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.

Defining the orientation of the tandem fusions that occurred during the evolution of Indian muntjac chromosomes by BAC mapping

The Indian muntjac (Muntiacus muntjak vaginalis) has a karyotype of 2n=6 in the female and 7 in the male, the karyotypic evolution of which through extensive tandem fusions and several centric fusions has been well-documented by recent molecular cytogenetic studies. In an attempt to define the fusion orientations of conserved chromosomal segments and the molecular mechanisms underlying the tandem fusions, we have constructed a highly redundant (more than six times of whole genome coverage) bacterial artificial chromosome (BAC) library of Indian muntjac. The BAC library contains 124,800 clones with no chromosome bias and has an average insert DNA size of 120 kb. A total of 223 clones have been mapped by fluorescent in situ hybridization onto the chromosomes of both Indian muntjac and Chinese muntjac and a high-resolution comparative map has been established. Our mapping results demonstrate that all tandem fusions that occurred during the evolution of Indian muntjac karyotype from the acrocentric 2n=70 hypothetical ancestral karyotype are centromere-telomere (head-tail) fusions.

Construction, characterization and chromosomal mapping of bacterial artificial chromosome (BAC) library of Yunnan snub-nosed monkey (Rhinopithecus bieti)

We constructed a high redundancy bacterial artificial chromosome library of a seriously endangered Old World Monkey, the Yunnan snub-nosed monkey (Rhinopithecus bieti) from China. This library contains a total of 136 320 BAC clones. The average insert size of BAC clones was estimated to be 148 kb. The percentage of small inserts (50-100 kb) is 2.74%, and only 2.67% non-recombinant clones were observed. Assuming a similar genome size with closely related primate species, the Yunnan snub-nosed monkey BAC library has at least six times the genome coverage. By end sequencing of randomly selected BAC clones, we generated 201 sequence tags for the library. A total of 139 end-sequenced BAC clones were mapped onto the chromosomes of Yunnan snub-nosed monkey by fluorescence in-situ hybridization, demonstrating a high degree of synteny conservation between humans and Yunnan snub-nosed monkeys. Blast search against human genome showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the BAC library. This library and the mapped BAC clones will serve as a valuable resource in comparative genomics studies and large-scale genome sequencing of nonhuman primates. The DNA sequence data reported in this paper were deposited in GenBank and assigned the accession number CG891489-CG891703.

Offshore geology of Pakistan and non-living resource prospects

Offshore geology of Pakistan is characterized by active and passive continental margins. These continental margins show very unique features such as an active Makran subduction zone in the west and the Indus delta and a submarine fan in the east. The geology of these features of Pakistan EEZ is inadequately known. This is a major obstacle in exploring mineral resources. Detailed study of coastal and shelf geology is needed for better understanding of the geology of the area and comprehensive evolution of its non-living resource potential. An understanding of the geological events including tectonic movements, sedimentation processes and geochemical history that comprise the geological history is very important to help in identification and estimation of resources. In Pakistan EEZ applying the current technology and undertaking research work to understand the seafloor features and mineral deposits associated with it will be very fruitful.

Status and distribution pattern of black crested gibbon (Nomaseas concolor jingdongensis) in Wuliang Mountains, Yunnan, China: implication for conservation

The western black crested gibbon (Nomascus concolor), or black gibbon, one of the lesser apes (Hylobatidae), is mainly distributed in Yunnan, China. Of the four recognized subspecies, N. c. jingdongensis is endemic to the Wuliang Mountain, central Yunnan,

Genetic diversity of the black crested gibbon (Nomascus concolor) from the Wuliang Mountains of Yunnan, China: preliminary results.

The authors thank Peng Shi, Scott Groom, and two anonymous reviewers for helpful comments. This work was supported by grants from the National Basic Research Program of China (973 Program, 2007CB411600), National Natural Science Foundation of China, and Bureau of Science and Technology of Yunnan Province (to Y.-P.Z.).

BAC及其转基因研究进展

本文综述了细菌人工染色体 (BacterialArtificialChromsomes ,BAC)的构建、物理图谱制作方法及其靶位精细操作策略的研究进展。同时 ,简要介绍了BAC转基因在基因功能以及基因表达与调控研究中的应用

Construction and characterization of a Lipotes vexillifer genomic DNA BAC library

We constructed a genomic DNA library for Lipotes vexillifer (L. vexillifer), the Baiji or Yangtze River dolphin, one of the most endangered mammals in the world. The library consists of 149,000 BAC clones, with an average insert size of 83 kb, representing approximately 3.4 haploid genome equivalents. PCR amplification of four known L. vexillifer genes yielded two to four positive clones each. To demonstrate the utility of this library, we isolated and sequenced the L. vexillifer alpha lactalbumin gene, which is a gene specific to mammals and one which has been widely used as molecular tool in phylogenetic analysis. We also end-sequenced 20 randomly selected clones, resulting in the identification of at least five new L. vexilliter genes, five SSR loci, and one SINE locus. These results suggest that this library is a valuable resource for candidate gene cloning, physical mapping, and genome sequencing of this important and threatened species.

Cymbellaceae and Gomphonemataceae (Bacillariophyta) from the Hengduan Mountains region (southwestern China)

We present a species list of the Gomphonemataceae and Cymbellaceae occurring in the Hengduan Mountains re-ion. These two families were found to be presented in the area by 117 species, varieties and forms belonging to four genera (Amphora, Cymbella, Didymosphenia and Gomphonema). Size, striae density, habitat and distribution in China are given for each taxon. The common taxa were Cymbella aequalis var. piscicultis. C. affinis, C. cesatii, C. cistula var. gibbosa, C. delicatula. C. gracilis, C. hustedtii, C. minuta f. latens, C. minita var. silesiaca, C. naviculiformis, C. parva. C. turgidida, Gomphonema acuminatum var. acuminatum, G. gracile, G. intricatum, G. olivaceum. G. parvulum and G. truncatum var. capitatum. Some morphological features of Cymbella cistula var. capitata, Cymbella sinica var. miyiensis, Gomphonema hedinii and G. kaznakowii were found to differ from previously published descriptions. Taxa typical of high latitude climates encountered during the present study were Cymbella affinis, C. alpina, C. cistula var. cistida, C. delicatula. C. naviculiformis. Didymosphenia geminata, Gomphonema acuminatum var. pusillum, G. constrictum var. capitatum f. turgidum, G. kaznakowii, G. olivaceum, G. subtile var. subtile, G. tergestinum and G. ventricosum.