Electrophoresis karyotype and chromosome-length polymorphism of Histoplasma capsulatum clinical isolates from Latin America

Intact chromosomes of 19 clinical isolates of Histoplasma capsulatum recently obtained in Argentina, Mexico and Guatemala and the laboratory reference strain G186B from Panama were analyzed using pulsed-field gel electrophoresis. Chromosomal banding patterns of the human isolates revealed 5-7 bands, ranging from 1.3 to 10 Mbp in size. Strain G186B showed five bands of approximately 1.1, 2.8, 3.3, 5.4 and 9.7 Mbp. Thirteen different electrokaryotypes were identified, indicating that the genome of H. capsulatum varies widely in nature, as observed previously in laboratory strains. No definite association was found between electrokaryotype and geographical or clinical source.     

Variation in green hydra. A description of three cloned strains of Hydra viridissima Pallas 1766 (Gnidaria: Hydrozoa) isolated from a single site

Three different strains of green hydra were isolated in successive years from a single site in the River Frome, Bristol, England. The strains resembled each other in important taxonomic characters, and were identified as Hydra viridissima by their possession of smooth-walled single-chambered embryothecas, but were smaller, possessed smaller nematocysts and produced fewer eggs per individual than the Western European holotype. It is possible that English green hydra represent a geographical subspecies.
The three strains could be distinguished from each other by differences in rates of bud production and in characters associated with their symbiotic algae. These differences are considered varietal, and it is suggested that H. viridissima is a polytypic species. The possible origins of these variations and their significance is discussed.     

Variation in genome size of argasid and ixodid ticks

The suborder Ixodida includes many tick species of medical and veterinary importance, but little is known about the genomic characteristics of these ticks. We report the first study to determine genome size in two species of Argasidae (soft ticks) and seven species of Ixodidae (hard ticks) using flow cytometry analysis of fluorescent stained nuclei. Our results indicate a large haploid genome size (1C>1000 Mbp) for all Ixodida with a mean of 1281 Mbp (1.31+/-0.07 pg) for the Argasidae and 2671 Mbp (2.73+/-0.04 pg) for the Ixodidae. The haploid genome size of Ixodes scapularis was determined to be 2262 Mbp. We observed inter- and intra-familial variation in genome size as well as variation between strains of the same species. We explore the implications of these results for tick genome evolution and tick genomics research.     

Electrophoretic karyotype ofTrichoderma reesei

Summary Pulsed field electrophoresis was used to separate the intact chromosomes of the fungi imperfectiTrichoderma reesei for which no previous karyotype has been available.T. reesei was shown to have six chromosomes with molecular weights ranging from 3.3 to 11.9 megabasepairs (Mbp). The genome size was estimated to be 38 Mbp, indicating thatTrichoderma has a genome larger thanAspergillus nidulans (31 Mbp) but smaller thanNeurospora crassa (47 Mbp).     

Three new genera and five new species of misophrioid copepods (Crustacea) from anchialine caves on Indo-West Pacific and North Atlantic Islands

Hydra lirosoma sp. nov. is a small, hermaphroditic species possessing broad holotrichous isorhiza nematocysts. The spherical embryo and cobbled embryotheca set it apart from similar species. Hydras with broad holotrichous isorhizas form a distinct cluster of species, but one which was not explicitly represented in the three genera ( Pelmatohydra, Hydra and Chlorohydra ) recognized by Schulze (1917, Archiv für Biontologie, 4(2 ): 29). Schulze failed to recognize this group because of the small number of species known at that time. The hydras that are known now fit naturally into four clusters of species termed, in this paper, the oligactis, vulgaris, viridissima, and braueri groups.     

Electrophoresis karyotype and chromosome-length polymorphism of Histoplasma capsulatum clinical isolates from Latin America

Intact chromosomes of 19 clinical isolates of Histoplasma capsulatum recently obtained in Argentina, Mexico and Guatemala and the laboratory reference strain G186B from Panama were analyzed using pulsed-field gel electrophoresis. Chromosomal banding patterns of the human isolates revealed 5–7 bands, ranging from 1.3 to 10 Mbp in size. Strain G186B showed five bands of approximately 1.1, 2.8, 3.3, 5.4 and 9.7 Mbp. Thirteen different electrokaryotypes were identified, indicating that the genome of H. capsulatum varies widely in nature, as observed previously in laboratory strains. No definite association was found between electrokaryotype and geographical or clinical source.     

