Umbilical cord blood (UCB) transplant is a therapeutic option for both pediatric and adult patients with a variety of hematologic diseases such as several types of blood cancers, myeloproliferative disorders, genetic diseases, and metabolic disorders. However, the level of cellular heterogeneity and diversity of nucleated cells in the UCB has not yet been assessed in an unbiased and systemic fashion. In the current study, nucleated cells from UCB were subjected to single-cell RNA sequencing, a technology enabled simultaneous profiling of the gene expression signatures of thousands of cells, generating rich resources for further functional studies. Here, we report the transcriptome of 17,637 UCB cells, covering twelve major cell types. Many of these cell types are comprised of distinct subpopulations. Pseudotemporal ordering of nucleated red blood cells (NRBC) identifies wave-like activation and suppression of transcription regulators, leading to a polarized cellular state, which may reflect NRBC maturation. Progenitor cells in UCB also consist two subpopulations with divergent transcription programs activated, leading to specific cell-fate commitment. Detailed profiling of cytotoxic cell populations unveiled granzymes B and K signatures in NK and NKT cell types in UCB. Collectively, we provide this comprehensive single-cell transcriptomic landscape and show that it can uncover previously unrecognized cell types, pathways and gene expression regulations that may contribute to the efficacy and outcome of UCB transplant, broadening the scope of research and clinical innovations.

Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population.
Herein, we present a novel and efficient computational tool named Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high depth whole-genome sequencing (WGS) data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population of 90 Han Chinese individuals with a mean 68× depth per individual. In total, we identify 9342 recent RIPs, and 8433 of these RIPs are novel compared with dbRIP, including 5826 Alu, 2169 long interspersed nuclear element 1 (L1), 383 SVA, and 55 long terminal repeats (LTR). Among the 9342 RIPs, 4828 were located in gene regions and five were located in protein-coding regions. We demonstrate that RIPs can, in principle, be an informative resource to perform population evolution and phylogenetic analyses. Taking the demographic effects into account, we identify a weak negative selection on SVA and L1 but approximately neutral selection for Alu elements based on the frequency spectrum of RIPs.
SID is a powerful open-source program for the detection of non-reference RIPs. We built a non-reference RIP dataset that greatly enhanced the diversity of RIPs detected in the general population and should be invaluable to researchers interested in many aspects of human evolution, genetics, and disease. As a proof-of-concept, we demonstrate that the RIPs can be used as biomarkers in a similar way as single nucleotide polymorphisms (SNPs).

Nanorana parkeri (also known as the high Himalaya frog, Xizang Plateau frog, Parker's slow frog, or mountain slow frog) is a common frog living across the Tibetan Plateau. It occurs at elevations ranging from 2,850 to 5,000m. Because this species lives at such high elevations, it provides an additional excellent biological model to study the frogs adaptations to extreme conditions.
A female frog was collected from the Qinghai-Tibetan Plateau at an elevation of 4,900m, and genomic DNA was extracted from muscle tissue. Paired end DNA libraries with different insert-size lengths (170 bp to 20 kb) weresequenced on the Illumina HiSeq 2000 platform. After performing filtering steps to remove artificial duplication, adaptercontamination and low-quality reads, 190 Gbp of high-quality data (83× genome coverage) was obtained. This was assembled using SOAPdenovo and SSPACE, producing a final draft assembly of 2.0Gb with an N50 scaffold size of 1.05Mb. More than 20,000 genes were predicted. The Nanorana parkeri genome should help offer new insights into the amphibian evolution and Tibetan high-altitude adaptation.

Schistosoma haematobium is an important digenetic trematode, and is found in the Middle East, India, Portugal and Africa. It is a major agent of schistosomiasis. More specifically, it is associated with urinary schistosomiasis. Adults are found in the Venous plexuses around the urinary bladder and the released eggs traverse the wall of the bladder causing haematuria and fibrosis of the bladder. The bladder becomes calcified, and there is increased pressure on ureters and kidneys otherwise known as hydronephrosis. Inflammation of the genitals due to S.haematobium may contribute to the propagation of HIV. In this study, we sequenced the S.haematobium genome from 200 ng of genomic DNA template isolated from a single, mated pair of adult worms, and produced 33.5 Gb of usable sequence data, using Illumina-based technology at 74-fold coverage and comparedit to sequences from related parasites. We consistently showed low sequence heterozygosity and estimated the genome size to be 431-452 Mb, then assembled the data and used local assemblies to close most (96.1%) of the remaining gaps, achieving a final assembly of 385 Mb (365 contigs; N50 scaffold size 307 Kb). Also we included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.

