Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype

The Afrotheria, a supraordinal grouping of mammals whose radiation is rooted in Africa, is strongly supported by DNA sequence data but not by their disparate anatomical features. We have used flow-sorted human, aardvark, and African elephant chromosome painting probes and applied reciprocal painting schemes to representatives of two of the Afrotherian orders, the Tubulidentata (aardvark) and Proboscidea (elephants), in an attempt to shed additional light on the evolutionary affinities of this enigmatic group of mammals. Although we have not yet found any unique cytogenetic signatures that support the monophyly of the Afrotheria, embedded within the aardvark genome we find the strongest evidence yet of a mammalian ancestral karyotype comprising 2n = 44. This karyotype includes nine chromosomes that show complete conserved synteny to those of man, six that show conservation as single chromosome arms or blocks in the human karyotype but that occur on two different chromosomes in the ancestor, and seven neighbor-joining combinations (i.e., the synteny is maintained in the majority of species of the orders studied so far, but which corresponds to two chromosomes in humans). The comparative chromosome maps presented between human and these Afrotherian species provide further insight into mammalian genome organization and comparative genomic data for the Afrotheria, one of the four major evolutionary clades postulated for the Eutheria.

Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora

Cross-species painting (fluorescence in situ hybridization) with 23 human (Homo sapiens (HSA)) chromosome-specific painting probes (HSA 1-22 and the X) was used to delimit regions of homology on the chromosomes of the golden mole (Ghrysochloris asiaticus) and elephant-shrew (Elephantulus rupestris). A cladistic interpretation of our data provides evidence of two unique associations, HSA 1/19p and 5/21/3, that support Afrotheria. The recognition of HSA 5/3/21 expands on the 3/21 synteny originally designated as an ancestral state for all eutherians. We have identified one adjacent segment combination (HSA2/8p/4) that is supportive of Afroinsectiphillia (aardvark, golden mole, elephant-shrew). Two segmental combinations (HSA 10q/17 and HSA 3/20) unite the aardvark and elephant-shrews as sister taxa. The finding that segmental syntenies in evolutionarily distant taxa can improve phylogenetic resolution suggests that they may be useful for testing sequence-based phylogenies of the early eutherian mammals. They may even suggest clades that sequence trees are not recovering with any consistency and thus encourage the search for additional rare genomic changes among afrotheres.

Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations

The red panda (Ailurus fulgens) is one of the flagship species in worldwide conservation and is of special interest in evolutionary studies due to its taxonomic uniqueness. We sequenced a 236-bp fragment of the mitochondrial D-loop region in a sample of 5

Construction of a BAC library for Chinese amphioxus Branchiostoma belcheri and identification of clones containing Amphi-pax genes

Amphioxus is a crucial organism for the study of vertebrate evolution. Although a genomic BAC library of Branchiostoma floridae has been constructed, we report here another BAC library construction of its distant relative species Branchiostoma belcheri. The amphioxus BAC library established in present study consists of 45,312 clones arrayed in one hundred and eighteen 384-well plates. The average insert fragment size was 120 kb estimated by Pulsed Field Gel Electrophoresis (PFGE) analysis of 318 randomly selected clones. The representation of the library is about 12 equivalent to the genome, allowing a 99.9995% probability of recovering any specific sequence of interest. We further screened the library with 4 single copied Amphi-Pax genes and identified total of 26 positive clones with average of 6.5 clones for each gene. The result indicates this library is well suited for many applications and should also serve as a useful complemental resource for the scientific community.

Mitochondrial DNA hypervariable region-1 sequence variation and phylogeny of the concolor gibbons, Nomascus

The still little known concolor gibbons are represented by 14 taxa (five species, nine subspecies) distributed parapatrically in China, Myanmar, Vietnam, Laos and Cambodia. To set the stage for a phylogeographic study of the genus we examined DNA sequence

CpG island density and its correlations with genomic features in mammalian genomes