Chromosome identification for the carnivorous plant <Emphasis Type="Italic">Genlisea margaretae</Emphasis>

Genlisea margaretae, subgenus Genlisea, section Recurvatae (184 Mbp/1C), belongs to a plant genus with a 25-fold genome size difference and an extreme genome plasticity. Its 19 chromosome pairs could be distinguished individually by an approach combining optimized probe pooling and consecutive rounds of multicolor fluorescence in situ hybridization (mcFISH) with bacterial artificial chromosomes (BACs) selected for repeat-free inserts. Fifty-one BACs were assigned to 18 chromosome pairs. They provide a tool for future assignment of genomic sequence contigs to distinct chromosomes as well as for identification of homeologous chromosome regions in other species of the carnivorous Lentibulariaceae family, and potentially of chromosome rearrangements, in cases where more than one BAC per chromosome pair was identified.     

海三棱藨草及其近缘种基因组大小的测定

基因组大小是物种基因组的重要特征,通常用DNA C值来衡量,能够用于快速判断基因组倍性,并为分类学与进化生物学提供重要依据。海三棱藨草(Scirpus mariqueter)是长江口和杭州湾具有重要生态意义的标志性物种,被认为是扁秆藨草(S. planiculmis)和藨草(S. triqueter)的杂交种,因染色体小而难以准确确定倍性。近年来,部分研究者指出该物种的分类和命名存在疑点。该研究通过基因组Survey分析检测海三棱藨草样本CJ1的基因组特征,测序深度约为120 ×,并以绿豆(Vigna radiata)为参考标准,利用流式细胞术测定了海三棱藨草及其同域近缘种扁秆藨草和藨草以及海三棱藨草和扁秆藨草的杂交F1共13个样本的DNA C值和相对倍性。结果表明:(1)基因组Survey分析测得CJ1的基因组大小为244.12 Mbp,杂合率为0.68%,重复序列比例为42.38%,GC含量为37.25%。(2)流式细胞术测得来自不同区域的海三棱藨草各样本的基因组倍性相同,1C值在234.87 ～ 242.5 Mbp之间,其中CJ1的基因组大小与基因组Survey检测结果高度一致。(3)扁秆藨草的1C值在251.77 ～ 264.13 Mbp之间,藨草1C值为537.33 Mbp。根据上述基因组大小,认为海三棱藨草不可能是这两者的杂交种。该研究补充了海三棱藨草及其近缘种的基因组特征,为后续全基因组测序奠定基础,同时也否定了海三棱藨草起源于扁杆藨草和藨草杂交的假说。     

The expected nucleotide sequence of the human genome should be shortened about twofold

The sizes of nucleotide sequences of chromosomes 21 and 22 of the human genome established in three independent laboratories were compared with the sizes expected from the accurately determined contribution of these chromosomes to the genome mass. It was found that the expected haploid mass of the genome is about twofold smaller than the lowest of the figures published. This strongly contradicts the current notions about the genome size. With the bineme model of chromosome, the expected overall length of the human genome is close to 2100 Mbp and the haploid mass is close to 4200 Mbp. According to the calculations performed, the bineme chromosome structure enhances the reliability of the genome about 1.6 x 10(8)-fold (the computations are given in the paper).     

