Electrophoretic investigation of genetic variation in two krill species Euphausia superba and E. crystallorophias (Euphausiidae)

Summary Specimens of Euphausia superba and of E. crystallorophias from different locations were analyzed electrophoretically for protein variation. The present study extends previous genetic studies on E. superba by analyzing samples from the East Wind Drift and repeat samples from the Bransfield Strait, Elephant Island and the Weddell Sea. E. crystallorophias was collected in the Weddell Sea and around the Antarctic Peninsula in order to provide information on the breeding structure of the species in this region. For all loki taking all sampling sites together for both species except GPI in E. crystallorophias no significant deviation of phenotype distributions from random mating expectations was observed. Furthermore, the allele distributions in all polymorphic loci for both species were found to be homogeneous. Estimates of genetic distance between samples within each species are low (0.0001 to 0.0003 in E. superba and 0.0001 to 0.0002 in E. crystallorophias), and are consistent with results expected for samples from a single interbreeding population. Estimate of genetic distance between these two species was 0.9729. These results suggest that for each species specimens from all locations investigated in the Bransfield Strait and Weddell Sea belong to a single genetically homogeneous population. A possible mechanism for maintaining such homogeneity and the implications for fishery management are discussed.     

Straight Walk: A modified method of ligation-mediated genome walking for plant species with large genomes

Polymerase chain reaction (PCR)-based genome walking techniques are commonly used to clone unknown genomic regions flanking known sequences. However, these methods are typically problematic when applied to highly complex DNA templates isolated from plants with large genomes. Here we describe a reliable and efficient genome walking method that is particularly effective for plants with large genomes. Our ligation-mediated PCR method, Straight Walk, has improved sensitivity and specificity due to optimization of sequences of adaptors and adaptor primers. Successful genome walking in lily, which has one of the largest genomes in plants, indicates that Straight Walk is applicable for most plant species.     

Isolation of highly polymorphic microsatellite loci for a species with a large genome size: sharp-ribbed salamander (Pleurodeles waltl)

Fourteen highly polymorphic microsatellite markers were developed and characterized for the sharp-ribbed salamander, Pleurodeles waltl. Isolating microsatellites with more than 12 single repeat type units was only successful for a tetranucleotide repeat (ATAG). Compared to microsatellite libraries constructed simultaneously for two anuran amphibian species, a greater number of primer pairs designed for P. waltl had to be discarded, due to consistent amplification problems. Low amplification success rate for P. waltl may be due to its larger genome size. Consequently, to avoid nonspecific binding and to increase amplification success, polymerase chain reaction programmes with touchdown cycles were used. For 14 microsatellite markers, amplification was successful and consistent with number of alleles and expected heterozygosity ranging from seven to 22 and from 0.79 to 0.94, respectively. All 14 microsatellite markers will be extremely useful for metapopulation studies of this unique amphibian species.     

Limb ontogeny and trunk segmentation in Nebalia species (Crustacea, Malacostraca, Leptostraca)

The ’egg-larval’ development of two species of Nebalia has been examined with SEM. Various details concerning limb ontogeny and trunk segmentation are described. The most important of these are the following. The tripartite state of the peduncle of antenna 2 in the adult of Nebalia species is derived from the fusion of the third and fourth podomeres, present in late larvae. The proximal portion of the mandible in the adult of Nebalia brucei, carrying the ’coxal process’, is, based on the ontogenetic evidence, interpreted as the combined basis and coxa, and the bipartite palp is interpreted as the endopod. The early development of the thoracopods and the three anteriormost pleopods is identical. They all start as laterally directed, biramous limb buds. This suggests that tagmatisation of the trunk of the Leptostraca (and other Malacostraca) has been developed from an ancestor with an undivided trunk region with serially similar limbs. Certain early stages reveal an extra, ’eighth’, limbless pleon segment, as compared with the normal number of seven pleomeres of adult Leptostraca. The presence of a row of ventral, sternitic, triangular processes between the bases of the thoracopods, as they are found in certain stages of a species of Nebalia, is suggested as a possible ground pattern for the Malacostraca. Accepted: 1 February 2000     

The UniMarker (UM) method for synteny mapping of large genomes

MOTIVATION: Synteny mapping, or detecting regions that are orthologous between two genomes, is a key step in studies of comparative genomics. For completely sequenced genomes, this is increasingly accomplished by whole-genome sequence alignment. However, such methods are computationally expensive, especially for large genomes, and require rather complicated post-processing procedures to filter out non-orthologous sequence matches. RESULTS: We have developed a novel method that does not require sequence alignment for synteny mapping of two large genomes, such as the human and mouse. In this method, the occurrence spectra of genome-wide unique 16mer sequences present in both the human and mouse genome are used to directly detect orthologous genomic segments. Being sequence alignment-free, the method is very fast and able to map the two mammalian genomes in one day of computing time on a single Pentium IV personal computer. The resulting human-mouse synteny map was shown to be in excellent agreement with those produced by the Mouse Genome Sequencing Consortium (MGSC) and by the Ensembl team; furthermore, the syntenic relationship of segments found only by our method was supported by BLASTZ sequence alignment.     

