scholarly journals Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection

2021 ◽  
Vol 7 (10) ◽  
pp. 864
Author(s):  
Lajos Acs-Szabo ◽  
Laszlo Attila Papp ◽  
Matthias Sipiczki ◽  
Ida Miklos
Keyword(s):  
Natural Selection ◽  
Gene Order ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Last Common Ancestor ◽  
Cleavage Sites ◽  
Evolutionary Patterns ◽  
Ancestral Gene ◽  
Gene Structures ◽  
Stable Genome

Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Our results provided evidence that the structural and sequence evolution of the fission yeasts were correlated. Moreover, we revealed ancestral locally collinear blocks (aLCBs), which could have been inherited from their last common ancestor. These aLCBs proved to be the most conserved regions of the genomes as the aLCBs contain almost eight genes/blocks on average in the same orientation and order across the species. Gene order of the aLCBs is mainly fission-yeast-specific but supports the idea of filamentous ancestors. Nevertheless, the sequences and gene structures within the aLCBs are as mutable as any sequences in other parts of the genomes. Although genes of certain Gene Ontology (GO) categories tend to cluster at the aLCBs, those GO enrichments are not related to biological functions or high co-expression rates, they are, rather, determined by the density of essential genes and Rec12 cleavage sites. These data and our simulations indicated that aLCBs might not only be remnants of ancestral gene order but are also maintained by natural selection.

scholarly journals iHam and pyHam: visualizing and processing hierarchical orthologous groups

2018 ◽  
Vol 35 (14) ◽  
pp. 2504-2506 ◽  
Author(s):  
Clément-Marie Train ◽  
Miguel Pignatelli ◽  
Adrian Altenhoff ◽  
Christophe Dessimoz
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Gene Families ◽  
Comparative Genomic ◽  
Last Common Ancestor ◽  
Analysis Method ◽  
Ancestral Gene ◽  
Genomic Analyses ◽  
History Of ◽  
Multiple Species

Abstract Summary The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species. Availability and implementation iHam’s code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam’s code is available at https://github.com/DessimozLab/pyHam and or via the pip package ‘pyham’.

scholarly journals Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order

Algorithms ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 160
Author(s):  
Qiaoji Xu ◽  
Lingling Jin ◽  
James H. Leebens-Mack ◽  
David Sankoff
Keyword(s):  
Phylogenetic Tree ◽  
Gene Order ◽  
Evolutionary Process ◽  
Gene Content ◽  
Ancestral Genome ◽  
Maximum Weight ◽  
Ancestral Gene ◽  
Maximum Weight Matching

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.

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

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.

scholarly journals Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

scholarly journals Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2982 ◽  
Author(s):  
Mun Hua Tan ◽  
Han Ming Gan ◽  
Yin Peng Lee ◽  
Gary C.B. Poore ◽  
Christopher M. Austin
Keyword(s):  
Codon Usage ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Decapod Crustacean ◽  
Illumina Miseq ◽  
Comparative Genomic ◽  
Decapod Crustaceans ◽  
Phylogenetic Studies ◽  
Significant Gene ◽  
Taxonomic Groups

BackgroundWhole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information.MethodsSequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements.ResultsWe present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps,Callianassa ceramicaandTrypaea australiensis, along with three caridean shrimps,Macrobrachium bullatum,Alpheus lobidens, andCaridinacf.nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders.DiscussionOur findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

scholarly journals Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise

2018 ◽  
Author(s):  
Russell A. Ligon ◽  
Christopher D. Diaz ◽  
Janelle L. Morano ◽  
Jolyon Troscianko ◽  
Martin Stevens ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Natural Selection ◽  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Functional Integration ◽  
Empirical Support ◽  
Evolutionary Patterns ◽  
Evolutionary Innovation ◽  
Birds Of Paradise ◽  
Analytical Approaches