Development and population growth of Hydra viridissima Pallas, 1766 (Cnidaria, Hydrozoa) in the laboratory

Hydras, the most representative freshwater Cnidaria, are of common occurrence in bodies of water in every continent except Antarctica. This study was planned with the aim of maintaining a population of Hydra viridissima in laboratory culture to enable the determination of the individual and population growth-rates of this species, as well as its population doubling time and generation time, with a view to employing these common animals as test-organisms in ecotoxicological assays. The organisms were maintained in reconstituted water at 20 +/- 2 degrees C, illuminated at 800 lux with a photoperiod of 12 hours light: 12 hours dark, and were fed on neonates of the cladoceran Ceriodaphnia silvestrii (3 or 4 neonates per hydra, 3 times a week). The individual growth-rate (k) of the species was 0.43, the maximum length of the column 2.53 mm and the generation time 6.6 +/- 1.5 days on average. The hydra population showed an intrinsic growth-rate (r) of 0.0468, according to the fitted curve, and a doubling time of 14.8 +/- 2.63 days. Hydra viridissima is easy to grow in the laboratory and performs well in the conditions used in this study. It is thus a promising candidate test-organism for ecotoxicological studies.     

Evolutionary analysis identifies multiple genome expansions and contractions in Sepsidae (Diptera) and suggests targets for future genomic research

We here argue that data from comparative studies of genome size and karyotypes provide important information for planning comparative research on genome evolution. We document for 39 species of sepsids that there is a four‐fold difference in genome size (151–618 Mbp). Mapping genome sizes onto a phylogenetic hypothesis identifies that this range is the result of five genome expansions and four genome contractions that we here define as changes in genome size of more than 50 Mbp. We then generate karyotype data for 10 species and find no changes in chromosome number. The study reveals that the “Oriental” clade of sepsids is a promising system for studying genome evolution because it has experienced three genome expansion events. These events can be compared with an expansion in the “Neotropical” clade in order to reveal the mechanisms that underlie genome expansion in Sepsidae. A review of the literature on genome sizes and karyotypes reveals that they have been poorly documented in Metazoa. This means that researchers interested in the evolution of genome expansions and contractions are currently not being able to identify appropriate target taxa for genome sequencing. We thus argue for more comparative research on genome sizes and karyotypes and point out that historically species were chosen for genome sequencing for reasons not related to genome evolution (e.g. small genome size, model species status, phylogenetic position, interesting phenotypes). We believe that it is now time to use a more genome‐centric selection criterion, where species for whole genome sequencing are selected based on their importance for understanding genome evolution.     

Investigation of the physiological properties and synthesis of PUFAs from Thraustochytrids and its electrophoretic karyotypes

Physiological properties of organism, such as the number of chromosomes, genome size, fatty acid profile and the activities of desaturases and elongases were investigated for four differentThraustochytrium species. The investigation revealed thatThraustochytrium aureum could synthesize a significant level of polyunsaturated fatty acids (PUFAs), particularly docosa-hexaenoic acid (DHA), when compared to the other threeThraustochytrium species tested. A higher level of saturated fatty acids was observed byT. striatum followed byThraustochytrium sp. ATCC 26185. The PUFA accumulation rate was higher in the n-3 than in the n-6 pathway. A comparison of the activities for these desaturases and elongases of the four different species were also studied. Further, the electrophoretic karyotypes of Thraustochytrids were separated by pulsed-field gel electrophoresis (PFGE). The separation condition of PFGE was developed to obtain the different chromosomes from the variousThraustochytrium species. The number of chromosomes inT. aureum, T. striatum, Thraustochytrium sp. ATCC 20891 andThraustochytrium sp. ATCC 26185 were 13, 17, 10. 8, and the whole genome size of those species were estimated to be 12.9, 11.7, 11.3 and 9.93 Mbp, respectively.     

Genomic characterization of Neoparamoeba pemaquidensis (Amoebozoa) and its kinetoplastid endosymbiont

We have performed a genomic characterization of a kinetoplastid protist living within the amoebozoan Neoparamoeba pemaquidensis. The genome of this "Ichthyobodo-related organism" was found to be unexpectedly large, with at least 11 chromosomes between 1.0 and 3.5 Mbp and a total genome size of at least 25 Mbp.     

