The teleost fish Monopterus albus is emerging as a new model for biological studies due to its natural sex transition and small genome, in addition to its enormous economic and potential medical value. However, no genomic information for the Monopterus is currently available.
Here, we sequenced and de novo assembled whole genome of the Monopterus, and report the de novo chromosome assembly by FISH walking assisted by conserved synteny (Cafs). Using Cafs, 328 scaffolds were assembled into 12 chromosomes, which cover genomic sequences of 555 Mb, accounting for 81.3% of the sequences assembled in scaffolds (~689 Mb). A total of 18,660 genes were mapped on the chromosomes and show a non-random distribution along chromosomes.
We report the first reference genome of the Monopterus and provided an efficient Cafs strategy for a de novo chromosome-level assembly of the Monopterus genome which provides a valuable resource, not only for further studies in genetics, evolution and development, particularly sex determination, but also for breed improvement of the species.

As one of the most recognizable characteristics in birds, plumage colour has a high impact on understanding the evolution and mechanisms of colouration. Feather and skin are ideal tissues to explore the genomics and complexity of colour patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amhersts pheasant (Chrysolophus amherstiae), exhibit brilliant colours in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage colouration mechanisms in birds.
We sequence and assemble a genome of golden pheasant with high-coverage and annotate 15,552 protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage. Based on the feather pigment identification, a series of genomic and transcriptomic comparisons are conducted to investigate the complex features of plumage colouration. Through identifying the lineage-specific sequence variations in Chrysolophus and golden pheasant, against different backgrounds, we find that four melanogenesis biosynthesis genes and some lipid-related genes might be candidate genomic factors for the evolution of melanin and carotenoid pigmentation, respectively. In addition, a study among 47 birds shows some candidate genes related to carotenoid colouration in a broad range of birds. The transcriptome data further reveal important regulators of the two colourations, particularly one splicing transcript of the microphthalmia-associated transcription factor (MITF) gene for pheomelanin synthesis.
Analysis of the golden pheasant and its sister pheasant genomes, as well as comparison with other avian genomes, are helpful to reveal the underlying regulation of their plumage colouration. The present study provides important genomic information and insights for further studies of avian plumage evolution and diversity.

Longan (Dimocarpus longan), an important subtropical fruit, is grown in more than 10 countries of the world. Longan is an edible drupe fruit and source of traditional medicine with polyphenol-rich traits, while tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled.The draft genome (about 471.88 Mb) of a China longan cultivar Honghezi was estimated to contain 31,007 high- quality genes and 261.88 Mb of repetitive sequences. No recent whole-genome wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen-resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3H, ANR, and UFGT) and contracted (PAL, CHS, and F35H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine- rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, and the recent expansion and contraction of the NBS-LRR family suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen- resistance characteristics.

The blunt snout bream, Megalobrama amblycephala, is an economically important cyprinid fish species. As a herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is a less desirable feature for fish meat processing and consumption.
As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala, with 779.54 Mb anchored on 24 linkage groups. Integrating spatiotemporal transcriptome analyses we show that intermuscular bone is formed in the more basal teleosts by intramembranous ossification, and may be involved in muscle contractibility and coordinating cellular events. Comparative analysis revealed that olfactory receptor genes, especially of the beta type, underwent an extensive expansion in herbivorous cyprinids, whereas the gene for the umami receptor T1R1 was specifically lost in M. amblycephala. The composition of gut microflora, which contributes to the herbivorous adaptation of M. amblycephala, was found to be similar to that of other herbivores.
As a valuable resource for improvement of M. amblycephala livestock, the draft genome sequence offers new insights into the development of intermuscular bone and herbivorous adaptation.

Watermelon (Citrullus lanatus is an important cucurbit crop grown throughout the world. The annual world production of watermelon is about 90 million tons, making it among the top five most consumed fresh fruits (http://faostat.fao.org/).
We sequenced the 0.425 Gb genome to a depth of approximately 108.6 x with short reads from a series of libraries with various insert sizes ( 100-200 bp, 400 bp, 2 kb, 5 kb, 10 kb and 20 kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 46.18 Gb, with the contig and scaffold N50 values of 26.38 kb and 2.38 Mb respectively. We identified 23,440 protein-coding genes.

The domestic donkey is derived from the African Wild Ass. As with most domesticated species there are a wide variety of coat colours and sizes. They can live for upto 40years.
We sequenced the genome to a depth of approximately 19.4 X with short reads from a series of libraries with various insert sizes ( 800bp and 2kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 48.6 Gb.

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.

Available here is genomic data for the polyploid plant Brassica rapa ssp. pekinensis line Chiifu-401-42, a Chinese cabbage. As there are several oil and vegetable crop species in the Brassica family, this genome is of great agricultural relevance. It also provides an important resource for studying the evolution of polyploid genomes.The Brassica rapa Genome Sequencing Project Consortium assembled a 283.8 Mb genome estimated to cover >98% of the gene space. Using 72X coverage of paired short read sequences generated by Illumina GA II technology and 199,452 BAC-end sequences, 159 super scaffolds were produced, representing 90% of the assembled sequences with an N50 scaffold size of 1.97 Mb. Using genetic mapping of 1,427 markers in B. rapa, ten pseudo chromosomes that included 90% of the assembly were produced. A total of 41,174 protein-coding genes in the B. rapa genome were modeled, and the genome was found to have undergone genome triplication.