Hox genes in a pentameral animal

There is renewed interest in how the different body plans of extant phyla are related. This question has traditionally been addressed by comparisons between vertebrates and Drosophila. Fortunately, there is now increasing emphasis on animals representing other phyla. Pentamerally symmetric echinoderms are a bilaterian metazoan phylum whose members exhibit secondarily derived radial symmetry. Precisely how their radially symmetric body plan originated from a bilaterally symmetric ancestor is unknown, however, two recent papers address this subject. Peterson et al. propose a hypothesis on evolution of the anteroposterior axis in echinoderms, and Arenas-Mena et al. examine expression of five posterior Hox genes during development of the adult sea urchin.     

Homology of ciliary bands in Spiralian Trochophores

A number of hypotheses have been presented regarding the originsof the metazoans and, more specifically, the Bilateria. Usingvarious phylogenetic analyses, characteristics have been mappedon phylogenetic trees to infer ancestral body plans and lifehistory strategies of those ancestors. Many arguments on theevolution of the Bilateria are based on the presumed homologyof certain characteristics of extant larva and adults, includingvarious ciliated bands involved in feeding and locomotion. Thisarticle considers a recent study indicating that the second,downstream-collecting, ciliated band in the veliger larva ofthe gastropod mollusc, Crepidula fornicata, is actually derivedfrom secondary trochoblasts (derived from second quartet micromeres),that normally form part of the prototrochal band found in otherspiralian phyla (Hejnol et al. 2007). Despite previous arguments,these new findings suggest that the second ciliated band inthe veliger larva is not homologous to the metatroch found inthe trochophore larva of some other spiralians, such as theannelid, Polygordius lacteus. In the latter case, the metatrochwas reported to be formed by a different set of lineage precursors(derived from third quartet micromeres) (Woltereck 1904). Thesefindings have important implications for the interpretationof various hypotheses related to the evolution of metazoan phyla.     

CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species

In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/.The Brassicaceae (crucifer) plant family contains more than 3,700 species, including the model plant organism Arabidopsis (Arabidopsis thaliana); economically important crop species, such as Brassica rapa and Brassica napus; and close relatives of Arabidopsis used in abiotic stress research, such as Eutrema salsugineum and Schrenkiella parvula. Because Brassicaceae plants have high scientific and economic importance, several whole-genome sequencing projects of the species in this family have been recently launched (http://www.brassica.info). Moreover, Brassicaceae is also a good system for population genomics. The 1001 Arabidopsis Genomes Project (http://www.1001genomes.org/) plans to generate complete genome sequences for 1,001 Arabidopsis strains to study the associations between genetic variation and phenotypic diversity. The Value-directed Evolutionary Genomics Initiative project aims to understand the genome evolution of Brassicaceae species by sequencing several close relatives of Arabidopsis, such as Arabidopsis lyrata and Capsella rubella. Recent advances in high-throughput sequencing technology have greatly expedited these whole-genome sequencing projects of versatile nonmodel organisms. Although increasingly longer reads can now be produced from high-throughput sequencing experiments, de novo assembler tools can only generate contig and/or scaffold sequences from high-throughput sequencing reads. These tools cannot generate complete chromosome sequences without genetic and/or physical maps that typically require years to create. This limitation makes chromosome-scale structural variation (i.e. translocation, inversion, deletion and insertion, and segmental and tandem duplication) and genomic macrosynteny analyses difficult to perform.In both plants and animals, genomes of species within the same family have evolved with conserved karyotype patterns due to the rearrangements of large chromosomal segments. Chromosomal karyotypes can be obtained from comparative chromosomal painting (CCP) experiments by performing in situ hybridization experiments on bacterial artificial chromosome sequences between related species. The genome of each Brassicaceae member is composed of 24 conserved genomic blocks that have been considered as the basic units of chromosomal rearrangement during genome evolution (Lysak et al., 2006). The sizes of these conserved blocks range from several to dozens of megabases. Currently, karyotypes profiled by CCP experiments in approximately 20 Brassicaceae species are available; such karyotypes include those from Arabidopsis (n = 5), Homungia alpine (n = 6), Eutrema spp. (n = 7), A. lyrata (n = 8), B. rapa (n = 10), and Polyctenium fremontii (n = 14). By utilizing the karyotype information in Brassicaceae, we have developed a tool, KGBassembler (for Karyotype-based Genome assembler for Brassicaceae), to finalize the assembly of chromosomes from scaffolds/contigs without relying on a genetic/physical map (Ma et al., 2012).Over the past 2 years, complete whole-genome sequences of several Brassicaceae species have been released, including the aforementioned A. lyrata, S. parvula, B. rapa, and E. salsugineum (Dassanayake et al., 2011; Hu et al., 2011; Wang et al., 2011; Wright and Agren, 2011; Wu et al., 2012; Yang et al., 2013). These genomic resources have opened a new era of comparative genomics in Brassicaceae to better understand the genomic evolution (Cheng et al., 2012). Numerous tools and databases are available for performing comparative genomics analysis in plants. CoGe is a comparative genomics analysis platform that is now a part of the iPlant Collaborative Project (Goff et al., 2011). The CoGe database currently includes nearly 2,000 genome sequences of approximately 1,500 organisms, allowing users to perform online visual analyses of genome synteny and duplication events (Tang and Lyons, 2012). PLAZA and Vista are also Web-based databases that provide comparative analysis services on the genomic data deposited in the databases (Frazer et al., 2004; Van Bel et al., 2012). Other stand-alone bioinformatic applications for comparative genomic analysis, such as Easyfig and genoPlotR, are commonly used to generate synteny plots of given genome segments at a scale ranging from a single gene to one chromosome (Guy et al., 2010; Sullivan et al., 2011).In this work, we present a Java-based bioinformatic application, CrusView, for performing visualized analyses of genome synteny and karyotype evolution in Brassicaceae species. CrusView features a user-friendly graphical user interface (GUI) implemented with Standard Widget Toolkit (SWT)/Swing graphics libraries and a SQLite database used to manage local genomic data. Compared with the most commonly used tools in comparative genomics, one of the unique features of CrusView is that available karyotype data of a Brassicaceae species are incorporated to facilitate karyotype-based chromosome assembly and analyses of chromosomal structural evolution. Compared with Web-based tools, the stand-alone CrusView tool was also designed to give users higher flexibility in analyzing currently unpublished genome data and integrating self-defined genomic information based on the users’ interests, such as gene families, gene duplications, chromosomal break points, Gene Ontology terms, and groups of orthologs/paralogs, with the genomic synteny maps. In addition, CrusView can generate images representing genomic synteny between two compared genomes in PNG/SVG/PDF high-resolution formats that are suitable for publication.     