Flow cytometry reveals that the rust fungus,Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported—2489 Mbp

Among the Eukaryotes, Fungi have relatively small genomes (average of 44.2 Mbp across 1850 species). The order Pucciniales (Basidiomycota) has the largest average genome size among fungi (305 Mbp), and includes the two largest fungal genomes reported so far (Puccinia chrysanthemi and Gymnosporangium confusum, with 806.5 and 893.2 Mbp, respectively). In this work, flow cytometry was employed to determine the genome size of the Bidens pilosa rust pathogen, Uromyces bidentis. The results obtained revealed that U. bidentis presents a surprisingly large haploid genome size of 2489 Mbp. This value is almost three times larger than the previous largest fungal genome reported and over 50 times larger than the average fungal genome size. Microscopic examination of U. bidentis nuclei also showed that they are not as different in size from the B. pilosa nuclei when compared with the differences between other rusts and their host plants. This result further reinforces the position of the Pucciniales as the fungal group with the largest genomes, prompting studies addressing the role of repetitive elements and polyploidy in the evolution, pathological specialization and diversity of fungal species.     

REPLICATION OF CHLORELLA VIRUS PBCV-1 AND HOST KARYOTYPE DETERMINATION STUDIED WITH PULSED-FIELD GEL ELECTROPHORESIS1

We demonstrated the time-course of DNA replication of the 330-kbp Chlorella virus PBCV-1 by pulsed-field gel electrophoresis. Viral DNA replication began between 90 and 120 min postinfeclion in cell samples produced without first removing cell walls. The host nuclear genome was degraded beginning almost immediately after infection, but some host DNA remained even after 360 min postinfection. The karyotype of the host alga consisted of nine resolvable bands that we presume to represent 13 chromosomes based on band intensity. The chromosomes ranged in size from 1.1 to 6.5 megabase pairs (Mbp). A summation of the sizes of the bands predicts a genome size of 39–45 Mbp of DNA.     

Value of the Hydra model system for studying symbiosis

Green Hydra is used as a classical example for explaining symbiosis in schools as well as an excellent research model. Indeed the cosmopolitan green Hydra (Hydra viridissima) provides a potent experimental framework to investigate the symbiotic relationships between a complex eumetazoan organism and a unicellular photoautotrophic green algae named Chlorella. Chlorella populates a single somatic cell type, the gastrodermal myoepithelial cells (also named digestive cells) and the oocyte at the time of sexual reproduction. This symbiotic relationship is stable, well-determined and provides biological advantages to the algal symbionts, but also to green Hydra over the related non-symbiotic Hydra i.e. brown hydra. These advantages likely result from the bidirectional flow of metabolites between the host and the symbiont. Moreover genetic flow through horizontal gene transfer might also participate in the establishment of these selective advantages. However, these relationships between the host and the symbionts may be more complex. Thus, Jolley and Smith showed that the reproductive rate of the algae increases dramatically outside of Hydra cells, although this endosymbiont isolation is debated. Recently it became possible to keep different species of endosymbionts isolated from green Hydra in stable and permanent cultures and compare them to free-living Chlorella species. Future studies testing metabolic relationships and genetic flow should help elucidate the mechanisms that support the maintenance of symbiosis in a eumetazoan species.     

强壮水螅的特征及其与寡水螅的种间差别问题

一种广泛分布于黑龙江省的大型具柄水螅被暂定为强壮水螅Hydra robusta(IT(?) 1947)。这一中国品系与IT(?)(1947)在日本报告的新种主要特征相同,包括具有精巢乳头。只是精巢乳头不稳定。在实验室条件下第一次有性生殖时每个雄体都发生精巢乳头,但第二次有性生殖时,同一群的后代可全部失去精巢乳头。这是介于强壮水螅与寡水螅Hydra oligactis Pallas(1766)之间的中间性状。从而导致作者做出结论,认为过去其他学者所主张的,以精巢乳头的有无做为鉴别特征来区分强壮水螅和寡水螅是不可靠的。因此,本文又检验了此种水螅的体细胞染色体,证明2n=30,其中第二对染色体上有明显近中位置的次缢痕,最小染色体的长度为最大染色体长度的二分之一以上。这些可做为此种水蝗的鉴别特征。对Niiyama(1944)和Datta(1970)在寡水螅上所做的染色体研究也做了比较及讨论。