Ornaments used in courtship often vary wildly among species, reflecting the evolutionary interplay between mate preference functions and the constraints imposed by natural selection. Consequently, understanding the evolutionary dynamics responsible for ornament diversification has been a longstanding challenge in evolutionary biology. However, comparing radically different ornaments across species, as well as different classes of ornaments within species, is a profound challenge to understanding diversification of sexual signals. Using novel methods and a unique natural history dataset, we explore evolutionary patterns of ornament evolution in a group - the birds-of-paradise - exhibiting dramatic phenotypic diversification widely assumed to be driven by sexual selection. Rather than the tradeoff between ornament types originally envisioned by Darwin and Wallace, we found positive correlations among cross-modal (visual/acoustic) signals indicating functional integration of ornamental traits into a composite unit - the courtship phenotype. Furthermore, given the broad theoretical and empirical support for the idea that systemic robustness - functional overlap and interdependency - promotes evolutionary innovation, we posit that birds-of-paradise have radiated extensively through ornamental phenotype space as a consequence of the robustness in the courtship phenotype that we document at a phylogenetic scale. We suggest that the degree of robustness in courtship phenotypes among taxa can provide new insights into the relative influence of sexual and natural selection on phenotypic radiations.Author SummaryAnimals frequently vary widely in ornamentation, even among closely related species. Understanding the patterns that underlie this variation is a significant challenge, requiring comparisons among drastically different traits - like comparing apples to oranges. Here, we use novel analytical approaches to quantify variation in ornamental diversity and richness across the wildly divergent birds-of-paradise, a textbook example of how sexual selection can profoundly shape organismal phenotypes. We find that color and acoustic complexity, along with behavior and acoustic complexity, are positively correlated across evolutionary time-scales. Positive covariation among ornament classes suggests that selection is acting on correlated suites of traits - a composite courtship phenotype - and that this integration may be partially responsible for the extreme variation we see in birds-of-paradise.

scholarly journals Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 358
Author(s):  
Joan Pedrola-Monfort ◽  
David Lázaro-Gimeno ◽  
Carlos G. Boluda ◽  
Laia Pedrola ◽  
Alfonso Garmendia ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Evolutionary Biology ◽  
Repetitive Sequences ◽  
Gc Content ◽  
Nuclear Genome ◽  
Nuclear Ribosomal Dna ◽  
Sequence Evolution ◽  
Evolutionary Trends ◽  
Genome Length ◽  
Evolutionary Patterns

Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three genetic compartments, particularly during the transition from water to land. To clarify the evolutionary trends in the mitochondrial genome of Archaeplastida, we analyzed the sequences from 37 complete genomes. Therefore, we utilized mitochondrial, plastidial and nuclear ribosomal DNA molecular markers on 100 species of Streptophyta for each subunit. Hierarchical models of sequence evolution were fitted to test the heterogeneity in the base composition. The best resulting phylogenies were used for reconstructing the ancestral Guanine-Cytosine (GC) content and equilibrium GC frequency (GC*) using non-homogeneous and non-stationary models fitted with a maximum likelihood approach. The mitochondrial genome length was strongly related to repetitive sequences across Archaeplastida evolution; however, the length seemed not to be linked to the other studied variables, as different lineages showed diverse evolutionary patterns. In contrast, Streptophyta exhibited a powerful positive relationship between the GC content, non-coding DNA, and repetitive sequences, while the evolution of Chlorophyta reflected a strong positive linear relationship between the genome length and the number of genes.

First partial mitogenome of a new Seira Lubbock species (Collembola,Entomobryidae, Seirinae) from Cambodia reveals a possible separate lineage from the Neotropical Seirinae

Zootaxa ◽  
2020 ◽  
Vol 4890 (4) ◽  
pp. 451-472
Author(s):  
NERIVANIA NUNES GODEIRO ◽  
FENG ZHANG ◽  
NIKOLAS GIOIA CIPOLA
Keyword(s):  
New Species ◽  
Gene Order ◽  
Colour Pattern ◽  
Protein Coding ◽  
Ancestral Gene ◽  
Protein Coding Genes ◽  
The Third ◽  
Maximum Likelihood Phylogenetic Tree ◽  
Genome Information ◽  
A New Species

A new species of Seira from Koh Rong Sanloem Island, Cambodia, as well as its mitochondrial genome information, are herein described. Seira sanloemensis sp. nov. has a similar colour pattern compared to nine other species of Seira worldwide distributed, but the dorsal chaetotaxy is more similar to S. arunachala Mitra from India, S. camgiangensis Nguyễn from Vietnam, and S. gobalezai Christiansen & Bellinger from Hawaii. However, the new species differs from these species by dorsal chaetotaxy of head, Th II–III and Abd II, collophore chaetotaxy, and morphology of the empodial complex. This is the third Collembola species described for Cambodia. Its assembled incomplete mitogenome from MGI reads, has a length of 13,953 bp, and contains all protein-coding genes except for tree tRNAs missing; the gene order is the same of the Pancrustacean ancestral gene order. Based on the alignment of the 13 coding genes, a maximum likelihood phylogenetic tree of medium bootstrap values suggested that the Asian Seira species can represent a different lineage from the Neotropical Seirinae, but further biogeographic and divergence estimation analyses plus the inclusion of more Asian taxa are necessary to test such hypothesis. 

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