A Brief Review of Metazoan Phylogeny and Future Prospects in Hox-Research

Underlying any analysis on the evolution of development is aphylogenetic framework, whether explicitly stated or implied.As such, differing views on phylogenetic relationships leadto variable interpretations of how developmental mechanismshave changed through time. Over the past decade, many long-standinghypotheses about animal evolution have been questioned causingsubstantial changes in the assumed phylogenetic framework underlyingcomparative developmental studies. Current hypotheses aboutearly metazoan history suggest that three, not two, major lineagesof bilateral animals originated in the Precambrian: the Deuterostomes(e.g., seastars, acorn worms, and vertebrates), the Ecdysozoans(e.g., nematodes and arthropods), and the Lophotrochozoans (e.g.,annelids, mollusks, and lophophorates). Although informationin Hox-genes bears directly on our understanding of early metazoanevolution and the formation of body plans, research effort hasbeen focused primarily on two taxa, insects and vertebrates.By sampling a greater diversity of metazoan taxa and takingadvantage of biotechnological advances in genomics, we willnot only learn more about metazoan phylogeny, but will alsogain valuable insight as to the key evolutionary forces thatestablished and maintained metazoan bauplans.     

Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer

Trehalose is a versatile non-reducing sugar. In some animal groups possessing its intrinsic production machinery, it is used as a potent protectant against environmental stresses, as well as blood sugar. However, the trehalose biosynthesis genes remain unidentified in the large majority of metazoan phyla, including vertebrates. To uncover the evolutionary history of trehalose production machinery in metazoans, we scrutinized the available genome resources and identified bifunctional trehalose-6-phosphate synthase-trehalose-6-phosphate phosphatase (TPS–TPP) genes in various taxa. The scan included our newly sequenced genome assembly of a desiccation-tolerant tardigrade Paramacrobiotus sp. TYO, revealing that this species retains TPS–TPP genes activated upon desiccation. Phylogenetic analyses identified a monophyletic group of the many of the metazoan TPS–TPP genes, namely ‘pan-metazoan’ genes, that were acquired in the early ancestors of metazoans. Furthermore, coordination of our results with the previous horizontal gene transfer studies illuminated that the two tardigrade lineages, nematodes and bdelloid rotifers, all of which include desiccation-tolerant species, independently acquired the TPS–TPP homologues via horizontal transfer accompanied with loss of the ‘pan-metazoan’ genes. Our results indicate that the parallel evolution of trehalose synthesis via recurrent loss and horizontal transfer of the biosynthesis genes resulted in the acquisition and/or augmentation of anhydrobiotic lives in animals.     

