Regulatory genes in the ancestral chordate genomes

Changes or innovations in gene regulatory networks for the developmental program in the ancestral chordate genome appear to be a major component in the evolutionary process in which tadpole-type larvae, a unique characteristic of chordates, arose. These alterations may include new genetic interactions as well as the acquisition of new regulatory genes. Previous analyses of the Ciona genome revealed that many genes may have emerged after the divergence of the tunicate and vertebrate lineages. In this paper, we examined this possibility by examining a second non-vertebrate chordate genome. We conclude from this analysis that the ancient chordate included almost the same repertory of regulatory genes, but less redundancy than extant vertebrates, and that approximately 10% of vertebrate regulatory genes were innovated after the emergence of vertebrates. Thus, refined regulatory networks arose during vertebrate evolution mainly as preexisting regulatory genes multiplied rather than by generating new regulatory genes. The inferred regulatory gene sets of the ancestral chordate would be an important foundation for understanding how tadpole-type larvae, a unique characteristic of chordates, evolved.     

Adaptive evolution of chloroplast genomes in ancestral grasses

The grass family, Poaceae, is one of the most successful families among angiosperms. Although it has long been suggested that the chloroplast genomes of the Poaceae have undergone an elevated evolutionary rate compared to other angiosperms, little was known about the details of this phenomenon. By using chloroplast genome data from 31 seed plants species, we recently showed that episodic rate acceleration occurred in the common ancestral branch of the core Poaceae (a clade formed by rice Oryza sativa, wheat Triticum aestivum, maize Zea mays and their allies) accompanied by elevated non-synonymous/synonymous rate ratio, while the rate and the non-synonymous/synonymous rate ratio reverted to the low level typical of most monocot species in the terminal branches. It was further shown that positive selection or adaptive evolution operated in several chloroplast proteins during the evolution of ancestral grasses, and the amino acid sites which putatively experienced positive selection have been identified. These findings illustrate the importance of future works of structural biological research of chloroplasts to understand the background of the evolution of the successful group, Poaceae.Key words: rate acceleration, positive selection, non-synonymous/synonymous rate ratio, Poaceae, structural biologyThe grass family, Poaceae, is one of the largest plant families, comprising about 10,000 species including the most important agricultural plants, rice, wheat and maize, as well as grass-dominated ecosystems which comprise about one-third of Earth''s vegetative cover and support a vast number of animals.¹ The chloroplast genes of the grass family Poaceae are known to have undergone accelerations in their evolutionary rates,^2,3 yet little was known about the details of this acceleration. It has become increasingly feasible to estimate the phylogenetic tree of angiosperms and to clarify the tempo and model of molecular evolution by using chloroplast genome sequences.^4–6 By using chloroplast genome data from 13 monocot species and 18 species from dicots and gymnosperms (31 species in total), we recently examined the details of this phenomenon from several aspects.Figure 1 shows the Poales + Musa part of the chloroplast ML tree of the 31 species, and the elongated branches of Poaceae show the rate acceleration in that particular group. Moreover, longer distances of the Poaceae species from Musa than the Typha/Musa distance by more than two times both in terms of non-synonymous and synonymous substitutions (Fig. 1) indicate that both types of substitutions have undergone rate acceleration along the line leading to Poaceae. To explore the pattern of rate change during the course of grass evolution more in detail, we estimated the time-scale of Angiosperm phylogeny with a relaxed clock based on the Bayesian method implemented in MCMCTREE program of PAML.⁷ As is apparent from Figure 1, the molecular evolutionary rate (substitution rate) differs among different lineages, and therefore we used the relaxed clock method which takes account of the evolution of the evolutionary rate in estimating the divergence times and the pattern of rate change. Based on fossil evidence, we assumed the followings in calibrating the relaxed clock; (1) the Gymnosperm/Angiosperm divergence occurred at 280–310 Ma (million years ago),^5,6 (2) the divergence of Poales from other monocots occurred before 115 Ma,^8,9 and (3) the most basal divergence in eudicots occurred before 125 Ma.⁵Open in a separate windowFigure 1Poales + Musa part of the chloroplast genome tree from 31 seed plant species. The branch lengths are proportional to the estimated lengths by the ML with the codon-substitution model (CODEML in PAML⁷). Non-synonymous (d_N) and synonymous (d_S) distances of Poales from Musa and ω = d_N/d_S (along branches) were estimated by the same program.We further gave a constraint of >65 Ma for the Zea/Oryza divergence based on the recent finding of 65 Ma grass phytoliths in dinosaur coprolites which places the diversification of the grasses to the Cretaceous period.^10,11 As a result, it was found that the rate acceleration was limited to the common ancestral branch of Poaceae after they diverged from Musa and that the rate reverted to the slow rate typical of most monocot species in the terminal branches. Even when the constraint was removed, almost the same pattern of rate change was obtained, suggesting that our conclusion regarding accelerated rate in the ancestral grasses followed by the reverted slow rate in contemporary Poaceae is robust.Non-synonymous/synonymous rate ratio (ω = d_N/d_S) is widely used as an indicator of positive selection or adaptive evolution.¹² Figure 1 also indicates a pronounced increase of ω ratio in the common ancestral branch of Poaceae after their divergence from Typha, followed by reversion in the terminal branches to the lower level typical of basal lineages. The elevation of the ω ratio can be due either by adaptive evolution or by relaxation of selective constraints. An ω value higher than 1 is usually regarded as an evidence of adaptive evolution, but since the ω values shown in the figure averages over the entire protein-encoding genes, we would not obtain such a high value even if positive selection operated in some regions of some proteins. To identify positively selected sites, among 75 protein-encoding genes, we at first selected 14 genes, for which the model with higher ω in the ancestral grass branch than others is significantly better than the model with homogeneous ω, and by using the branch-site model,^13,14 we identified 5 genes (atpE, cemA, clpP, rpoB and rps11) which have p value of the branch-site likelihood ratio test less than 0.05 and contain positively selected sites. The amino acid sites and substitutions identified to have experienced positive selection are as follows; atpE (2T→K, 17S→C, 41A→N, 64M→W, 132V→W), cemA (55N→R, 76Y→K, 161W→F, 190I→F, 204I→C), clpP (26R→V, 48V→T, 86F→T, 112I→P, 134E→R, 182T→D), rpoB (90R→F, 338G→K, 1026G→N), rps11 (54V→P, 62A→S, 82A→R, 105L→S, 115R→A, 120L→R) where the numberings of amino acid sites are those of Zea mays.¹⁵ We anticipate that these amino acid substitutions might have relevance to the successful evolution of grasses. To clarify the implication of these findings, structural biological studies of chloroplast proteins on how the amino acid changes affect their functions are needed.Rates of molecular evolution can be potentially linked to life history of organisms. By comparing evolutionary rates of chloroplast, nuclear and mitochondrial genes across five groups of angiosperms, Smith and Donoghue¹⁶ found that the rates are generally low in trees/shrubs compared to related herbs. Our finding, however, suggests that the pattern of rate change during evolution is more complicated than has previously been anticipated, and highlights the need for distinguishing rates of internal branches and those of terminal branches rather than averaging along a lineage in addressing this complicated problem.As Theodosius Dobzhansky¹⁷ wrote, nothing in biology makes sense except in the light of evolution, and the functional background of the molecular machinery in chloroplasts should be interpreted in the light of evolution. We hope our molecular evolutionary analysis of the chloroplast genomes is the first step towards this goal, and hope collaboration of molecular evolutionists with structural biologists becomes fruitful in the future.     

