽

Shou-Jin Fan ◽

Susann Wicke ◽

Ting-Shuang Yi

Keyword(s):

Inverted Repeat ◽

Chlorophyll Biosynthesis ◽

Housekeeping Genes ◽

Parasitic Plants ◽

Structural Features ◽

Regulation System ◽

Biosynthesis Pathway ◽

Plastid Genomes ◽

Plastome Evolution ◽

Selection For

Abstract Plastid genomes (plastomes) of parasitic plants undergo dramatic reductions as the need for photosynthesis relaxes. Here, we report the plastome of the only known heterotrophic gymnosperm Parasitaxus usta (Podocarpaceae). With 68 unique genes, of which 33 encode proteins, 31 tRNAs, and four rRNAs in a plastome of 85.3-kb length, Parasitaxus has both the smallest and the functionally least capable plastid genome of gymnosperms. Although the heterotroph retains chlorophyll, all genes for photosynthesis are physically or functionally lost, making photosynthetic energy gain impossible. The pseudogenization of the three plastome-encoded light-independent chlorophyll biosynthesis genes chlB, chlL, and chlN implies that Parasitaxus relies on either only the light-dependent chlorophyll biosynthesis pathway or another regulation system. Nesting within a group of gymnosperms known for the absence of the large inverted repeat regions (IRs), another unusual feature of the Parasitaxus plastome is the existence of a 9,256-bp long IR. Its short length and a gene composition that completely differs from those of IR-containing gymnosperms together suggest a regain of this critical, plastome structure-stabilizing feature. In sum, our findings highlight the particular path of lifestyle-associated reductive plastome evolution, where structural features might provide additional cues of a continued selection for plastome maintenance.

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Rapid Colorimetric Detection of Genome Evolution in SCRaMbLEd Synthetic Saccharomyces cerevisiae Strains

Microorganisms ◽

10.3390/microorganisms8121914 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1914

Author(s):

Elizabeth L. I. Wightman ◽

Heinrich Kroukamp ◽

Isak S. Pretorius ◽

Ian T. Paulsen ◽

Helena K. M. Nevalainen

Keyword(s):

Saccharomyces Cerevisiae ◽

Genome Evolution ◽

Colorimetric Detection ◽

Cre Recombinase ◽

Control Measures ◽

Genomic Rearrangements ◽

Industrial Yeast ◽

Poor Growth ◽

Yeast Strains ◽

Industrial Strains

Genome-scale engineering and custom synthetic genomes are reshaping the next generation of industrial yeast strains. The Cre-recombinase-mediated chromosomal rearrangement mechanism of designer synthetic Saccharomyces cerevisiae chromosomes, known as SCRaMbLE, is a powerful tool which allows rapid genome evolution upon command. This system is able to generate millions of novel genomes with potential valuable phenotypes, but the excessive loss of essential genes often results in poor growth or even the death of cells with useful phenotypes. In this study we expanded the versatility of SCRaMbLE to industrial strains, and evaluated different control measures to optimize genomic rearrangement, whilst limiting cell death. To achieve this, we have developed RED (rapid evolution detection), a simple colorimetric plate-assay procedure to rapidly quantify the degree of genomic rearrangements within a post-SCRaMbLE yeast population. RED-enabled semi-synthetic strains were mated with the haploid progeny of industrial yeast strains to produce stress-tolerant heterozygous diploid strains. Analysis of these heterozygous strains with the RED-assay, genome sequencing and custom bioinformatics scripts demonstrated a correlation between RED-assay frequencies and physical genomic rearrangements. Here we show that RED is a fast and effective method to evaluate the optimal SCRaMbLE induction times of different Cre-recombinase expression systems for the development of industrial strains.

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Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2019.05.030 ◽

2019 ◽

Vol 138 ◽

pp. 53-64 ◽

Cited By ~ 17

Author(s):

Bikash Shrestha ◽

Mao-Lun Weng ◽

Edward C. Theriot ◽

Lawrence E. Gilbert ◽

Tracey A. Ruhlman ◽

...

Keyword(s):

Genomic Rearrangements ◽

Nucleotide Substitutions ◽

Plastid Genomes

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Precise in-frame integration of exogenous DNA mediated by CRISPR/Cas9 system in zebrafish

Scientific Reports ◽

10.1038/srep08841 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 146

Author(s):

Yu Hisano ◽

Tetsushi Sakuma ◽

Shota Nakade ◽

Rie Ohga ◽

Satoshi Ota ◽

...