Taxonomic implications of genome size for all species of the genus Gasteria Duval (Aloaceae)

Nuclear DNA content (2C) is used as a new criterion to investigate all species of the genus Gasteria Duval including the three recently described species Gasteria polita van Jaarsv., G. pendulifolia van Jaarsv. and G. glauca van Jaarsv.. The 122 accessions investigated have the same chromosome number (2n=2x=14), with exception of three tetraploid plants found. The nuclear DNA content of the diploids, as measured by flow cytometry with Propidium Iodide, is demonstrated to range from 32.8–43.2 pg. This implies that the largest genome contains roughly 10¹⁰ more base pairs than the smallest. Based on DNA content the species could be divided in five groups: G. rawlinsonii Oberm. with 32.8 pg, 13 mostly inland species with 34.3–36.0 pg, five coastal species with 36.5–39.0 pg and Gasteria batesiana Rowley with 43.2 pg. The thirteen species with 34.3–36.0 pg could be divided further, in a group of eight species occupying mainly very restricted areas with 34.3–35.1 pg and a second group of five species with 35.2–36.0 pg mainly occupying large areas. These five groups did not coincide very well with the two sections and four series of Gasteria based on a cladistic analysis by van Jaarsveld et al. (1994). Based on its long leafy branches, location in the centre of Gasteria species distribution and its by far lowest DNA content, G. rawlinsonii might be the most primitive member of the genus. Nuclear DNA content as measured by flow cytometry is shown to be relevant to provide additional information on the relationships between Gasteria species.     

The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae)

BACKGROUND: In studies looking at individual polyploid species, the most common patterns of genomic change are that either genome size in the polyploid is additive (i.e. the sum of parental genome donors) or there is evidence of genome downsizing. Reports showing an increase in genome size are rare. In a large-scale analysis of 3008 species, genome downsizing was shown to be a widespread biological response to polyploidy. Polyploidy in the genus Nicotiana (Solanaceae) is common with approx. 40 % of the approx. 75 species being allotetraploid. Recent advances in understanding phylogenetic relationships of Nicotiana species and dating polyploid formation enable a temporal dimension to be added to the analysis of genome size evolution in these polyploids. METHODS: Genome sizes were measured in 18 species of Nicotiana (nine diploids and nine polyploids) ranging in age from <200,000 years to approx. 4.5 Myr old, to determine the direction and extent of genome size change following polyploidy. These data were combined with data from genomic in situ hybridization and increasing amounts of information on sequence composition in Nicotiana to provide insights into the molecular basis of genome size changes. KEY RESULTS AND CONCLUSIONS: By comparing the expected genome size of the polyploid (based on summing the genome size of species identified as either a parent or most closely related to the diploid progenitors) with the observed genome size, four polyploids showed genome downsizing and five showed increases. There was no discernable pattern in the direction of genome size change with age of polyploids, although with increasing age the amount of genome size change increased. In older polyploids (approx. 4.5 million years old) the increase in genome size was associated with loss of detectable genomic in situ hybridization signal, whereas some hybridization signal was still detected in species exhibiting genome downsizing. The possible significance of these results is discussed.     

Southern Ocean deep-sea isopod species richness (Crustacea, Malacostraca): influences of depth, latitude and longitude

