European maize genomes highlight intraspecies variation in repeat and gene content

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

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The Pan‐genome of the Cultivated Soybean (PanSoy) Reveals an Extraordinarily Conserved Gene Content

Plant Biotechnology Journal ◽

10.1111/pbi.13600 ◽

2021 ◽

Author(s):

Davoud Torkamaneh ◽

Marc‐André Lemay ◽

François Belzile

Keyword(s):

Gene Content ◽

Pan Genome ◽

Conserved Gene ◽

Cultivated Soybean

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Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

Scientific Reports ◽

10.1038/s41598-021-88160-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jiawei Zhou ◽

Shuo Zhang ◽

Jie Wang ◽

Hongmei Shen ◽

Bin Ai ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Population Level ◽

Gene Content ◽

Sequencing Data ◽

Cellular Functions ◽

Chloroplast Evolution ◽

Chloroplast Genomes ◽

Genome Features ◽

Genome Annotations ◽

Genome Analyses

AbstractThe chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.

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The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

BMC Plant Biology ◽

10.1186/s12870-021-03053-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yan-Yan Guo ◽

Jia-Xing Yang ◽

Ming-Zhu Bai ◽

Guo-Qiang Zhang ◽

Zhong-Jian Liu

Keyword(s):

Gene Order ◽

Inverted Repeat ◽

Single Copy ◽

Gene Content ◽

Comparative Genomic ◽

Substitution Rates ◽

Plastome Evolution ◽

Chloroplast Genomes ◽

Ideal System ◽

Small Single Copy

Abstract Background Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Results Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. Conclusions We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

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The cp genome characterization of Adenium obesum: gene content, repeat organization and phylogeny

Saudi Journal of Biological Sciences ◽

10.1016/j.sjbs.2021.03.048 ◽

2021 ◽

Author(s):

Khalid Mashay Alanazi ◽

Mohammad Ajmal Ali ◽

Soo-Yong Kim ◽

M. Oliur Rahman ◽

Mohammad Abul Farah ◽

...

Keyword(s):

Gene Content ◽

Genome Characterization ◽

Cp Genome

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Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

Scientific Reports ◽

10.1038/s41598-021-89091-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Guilherme B. Dias ◽

Musaad A. Altammami ◽

Hamadttu A. F. El-Shafie ◽

Fahad M. Alhoshani ◽

Mohamed B. Al-Fageeh ◽

...

Keyword(s):

Genome Assembly ◽

Control Strategies ◽

Insect Pest ◽

Single Copy ◽

Gene Content ◽

Rhynchophorus Ferrugineus ◽

Red Palm Weevil ◽

Transcriptomic Data ◽

Palm Trees ◽

Palm Weevil

AbstractThe red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage ($$\sim$$ ∼ 62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.

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Identification of lactobacilli by pheS and rpoA gene sequence analyses

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64711-0 ◽

2007 ◽

Vol 57 (12) ◽

pp. 2777-2789 ◽

Cited By ~ 201

Author(s):

Sabri M. Naser ◽

Peter Dawyndt ◽

Bart Hoste ◽

Dirk Gevers ◽

Katrien Vandemeulebroecke ◽

...

Keyword(s):

Gene Sequence ◽

Alpha Subunit ◽

Identification System ◽

Rrna Gene ◽

Gene Sequences ◽

Intraspecies Variation ◽

Reliable Identification ◽

Genomic Markers ◽

Identification Of Species ◽

Rpoa Gene

The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of members of the genus Lactobacillus. Two hundred and one strains representing the 98 species and 17 subspecies were examined. The pheS gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The rpoA gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all species of the genus Lactobacillus. The pheS and rpoA gene sequences provide a powerful tool for the detection of potential novel Lactobacillus species and synonymous taxa. In conclusion, the pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.

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