Recovery and characterization of a Citrus clementina Hort. ex Tan. 'Clemenules' haploid plant selected to establish the reference whole Citrus genome sequence

Background  

In recent years, the development of structural genomics has generated a growing interest in obtaining haploid plants. The use of homozygous lines presents a significant advantage for the accomplishment of sequencing projects. Commercial citrus species are characterized by high heterozygosity, making it difficult to assemble large genome sequences. Thus, the International Citrus Genomic Consortium (ICGC) decided to establish a reference whole citrus genome sequence from a homozygous plant. Due to the existence of important molecular resources and previous success in obtaining haploid clementine plants, haploid clementine was selected as the target for the implementation of the reference whole genome citrus sequence.     

Amitriptyline reduces olfactory neuron adenylyl cyclase activity

Adenylyl cyclase plays an important role in olfactory signaltransduction. Recently, a novel type III adenylyl cyclase hasbeen localized in olfactory neurons (Pfeuffer et al., 1989;Bakalyar and Reed, 1990). Because amitriptyline (AMI), a tricyclicantidepressant, appears to have an inhibitory effect on adenylylcyclase activity in other in other neuronal tissue (Yamaokaet al., 1988; Wong et al., 1991), we measured the effect ofAMI on forskolin-stimulated adenylyl cyclase activity in membranepreparations of olfactory mucosa from adult rats. In the presenceof 5'-guanylyl-imidodiphosphate, AMI (0.5–8.0 µM)inhibited forskolin-stimulated adenylyl cyclase activity ina dose-dependent manner. To determine whether this effect wasspecific for olfactory neurons, as opposed to other cells inthe olfactory epithelium, rats were unilaterally bulbectomizedin order to reduce selectively the number of olfactory neuronson the side ipsilateral to the bulbectomy. In membrane preparationsfrom unilaterally bulbectomized animals we saw significantlylower adenylyl cyclase activity in ipsilateral olfactory mucosa,compared with adenylyl cyclase activity from non-bulbectomizedmucosa. These results indicate that AMI inhibition of adenylylcyclase activity is primariy localized in olfactory neurons.     

Tick genomics: the Ixodes genome project and beyond

Ticks and mites (subphylum Chelicerata; subclass Acari) include important pests of animals and plants worldwide. The Ixodes scapularis (black-legged tick) genome sequencing project marks the beginning of the genomics era for the field of acarology. This project is the first to sequence the genome of a blood-feeding tick vector of human disease and a member of the subphylum Chelicerata. Genome projects for other species of Acari are forthcoming and their genome sequences will likely feature significantly in the future of tick research. Parasitologists interested in advancing the field of tick genomics research will be faced with specific challenges. The development of genetic tools and resources, and the size and repetitive nature of tick genomes are important considerations. Innovative approaches may be required to sequence, assemble, annotate and analyse tick genomes. Overcoming these challenges will enable scientists to investigate the genes and genome organisation of this important group of arthropods and may ultimately lead to new solutions for control of ticks and tick-borne diseases.     

Defining phyla: evolutionary pathways to metazoan body plans

SUMMARY Phyla are defined by two sets of criteria, one morphological and the other historical. Molecular evidence permits the grouping of animals into clades and suggests that some groups widely recognized as phyla are paraphyletic, while some may be polyphyletic; the phyletic status of crown phyla is tabulated. Four recent evolutionary scenarios for the origins of metazoan phyla and of supraphyletic clades are assessed in the light of a molecular phylogeny: the trochaea hypothesis of Nielsen; the clonal hypothesis of Dewel; the set-aside cell hypothesis of Davidson et al.; and a benthic hypothesis suggested by the fossil record. It is concluded that a benthic radiation of animals could have supplied the ancestral lineages of all but a few phyla, is consistent with molecular evidence, accords well with fossil evidence, and accounts for some of the difficulties in phylogenetic analyses of phyla based on morphological criteria.     