On the impossibility of reconstructing ancestral data and phylogenies.

We prove that it is impossible to reconstruct ancestral data at the root of "deep" phylogenetic trees with high mutation rates. Moreover, we prove that it is impossible to reconstruct the topology of "deep" trees with high mutation rates from a number of characters smaller than a low-degree polynomial in the number of leaves. Our impossibility results hold for all reconstruction methods. The proofs apply tools from information theory and percolation theory.     

Three founding ancestral genomes involved in the origin of sugarcane

Background and AimsModern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum.MethodsTo analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus.Key ResultsThe diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered.ConclusionsThis evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.     

Reconstruction of full-length LINE-1 progenitors from ancestral genomes

Sequences derived from the Long INterspersed Element-1 (L1) family of retrotransposons occupy at least 17% of the human genome, with 67 distinct subfamilies representing successive waves of expansion and extinction in mammalian lineages. L1s contribute extensively to gene regulation, but their molecular history is difficult to trace, because most are present only as truncated and highly mutated fossils. Consequently, L1 entries in current databases of repeat sequences are composed mainly of short diagnostic subsequences, rather than full functional progenitor sequences for each subfamily. Here, we have coupled 2 levels of sequence reconstruction (at the level of whole genomes and L1 subfamilies) to reconstruct progenitor sequences for all human L1 subfamilies that are more functionally and phylogenetically plausible than existing models. Most of the reconstructed sequences are at or near the canonical length of L1s and encode uninterrupted ORFs with expected protein domains. We also show that the presence or absence of binding sites for KRAB-C2H2 Zinc Finger Proteins, even in ancient-reconstructed progenitor L1s, mirrors binding observed in human ChIP-exo experiments, thus extending the arms race and domestication model. RepeatMasker searches of the modern human genome suggest that the new models may be able to assign subfamily resolution identities to previously ambiguous L1 instances. The reconstructed L1 sequences will be useful for genome annotation and functional study of both L1 evolution and L1 contributions to host regulatory networks.     

Testing the accuracy of methods for reconstructing ancestral states of continuous characters.

Many methods are available for estimating ancestral values of continuous characteristics, but little is known about how well these methods perform. Here we compare six methods: linear parsimony, squared-change parsimony, one-parameter maximum likelihood (Brownian motion), two-parameter maximum likelihood (Ornstein-Uhlenbeck process), and independent comparisons with and without branch-length information. We apply these methods to data from 20 morphospecies of Pleistocene planktic Foraminifera in order to estimate ancestral size and shape variables, and compare these estimates with measurements on fossils close to the phylogenetic position of 13 ancestors. No method produced accurate estimates for any variable: estimates were consistently less good as predictors of the observed values than were the averages of the observed values. The two-parameter maximum-likelihood model consistently produces the most accurate size estimates overall. Estimation of ancestral sizes is confounded by an evolutionary trend towards increasing size. Shape showed no trend but was still estimated very poorly: we consider possible reasons. We discuss the implications of our results for the use of estimates of ancestral characteristics.     

Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction

Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome‐scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR‐based Sanger sequencing, following the dawn of the second‐generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.     

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.     

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and AmphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.     

A hominoid-specific nuclear insertion of the mitochondrial D-loop: implications for reconstructing ancestral mitochondrial sequences

A nuclear integration of a mitochondrial control region sequence on human chromosome 9 has been isolated. PCR analyses with primers specific for the respective insertion-flanking nuclear regions showed that the insertion took place on the lineage leading to Hominoidea (gibbon, orangutan, gorilla, chimpanzee, and human) after the Old World monkey-Hominoidea split. The sequences of the control region integrations were determined for humans, chimpanzees, gorillas, orangutans, and siamangs. These sequences were then used to construct phylogenetic trees with different methods, relating them with several hominoid, Old Work monkey, and New World monkey mitochondrial control region sequences. Applying maximum-likelihood, neighbor-joining, and parsimony algorithms, the insertion clade was attached to the branch leading to the hominoid mitochondrial sequences as expected from the PCR-determined presence/absence of this integration. An unexpected long branch leading to the internal node that connects all insertion sequences was observed for the different phylogeny reconstruction procedures. This finding is not totally compatible with the lower evolutionary rate in the nucleus than in the mitochondrial compartment. We determined the unambiguous substitutions on the branch leading to the most recent common ancestor (MRCA) of the mitochondrial inserts according to the parsimony criterium. We propose that they are unlikely to have been caused by damage of the transposing nucleic acid and that they are probably due to a change in the evolutionary mode after the transposition.      

BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated peanut

Background

Cultivated peanut, Arachis hypogaea is an allotetraploid of recent origin, with an AABB genome. In common with many other polyploids, it seems that a severe genetic bottle-neck was imposed at the species origin, via hybridisation of two wild species and spontaneous chromosome duplication. Therefore, the study of the genome of peanut is hampered both by the crop's low genetic diversity and its polyploidy. In contrast to cultivated peanut, most wild Arachis species are diploid with high genetic diversity. The study of diploid Arachis genomes is therefore attractive, both to simplify the construction of genetic and physical maps, and for the isolation and characterization of wild alleles. The most probable wild ancestors of cultivated peanut are A. duranensis and A. ipaënsis with genome types AA and BB respectively.

Results

We constructed and characterized two large-insert libraries in Bacterial Artificial Chromosome (BAC) vector, one for each of the diploid ancestral species. The libraries (AA and BB) are respectively c. 7.4 and c. 5.3 genome equivalents with low organelle contamination and average insert sizes of 110 and 100 kb. Both libraries were used for the isolation of clones containing genetically mapped legume anchor markers (single copy genes), and resistance gene analogues.

Conclusion

These diploid BAC libraries are important tools for the isolation of wild alleles conferring resistances to biotic stresses, comparisons of orthologous regions of the AA and BB genomes with each other and with other legume species, and will facilitate the construction of a physical map.

     

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

Background

Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions.

Results

We present a computational method, ADseq, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADseq provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADseq to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes.

Conclusions

We demonstrate the method’s ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.

     

Neuromuscular development in Patellogastropoda (Mollusca: Gastropoda) and its importance for reconstructing ancestral gastropod bodyplan features

Within Gastropoda, limpets (Patellogastropoda) are considered the most basal branching taxon and its representatives are thus crucial for research into evolutionary questions. Here, we describe the development of the neuromuscular system in Lottia cf. kogamogai. In trochophore larvae, first serotonin‐like immunoreactivity (lir) appears in the apical organ and in the prototroch nerve ring. The arrangement and number of serotonin‐lir cells in the apical organ (three flask‐shaped, two round cells) are strikingly similar to those in putatively derived gastropods. First, FMRFamide‐lir appears in veliger larvae in the Anlagen of the future adult nervous system including the cerebral and pedal ganglia. As in other gastropods, the larvae of this limpet show one main and one accessory retractor as well as a pedal retractor and a prototroch muscle ring. Of these, only the pedal retractor persists until after metamorphosis and is part of the adult shell musculature. We found a hitherto undescribed, paired muscle that inserts at the base of the foot and runs towards the base of the tentacles. An apical organ with flask‐shaped cells, one main and one accessory retractor muscle is commonly found among gastropod larvae and thus might have been part of the last common ancestor.     

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

Background  

Genome size and complexity, as measured by the number of genes or protein domains, is remarkably similar in most extant eukaryotes and generally exhibits no correlation with their morphological complexity. Underlying trends in the evolution of the functional content and capabilities of different eukaryotic genomes might be hidden by simultaneous gains and losses of genes.