The giant panda (Ailuropoda melanoleuca) is considered a symbol of China and is a much loved animal all around the world. It is also one of the worlds most endangered species, making it a flagship species for conservation efforts. As the first fully sequenced Ursidae and the second fully sequenced carnivore after the dog, the whole genome sequence and annotation data provide an unparalleled amount of information to aid in understanding the genetic and biological underpinnings of this unique species, and will help contribute to disease control and conservation efforts.In 2008, BGI completed a first draft of the genome sequence of a three-year old female giant panda named Jingjing, who was used as a model for the 2008 Olympics in Beijing, China (doi: 10.1038/nature08696). Using second-generation Illumina GA sequencing data, the first de novo genome assembly was created using short-read sequencing technology. Here you will find the giant panda genome sequence assembly as well as annotation information, such as gene structure and function, non-coding RNAs, and repeat elements. Also presented are polymorphism information detected in the diploid genome, including SNPs, indels, and structural variations (SVs). The assembly was done using SOAPdenovo software and the panda genome data is visualized via MapView, which is powered by the Google Web Toolkit.

Here we present whole-genome resequencing data of 40 domesticated and wild silkworms (Bombyx). The domesticated silkworm (Bombyx mori) is of great economic interest and has been domesticated for more the 5,000 years. An organism with a mid-range genome size (~432 Mb), it often serves as a model insect for the order Lepidoptera. A number of wild varieties of silkworms exist as well, including the Chinese wild silkworm (Bombyx mandarina) from which the domesticated silkworm originated.Each of the silkworm varieties was sequenced to ~3X coverage, representing 99.88% of the genome. These sequences were then used to create a single-base pair resolution genetic variation map of the silkworm. SNP sets were obtained separately for the pool of 29 domesticated strains and the pool of 11 wild varieties. The number of SNPs in the domestic versus wild varieties was approximately 14 million and 13 million, respectively. In addition to SNPs, approximately 0.33 million small insertion-deletions (indels) and 35 thousand structural variants (SVs) were identified among the 40 varieties. Over three-fourths of the SVs overlapped with transposable elements.A total of 1,041 candidate regions Genomic Regions of Selective Signals (GROSS) were identified. These regions cover 12.5 Mb (2.9%) of the genome and may reflect genomic footprints left by artificial selection during domestication, as they include 354 protein-coding genes that were identified as good candidates for domestication genes.We observed that 159 genes from GROSS were expressed in on different B. mori tissues on day 3 of the fifth larval instar as a reference strain, and were enriched in tissues of silk gland, midgut, and testis. The genes expressed in silk gland are involved in the synthesis of silk proteins, including fibroin and sericin. Midgut-enriched genes are related to the metabolism of carbohydrates, amino acids and lipids. And genes enriched in the testis are annotated as having binding, catalytic, and motor activity related to reproduction.The reference genome for this project was the Japanese wild silkworm (NCBI Accession Number NC_003395).

Available here is the draft genome for Ascaris suum, a roundworm species that infects pigs. It is a valuable resource for therapy and diagnostic test development for both Ascaris suum infection of pigs, and also human infection by the closely related species A. lumbricoides.The A. suum genome was sequenced at ~80-fold coverage to generate an approximately 273 million base genome sequence encoding 18,542 protein-coding genes. Compared to other metazoan genomes, it has low repeat content (4.4%). Compared with other parasitic free-living roundworms and C. elegan, A. suum shares the highest homology with Brugia malayi, another animal parasite. The A. suum secretome (consisting of around 750 molecules) is rich in peptidases linked to the penetration and degradation of host tissue, and an assemblage of molecules likely to modulate or evade host immune responses. This genome provides a comprehensive resource to the scientific community and a foundation for developing new and urgently needed therapeutic intervention drugs, vaccines and diagnostic tests) against ascariasis and other nematodiases.