We examined deep-sea epibenthic sledge isopod data from the Atlantic sector of the Southern Ocean (SO) (depth range=742–5,191 m). Samples were taken during the expeditions EASIZ II (ANT XV-3) in 1998 and ANDEEP I and II (ANT XIX3/4) in 2002. A total of 471 isopod species were recorded from 28 sites. The species richness of the epibenthic sledge samples was highly variable (6–82 species). Species richness was highest at site 131-3 in 3,053 m depth in the north-eastern Weddell Sea. The highest numbers of species were sampled in the middle depth range and lower species richness was found in the shallower and deeper parts of the study area. Depth is suggested to explain isopod species richness better than both latitude and longitude. Between 58°S and 65°S, the number of species ranged from 9 to 82 (mean=35.9). Further south in the Weddell Sea, between 73°S and 74°S, species richness was lower and the number of species ranged from 6 to 35 (mean=19.2). With regard to longitude, the highest species richness (up to 82 species) was found between 50°W and 60°W in the area of the South Shetland Islands and around the Antarctic Peninsula, while numbers did not exceed 50 species in the eastern Weddell Sea. The haul length, ranging from 807 to 6,464 m, was positively correlated with depth; however, there was no linear relationship between haul length and species richness. We therefore suggest that depth was the most important factor explaining isopod species richness. However, only 28 sites were visited and the statistical power is thus limited. Sampling in the deep sea is expensive and time consuming and as yet this is the best isopod data set available from the Atlantic sector of the SO. Future expeditions are therefore important to better explain the current patterns of benthic diversity in Antarctica.     

The maize genome as a model for efficient sequence analysis of large plant genomes

The genomes of flowering plants vary in size from about 0.1 to over 100 gigabase pairs (Gbp), mostly because of polyploidy and variation in the abundance of repetitive elements in intergenic regions. High-quality sequences of the relatively small genomes of Arabidopsis (0.14 Gbp) and rice (0.4 Gbp) have now been largely completed. The sequencing of plant genomes that have a more representative size (the mean for flowering plant genomes is 5.6 Gbp) has been seen as a daunting task, partly because of their size and partly because of the numerous highly conserved repeats. Nevertheless, creative strategies and powerful new tools have been generated recently in the plant genetics community, so that sequencing large plant genomes is now a realistic possibility. Maize (2.4-2.7 Gbp) will be the first gigabase-size plant genome to be sequenced using these novel approaches. Pilot studies on maize indicate that the new gene-enrichment, gene-finishing and gene-orientation technologies are efficient, robust and comprehensive. These strategies will succeed in sequencing the gene-space of large genome plants, and in locating all of these genes and adjacent sequences on the genetic and physical maps.     

Chromosome numbers and genome size variation in Indian species of Curcuma (Zingiberaceae)

BACKGROUND AND AIMS: Genome size and chromosome numbers are important cytological characters that significantly influence various organismal traits. However, geographical representation of these data is seriously unbalanced, with tropical and subtropical regions being largely neglected. In the present study, an investigation was made of chromosomal and genome size variation in the majority of Curcuma species from the Indian subcontinent, and an assessment was made of the value of these data for taxonomic purposes. METHODS: Genome size of 161 homogeneously cultivated plant samples classified into 51 taxonomic entities was determined by propidium iodide flow cytometry. Chromosome numbers were counted in actively growing root tips using conventional rapid squash techniques. KEY RESULTS: Six different chromosome counts (2n = 22, 42, 63, >70, 77 and 105) were found, the last two representing new generic records. The 2C-values varied from 1.66 pg in C. vamana to 4.76 pg in C. oligantha, representing a 2.87-fold range. Three groups of taxa with significantly different homoploid genome sizes (Cx-values) and distinct geographical distribution were identified. Five species exhibited intraspecific variation in nuclear DNA content, reaching up to 15.1 % in cultivated C. longa. Chromosome counts and genome sizes of three Curcuma-like species (Hitchenia caulina, Kaempferia scaposa and Paracautleya bhatii) corresponded well with typical hexaploid (2n = 6x = 42) Curcuma spp. CONCLUSIONS: The basic chromosome number in the majority of Indian taxa (belonging to subgenus Curcuma) is x = 7; published counts correspond to 6x, 9x, 11x, 12x and 15x ploidy levels. Only a few species-specific C-values were found, but karyological and/or flow cytometric data may support taxonomic decisions in some species alliances with morphological similarities. Close evolutionary relationships among some cytotypes are suggested based on the similarity in homoploid genome sizes and geographical grouping. A new species combination, Curcuma scaposa (Nimmo) Skornick. & M. Sabu, comb. nov., is proposed.     