Keyword(s):

High Efficiency ◽

Model Organisms ◽

Cleavage Sites ◽

Simple Method ◽

Exogenous Dna ◽

Dna Integration ◽

Homologous Sequences ◽

Genome Modification ◽

Vector Sequences ◽

The Right

Abstract The CRISPR/Cas9 system provides a powerful tool for genome editing in various model organisms, including zebrafish. The establishment of targeted gene-disrupted zebrafish (knockouts) is readily achieved by CRISPR/Cas9-mediated genome modification. Recently, exogenous DNA integration into the zebrafish genome via homology-independent DNA repair was reported, but this integration contained various mutations at the junctions of genomic and integrated DNA. Thus, precise genome modification into targeted genomic loci remains to be achieved. Here, we describe efficient, precise CRISPR/Cas9-mediated integration using a donor vector harbouring short homologous sequences (10–40 bp) flanking the genomic target locus. We succeeded in integrating with high efficiency an exogenous mCherry or eGFP gene into targeted genes (tyrosinase and krtt1c19e) in frame. We found the precise in-frame integration of exogenous DNA without backbone vector sequences when Cas9 cleavage sites were introduced at both sides of the left homology arm, the eGFP sequence and the right homology arm. Furthermore, we confirmed that this precise genome modification was heritable. This simple method enables precise targeted gene knock-in in zebrafish.

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SIZE DISTRIBUTION OF GENE FAMILIES IN A GENOME

Mathematical Models and Methods in Applied Sciences ◽

10.1142/s0218202513500644 ◽

2014 ◽

Vol 24 (04) ◽

pp. 697-717 ◽

Cited By ~ 11

Author(s):

RYSZARD RUDNICKI ◽

JERZY TIURYN

Keyword(s):

Size Distribution ◽

Genome Evolution ◽

Gene Mutation ◽

Probabilistic Model ◽

Gene Loss ◽

Genomic Data ◽

Gene Families ◽

Paralogous Gene ◽

A Genome ◽

Theoretical Results

We consider a probabilistic model of genome evolution. We are interested in size distribution of gene families. The model is based on three fundamental evolutionary events: gene loss, duplication and accumulated change. We assume that the probability of gene loss and duplication is constant and the probability of gene mutation mi depends on the size i of a family. We prove that size distribution of paralogous gene families in a genome converges to the equilibrium as time goes to infinity. Moreover, we show how this equilibrium depends on the sequence (mi). Theoretical results are compared with the available genomic data.

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Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”

Frontiers in Microbiology ◽

10.3389/fmicb.2016.00797 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 19

Author(s):

Sophie R. Ullrich ◽

Carolina González ◽

Anja Poehlein ◽

Judith S. Tischler ◽

Rolf Daniel ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Evolution ◽

Gene Loss

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Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae

PeerJ ◽

10.7717/peerj.7830 ◽

2019 ◽

Vol 7 ◽

pp. e7830 ◽

Cited By ~ 1

Author(s):

Eugeny V. Gruzdev ◽

Vitaly V. Kadnikov ◽

Alexey V. Beletsky ◽

Andrey V. Mardanov ◽

Nikolai V. Ravin

Keyword(s):

Genome Evolution ◽

Plastid Genome ◽

Housekeeping Genes ◽

Parasitic Plants ◽

Rrna Genes ◽

Phylogenetic Position ◽

Trna Genes ◽

Protein Coding ◽

The Family ◽

Plastid Genome Evolution

Background Parasitic plants have the ability to obtain nutrients from their hosts and are less dependent on their own photosynthesis or completely lose this capacity. The reduction in plastid genome size and gene content in parasitic plants predominantly results from loss of photosynthetic genes. Plants from the family Orobanchaceae are used as models for studying plastid genome evolution in the transition from an autotrophic to parasitic lifestyle. Diphelypaea is a poorly studied genus of the Orobanchaceae, comprising two species of non-photosynthetic root holoparasites. In this study, we sequenced the plastid genome of Diphelypaea coccinea and compared it with other Orobanchaceae, to elucidate patterns of plastid genome evolution. In addition, we used plastid genome data to define the phylogenetic position of Diphelypaea spp. Methods The complete nucleotide sequence of the plastid genome of D. coccinea was obtained from total plant DNA, using pyrosequencing technology. Results The D. coccinea plastome is only 66,616 bp in length, and is highly rearranged; however, it retains a quadripartite structure. It contains only four rRNA genes, 25 tRNA genes and 25 protein-coding genes, being one of the most highly reduced plastomes among the parasitic Orobanchaceae. All genes related to photosynthesis, including the ATP synthase genes, had been lost, whereas most housekeeping genes remain intact. The plastome contains two divergent, but probably intact clpP genes. Intron loss had occurred in some protein-coding and tRNA genes. Phylogenetic analysis yielded a fully resolved tree for the Orobanchaceae, with Diphelypaea being a sister group to Orobanche sect. Orobanche.

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Tight association of genome rearrangements with gene expression in conifer plastomes

BMC Plant Biology ◽

10.1186/s12870-020-02809-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Chung-Shien Wu ◽

Edi Sudianto ◽

Shu-Miaw Chaw

Keyword(s):

Gene Expression ◽

Gene Order ◽

Genomic Rearrangements ◽

First Line ◽

Conifer Species ◽

Antisense Transcripts ◽

Plastid Genomes ◽

Rnaseq Data ◽

Tight Association ◽

Conserved Gene

Abstract Background Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. Results We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression. Conclusions Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

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