Incorporating Genomics into the Toolkit of Nematology

The study of nematode genomes over the last three decades has relied heavily on the model organism Caenorhabditis elegans, which remains the best-assembled and annotated metazoan genome. This is now changing as a rapidly expanding number of nematodes of medical and economic importance have been sequenced in recent years. The advent of sequencing technologies to achieve the equivalent of the $1000 human genome promises that every nematode genome of interest will eventually be sequenced at a reasonable cost. As the sequencing of species spanning the nematode phylum becomes a routine part of characterizing nematodes, the comparative approach and the increasing use of ecological context will help us to further understand the evolution and functional specializations of any given species by comparing its genome to that of other closely and more distantly related nematodes. We review the current state of nematode genomics and discuss some of the highlights that these genomes have revealed and the trend and benefits of ecological genomics, emphasizing the potential for new genomes and the exciting opportunities this provides for nematological studies.     

Nutrient-patch contrast in relation to clonal integration, with special reference to Glechoma longituba

Patch contrast, defined as the difference between patches, isamong the basic traits of environmental heterogeneity (Kolasa and Pickett 1991;Stuefer 1996). Clonal plants, especially those with long spacers,usually experience certain patches with different nutrient-patchcontrasts (de Kroon et al. 2005; Stuefer 1996). Clonal integrationhas been recognized as a basic strategy, by which clonal plantscan effectively cope with patchy resources and increase theirfitness in such habitats (de Kroon et al. 2005; Zhang et al. 2007).Glechoma longituba is distributed     

Organization of the psaH Gene Family of Photosystem I in Nicotiana sylvestris

The PSI-H subunit of photosystem I has two isoforms of differingmolecular mass in Nicotiana sylvestris [Obokata et al. (1993)Plant Physiol. 102: 1259], and is encoded by a nuclear gene,psaH. We identified three structurally distinct psaH genes inthe nuclear genome of N. sylvestris, designated psaHa, psaHb,and psaHc, and all three genes are expressed in young leaves.Each gene has two introns: one between sequences encoding atransit peptide and the N-terminal acidic domain, and one betweenthe N-terminal domain and a central hydrophobic domain. Thededuced amino acid sequences are identical in the mature proteinsand differ only in the transit peptides. Since PSI-H is presentin two isoforms in N. sylvestris, the psaH products may be subjectedto post-translational modifications. (Received November 8, 1993; Accepted December 28, 1993)     

Investigation of the Presence of Phenolic Compounds in Monocotyledonous Cell Walls, using UV Fluorescence Microscopy

Harris and Hartley (1976, 1980) demonstrated the presence offerulic acid in cell walls of certain monocotyledons using UVfluorescence microscopy (fluorescing green after treatment withammonium hydroxide solution). The presence or absence of thistype of fluorescence is apparently critical in higher levelsystematics of monocotyledons. In order to evaluate the significanceof this character, cell wall fluorescence was investigated ina range of monocotyledon species, particularly the AustralianXanthorrhoeaceae sensu lato (Bedford et al., 1986), which werenot investigated in earlier studies. This family is widely regardedas polyphyletic and was divided into several families by Dahlgren,Clifford and Yeo (1985). Some of its constituent genera, suchas Dasypogon, Kingia and Calectasia, have been linked with bothcommelinoid and non-commelinoid monocotyledons, and are of obscureaffinity. Some genera of Xanthorrhoeaceae sensu lato (Baxteria,Calectasia, Dasypogon and Kingia) show this type of green cellwall fluorescence and may therefore be more closely linked withthe commelinoid monocotyledons, rather than the Lilianae-Asparagales,as previously placed (Dahlgren et al., 1985).Copyright 1994,1999 Academic Press Asparagales, Dasypogonaceae, fluorescence, Hanguana, monocotyledons, systematics, Xanthorrhoeaceae     

Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer

The mitochondrial genome of grape (Vitis vinifera), the largestorganelle genome sequenced so far, is presented. The genomeis 773,279 nt long and has the highest coding capacity amongknown angiosperm mitochondrial DNAs (mtDNAs). The proportionof promiscuous DNA of plastid origin in the genome is also thelargest ever reported for an angiosperm mtDNA, both in absoluteand relative terms. In all, 42.4% of chloroplast genome of Vitishas been incorporated into its mitochondrial genome. In orderto test if horizontal gene transfer (HGT) has also contributedto the gene content of the grape mtDNA, we built phylogenetictrees with the coding sequences of mitochondrial genes of grapeand their homologs from plant mitochondrial genomes. Many incongruentgene tree topologies were obtained. However, the extent of incongruencebetween these gene trees is not significantly greater than thatobserved among optimal trees for chloroplast genes, the commonancestry of which has never been in doubt. In both cases, weattribute this incongruence to artifacts of tree reconstruction,insufficient numbers of characters, and gene paralogy. Thisfinding leads us to question the recent phylogenetic interpretationof Bergthorsson et al. (2003, 2004) and Richardson and Palmer(2007) that rampant HGT into the mtDNA of Amborella best explainsphylogenetic incongruence between mitochondrial gene trees forangiosperms. The only evidence for HGT into the Vitis mtDNAfound involves fragments of two coding sequences stemming fromtwo closteroviruses that cause the leaf roll disease of thisplant. We also report that analysis of sequences shared by bothchloroplast and mitochondrial genomes provides evidence fora previously unknown gene transfer route from the mitochondrionto the chloroplast.     