Evolution of the genome size inAkodon (Rodentia,Cricetidae)

Nuclear DNA contents were estimated by microdensitometry in five species of Akodon rodents: Arodon molinae, A. dolores, A. mollis, A. azarae, Bolomys obscurus) and in three chromosomal varieties of A. molinae (2n = 42; 2n = 43, 2n = 22). The data obtained showed that the species with the highest DNA content was B. obscurus, followed in order of decreasing genome size by A. molinae, A. mollis, A. dolores and A. azarae. In A. molinae the forms with 2n = 42 chromosomes had the lowest and the forms with 2n = 44 the highest amount of DNA, while the forms with 2n = 43 had intermediate DNA contents. The variation in DNA amount detected in A. molinae was interpreted as a phenomenon of amplification occurring in the chromosomal areas involved in the chromosomal rearrangement giving rise to the polymorphism exhibited by this species. The DNA contents of shared chromosomes (chromosomes with similar size, morphology and G banding pattern, which are found in two or more phylogenetically related species), were compared and correlated with values of total nuclear DNA. The information obtained indicates that: (a) shared chromosomes have variable amounts of DNA: (b) in a given species there is a correlation between the amount of nuclear and chromosomal DNA in most shared chromosomes (and perhaps in most of the chromosomal complement), e.g., the higher the amount of nuclear DNA, the higher the content of DNA in shared chromosomes; (c) some chromosomes may undergo processes of amplification or deletion restricted to certain regions and usually related with mechanisms of chromosomal rearrangements.(ABSTRACT TRUNCATED AT 250 WORDS)     

Complete mitochondrial genome of Acheilognathus signifer (Cypriniformes, Cyprinidae): comparison of light-strand replication origins from six Acheilognathus species

Acheilognathus signifer (Cypriniformes, Cyprinidae) is an endemic, endangered fresh water fish species in the Korean peninsula. In this study, the mitochondrial genome of A. signifer was completely sequenced, which is 16,566 bp in length. The characteristics of the complete mitochondrial genome were described in detail.     

Benthic isopods (Crustacea,Malacostraca) from the Ross Sea,Antarctica: species checklist and their zoogeography in the Southern Ocean

In this study isopod species of the Ross Sea were investigated. Literature until May 2008 was checked to provide an overview of all known and described species in the Ross Sea. This species checklist was then enlarged through material of the 19th Italica expedition in 2004. During this expedition for the first time a small mesh net (500 μm) was used. Nine thousand four hundred and eighty one isopod specimens were collected during this expedition. Through this material the number of isopod species in the Ross Sea increased from 42 to 117 species, which belong to 20 families and 49 genera. Fifty-six percentage of the isopods species collected during the Italica expedition are new to science. The zoogeography of the 117 species was investigated. A non-transformed binary presence-absence data matrix was constructed using the Bray–Curtis coefficient. The results were displayed in a cluster analysis and by nonmetric multidimensional scaling (MDS). This paper gives a first insight into the occurrence and distribution of the isopod species of the Ross Sea.     

Olfactory projection neuron pathways in two species of marine Isopoda (Peracarida,Malacostraca, Crustacea)

The neuroanatomy of the olfactory pathway has been intensely studied in many representatives of Malacostraca. Nevertheless, the knowledge about bilateral olfactory integration pathways is mainly based on Decapoda. Here, we investigated the olfactory projection neuron pathway of two marine isopod species, Saduria entomon and Idotea emarginata, by lipophilic dye injections into the olfactory neuropil. We show that both arms of the olfactory globular tract form a chiasm in the center of the brain, as known from several other crustaceans. Furthermore, the olfactory projection neurons innervate both the medulla terminalis and the hemiellipsoid body of the ipsi- and the contralateral hemisphere. Both protocerebral neuropils are innervated to a comparable extent. This is reminiscent of the situation in the basal decapod taxon Dendrobranchiata. Thus, we propose that an innervation by the olfactory globular tract of both the medulla terminalis and the hemiellipsoid body is characteristic of the decapod ground pattern, but also of the ground pattern of Caridoida.     

The considerable genome size variation of Hordeum species (poaceae) is linked to phylogeny, life form, ecology, and speciation rates

Genome size variation in plants is thought to be correlatedwith cytological, physiological, or ecological characters. However,conclusions drawn in several studies were often contradictory.To analyze nuclear genome size evolution in a phylogenetic framework,DNA contents of 134 accessions, representing all but one speciesof the barley genus Hordeum L., were measured by flow cytometry.The 2C DNA contents were in a range from 6.85 to 10.67 pg indiploids (2n = 14) and reached up to 29.85 pg in hexaploid species(2n = 42). The smallest genomes were found in taxa from theNew World, which became secondarily annual, whereas the largestdiploid genomes occur in Eurasian annuals. Genome sizes of polyploidtaxa equaled mostly the added sizes of their proposed progenitorsor were slightly (1% to 5%) smaller. The analysis of ancestralgenome sizes on the base of the phylogeny of the genus revealedlineages with decreasing and with increasing genome sizes. Correlationsof intraspecific genome size variation with the length of vegetationperiod were found in H. marinum populations from Western Europebut were not significant within two species from South America.On a higher taxonomical level (i.e., for species groups or theentire genus), environmental correlations were absent. Thiscould mostly be attributed to the superimposition of life-formchanges and phylogenetic constraints, which conceal ecogeographicalcorrelations.     