Background: CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one geno

Bacillus pallidus sp nov., isolated from forest soil

A Gram-positive bacterium, designated strain CW 7(T), was isolated from forest soil in Anhui Province, south-east China. Cells were strictly aerobic, motile with peritrichous flagella and rod-shaped. The strain grew optimally at 30-37 degrees C and pH 7.0-8.0. The major fatty acids of strain CW 7(T) were anteiso-C-15:0, iso-C-15:0 and anteiso-C-17:0. The predominant menaquinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G + C content of the genomic DNA was 42.3 mol%. Phylogenetic analysis indicated that strain CW 7(T) belonged to a monophyletic cluster within the genus Bacillus and showed 16S rRNA gene sequence similarities of less than 96.5% to recognized species of the genus Bacillus. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic and phylogenetic analyses, showed that strain CW 7(T) represents a novel species of the genus Bacillus, for which the name Bacillus pallidus sp. nov. is proposed. The type strain is CW 7(T) (=KCTC 13200(T)=CCTCC AB 207188(T)=LMG 24451(T)).

Pseudomonas duriflava sp nov., isolated from a desert soil

A Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain HR2(T) was isolated from a soil sample from the Talklimaken Desert in Xinjiang Province, China. Strain HR2(T) grew optimally at pH 7.0-8.0 and 30-37 degrees C in the presence of 0-1% (w/v) NaCl. An analysis of 16S rRNA gene sequences revealed that strain HR2(T) fell within the radiation of the genus Pseudomonas, the highest level of similarity being found with respect to Pseudomonas luteola IAM 13000(T) (97.5%); the levels of sequence similarity with respect to other recognized Pseudomonas species were < 96.4%. DNA-DNA hybridization showed that the genetic relatedness between strain HR2(T) and P. luteola IAM 13000(T) was 53.2%. The G + C content of the genomic DNA of strain HR2(T) was 55.2 mol%. The major fatty acids were 18: 1, summed feature 3 and 16:0. The hydroxylated fatty acids 10:0 3-OH, 12:0 3-OH and 12:0 2-OH were also present. The data obtained in this polyphasic study indicated that this isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas duriflava sp. nov. is proposed, The type strain is HR2(T) (=KCTC 221129(T) =CGMCC 1.6858(T)).

Molecular Cloning and Sequence Analysis of Two cDNAs Encoding Metalloproteinase2disintegrin from Trimeresurus jerdonii

　从菜花烙铁头蛇的毒腺中,利用RT2PCR 进行体外扩增,克隆到2 个金属蛋白酶2去整合素基 因,命名为TJM21、TJM22. TJM21 cDNA 全长为1 528 bp ,编码481 个氨基酸;TJM22 cDNA 全长为1 578 bp ,编码484 个氨基酸. TJM21 和TJM22 都属于Ⅱ型蛇毒金属蛋白酶,由信号肽、前肽、金属蛋白酶、 间隔肽和去整合素5 部分组成. Ⅱ型蛇毒金属蛋白酶氨基酸序列的比较及进化分析显示,它可进一 步分为两类,一类包括大多数Ⅱ型蛇毒金属蛋白酶(其中含有TJM21) ,而TJM22 和agkistin 则组成了 另一类. 并且TJM22 和agkistin 的第407 位和第426 位残基都是半胱氨酸,而在其它Ⅱ型金属蛋白酶 的相应位置,407 位是丝氨酸,426 位则缺失. TJM22 和agkistin 均有可与整合素α2 Ⅰ区域特异性结合 的片段QPNRKRHDNAQ(残基276～284) ,这个片段在其它Ⅱ型金属蛋白酶中并没有发现. 因此推 断, TJM22 和agkistin 可能属于一类新型的Ⅱ型蛇毒金属蛋白酶.

DIFFERENT RATES OF MITOCHONDRIAL-DNA SEQUENCE EVOLUTION IN KIRK DIK-DIK (MADOQUA-KIRKII) POPULATIONS

We have investigated evolutionary rates of the mitochondrial genome among individuals of Madoqua kirkii using the relative rate test. Our results demonstrate that individuals of two chromosome races, East African cytotype A and Southwest African cytotype D, evolve about 2.3 times faster than East African cytotype B. Cytogenetic changes, DNA repair efficiency, mutagens, and more likely, hitherto unrecognized factors will account for the rate difference we have observed. Our results suggest additional caution when using molecular clocks in the estimation of divergence time, even within lineages of closely related taxa. Rate heterogeneity in microevolutionary timescales represents a potentially important aspect of basic evolutionary processes and may provide additional insights into factors which affect genome evolution. (C) 1995 Academic Press, Inc.