Complete Nucleotide Sequence of the Chloroplast Genome from the Tasmanian Blue Gum, Eucalyptus globulus (Myrtaceae)

The complete nucleotide sequence of the chloroplast genome ofthe hardwood species Eucalyptus globulus is presented and comparedwith chloroplast genomes of tree and non-tree angiosperms andtwo softwood tree species. The 160 286 bp genome is similarin gene order to that of Nicotiana, with an inverted repeat(IR) (26 393 bp) separated by a large single copy (LSC) regionof 89 012 bp and a small single copy region of 18 488 bp. Thereare 128 genes (112 individual gene species and 16 genes duplicatedin the inverted repeat) coding for 30 transfer RNAs, 4 ribosomalRNAs and 78 proteins. One pseudogene (-infA) and one pseudo-ycf(-ycf15) were identified. The chloroplast genome of E. globulusis essentially co-linear with that of another hardwood treespecies, Populus trichocarpa, except that the latter lacks rps16and rpl32, and the IR has expanded in Populus to include rps19(part of the LSC in E. globulus). Since the chloroplast genomeof E. globulus is not significantly different from other treeand non-tree angiosperm taxa, a comparison of hardwood and softwoodchloroplasts becomes, in essence, a comparison of angiospermand gymnosperm chloroplasts. When compared with E. globulus,Pinus chloroplasts have a very small IR, two extra tRNAs andfour additional photosynthetic genes, lack any functional ndhgenes and have a significantly different genome arrangement.There does not appear to be any correlation between plant habitand chloroplast genome composition and arrangement.     

A Test for the Resource Remobilization Hypothesis: Tree Sprouting using Carbohydrates from Above-ground Parts

To test the resource remobilization hypothesis, i.e. the hypothesisthat some trees sprout from root-collars or from the lower partof trunks using resources obtained from above-ground parts ratherthan from resources reserved in their roots, we conducted cuttingexperiments forEuptelea polyandra, a frequently sprouting treespecies with little carbohydrate reserves in its roots,Quercusserrata,a frequently sprouting tree species with large reservesin the roots, andMallotus japonicus, a rarely sprouting treespecies. Trees of each species were cut down in winter leavingtwo kinds of stumps, those approx. 1.5 m in height and thosecut off near the ground. The number and total dry weight ofnewly sprouted shoots per stump were compared between the twotreatments and among the three species at the end of the followinggrowing season. InE. polyandra,both the number and total dryweight of sprouts per stump were very small for both treatmentsand were similar to, or less than, those ofM. japonicus. Onthe other hand,Q. serratasprouted abundantly in both treatments.These results indicate thatE. polyandracannot sprout sufficientlywithout a considerably large volume of above-ground parts orthat additional structures such as foliage and branches maybe necessary for sprouting. We conclude that the resource remobilizationhypothesis is supported for this species.Copyright 1998 Annalsof Botany Company Euptelea polyandraSieb. et Zacc,Quercus serrataThunb,Mallotus japonicus(Thunb.) Muell. Arg., tree sprouting, cutting experiment, resprouter, resource movement, carbohydrate allocation, ground-surface disturbance, root stock, resource remobilization hypothesis.     

A survey for body scales in dinoflagellates and a revision of Cachonina and Heterocapsa (Pyrrhophyta)

Small organic scales 0.2 to 0.4 µm in diameter have beenobserved to form a layer on the surface of three species ofmarine dinoflagellates. Two of the species were originally describedas members of the genus Cachonina; the third is Heterocapsapygmaea Loeblich et al., 1981. The body scales are very similarto those previously described covering cells of Heterocapsatriquetra (Ehrenberg) Stein, 1883. These scales are freely shedfrom the cells of the above four species and can be found inthe culture medium; no scales were observed in the culture mediumof 35 other dinoflagellate species representing 18 genera and11 families. The complete thecal plate pattern of H. triquetra,type species of Heterocapsa, has been determined, and on thebasis of similarities in body scale morphology and thecal platetabulation, the genus Cachonina is placed in the synonomy ofHeterocapsa. Cachonina illdefina and C. niei are transferredto Heterocapsa.