Cytotype diversity and genome size variation in eastern Asian polyploid Cardamine (Brassicaceae) species

Background and Aims

Intraspecific ploidy-level variation is an important aspect of a species'' genetic make-up, which may lend insight into its evolutionary history and future potential. The present study explores this phenomenon in a group of eastern Asian Cardamine species.

Methods

Plant material was sampled from 59 localities in Japan and Korea, which were used in karyological (chromosome counting) and flow cytometric analyses. The absolute nuclear DNA content (in pg) was measured using propidium iodide and the relative nuclear DNA content (in arbitrary units) was measured using 4,6-diamidino-2-phenylindole fluorochrome.

Key Results

Substantial cytotype diversity was found, with strikingly different distribution patterns between the species. Two cytotypes were found in C. torrentis sensu lato (4x and 8x, in C. valida and C. torrentis sensu stricto, respectively), which displays a north–south geographical pattern in Japan. Hypotheses regarding their origin and colonization history in the Japanese archipelago are discussed. In Korean C. amaraeiformis, only tetraploids were found, and these populations may in fact belong to C. valida. C. yezoensis was found to harbour as many as six cytotypes in Japan, ranging from hexa- to dodecaploids. Ploidy levels do not show any obvious geographical pattern; populations with mixed ploidy levels, containing two to four cytotypes, are frequently observed throughout the range. C. schinziana, an endemic of Hokkaido, has hexa- and octoploid populations. Previous chromosome records are also revised, showing that they are largely based on misidentified material or misinterpreted names.

Conclusions

Sampling of multiple populations and utilization of the efficient flow cytometric approach allowed the detection of large-scale variation in ploidy levels and genome size variation attributable to aneuploidy. These data will be essential in further phylogenetic and evolutionary studies.     

The organization of the olfactory lobes in Euphausiacea and Mysidacea (Crustacea,Malacostraca)

Summary The structural organization of the olfactory lobes in representatives of euphausiid and mysid crustaceans was investigated and compared, also with these structures described in other crustaceans and in insects. In the investigated euphasiid and mysid species, the olfactory-globular tract and the position of cell clusters associated with the olfactory lobes show a similar arrangement. This arrangement is in agreement with that described in decapod crustaceans. The olfactory lobe neuropil in representatives of both taxa shows glomerular arrangement. These glomeruli are partly enclosed in a glial wrapping, and they represent the only site where synaptic contacts are established within the olfactory lobes. This glomerular arrangement appears similar to that described in the antennal lobe of insects, but differs from the columnar arrangement described in decapod crustaceans. Furthermore, about 15–20 FMRFamide-like immunoreactive globuli cells were labeled and they occupy a similar position in the investigated species. Neurites from these cells terminate only in the olfactory lobe glomeruli, and they are therefore regarded as intrinsic interneurons. The absence of serotonin-like immunoreactivity in the olfactory lobes is a feature only ascribed to the euphausiids and mysids. A specific neuropil area is present in male mysids, and it occupy a position forward of the olfactory lobe. The male-specific neuropil in mysids and the macro-glomerular in insects complex are interpreted as analogous structures.     

The complete mitochondrial genome sequence of Euphausia pacifica (Malacostraca: Euphausiacea) reveals a novel gene order and unusual tandem repeats

Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. Euphausia pacifica (Malacostraca: Euphausiacea) is one of the most important and dominant crustaceans in the North Pacific Ocean. In this paper, we described the gene content, organization, and codon usage of the E. pacifica mitochondrial genome. The mitochondrial genome of E. pacifica is 16 898 bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Translocation of three transfer RNAs (trnL(1), trnL(2), and trnW) was found in the E. pacifica mitochondrial genome when comparing with the pancrustacean ground pattern. The rate of K(a)/K(s) in 13 protein-coding genes among three krill is much less than 1, which indicates a strong purifying selection within this group. The largest noncoding region in the E. pacifica mitochondrial genome contains one section with tandem repeats (4.7 x 154 bp), which are the largest tandem repeats found in malacostracan mitochondrial genomes so far. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, Brachyura, and Euphausiacea. The Bayesian analysis of nucleotide and amino acid datasets strongly supports the close relationship between Euphausiacea and Decapoda, which confirms traditional findings. The maximum likelihood analysis based on amino acid data strongly supports the close relationship between Euphausiacea and Penaeidae, which destroys the monophyly of Decapoda.