Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

A New Species of the Genus Garra from Nujiang River Basin, Yunnan, China (Teleostei: Cyprinidae)

2003年4月,于怒江二级支流镇康县境内的大叉河中采获一批墨头鱼属(Garra)鱼类标本,经鉴定为一新种,命名为怒江墨头鱼(G.nujiangensis Chen and Yang,sp.nov.).该新种主要鉴别特征:围尾柄鳞12～14:侧线鳞48～50:在小个体中有一对微小的吻须;背鳍分支鳍条8～9;侧线上鳞5～6,侧线下鳞3～4;体高小于头长;臀鳍起点处的小于眼后至吻端的距离;腹鳍前长为体长的50.0%～53.7%;肛门前长为体长的58.9%～63.9%:体宽为体长的16.7%～19.6%:体高为体长的19.2%～22.6%.本研究证实,在缺须的墨头鱼属的一些物种中,如高体墨头鱼(G.alticorpora)和怒江墨头鱼(G.nujiangensis),其幼体中往往具有一对很小的吻须.

GABA Transporter-1 Activity Modulates Hippocampal Theta Oscillation and Theta Burst Stimulation-Induced Long-Term Potentiation

The network oscillation and synaptic plasticity are known to be regulated by GABAergic inhibition, but how they are affected by changes in the GABA transporter activity remains unclear. Here we show that in the CA1 region of mouse hippocampus, pharmacolog

Microrasbora Annandale, a new genus record in China, with description of a new species (Teleostei: Cyprinidae)

A new species of genus Microrasbora Annandale (1918), M. microphthalma, is described from the Nanwan River, a tributary of the Ruili River, Irrawaddy drainage, in southwest Yunnan province, China. This new species is the first record of the genus Microras

The identity of Schizothorax griseus Pellegrin, 1931, with descriptions of three new species of schizothoracine fishes (Teleostei: Cyprinidae) from China

The identity of Schizothorax griseus Pellegrin, 1931, is clarified and the species redescribed. Three new species previously identified as S. griseus are described: S. nudiventris, from the Lancang Jiang, China; S. heterophysallidos, from the Nanpan Jiang

A new species of genus Pseudogyrinocheilus (Teleostei: Cyprinidae) from Guangxi, China

A new species, Pseudogyrinocheilus longisulcus, was discovered from a tributary of Pearl River in Jingxi Co., Guangxi, China, The new species can be distinguished from other species of Pseudogyrinocheilus by the following combination of characteristics: prolonged post-labial grooves, and extended antero-medially close to anterior end of middle lower lip, but not meeting with its counterpart; posterior margin of lower lip free; scales of abdomen from thorax to pectoral-fin base embedded under skin; lateral-line scales 40-42; dark stripe longitudinal along lateral line on flank. The key to the species of Pseudogyrinocheilus is provided.

The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake

Although new empirical evidence shows that sympatric speciation has occurred in some species, there are few indisputable model organisms for this process of speciation. The two subspecies (Gymnocypris eckloni eckloni and G. e. scoliostomus) of the schizothoracine Gymnocypris fish species complex from a small glacier lake in the Tibetan Plateau, Lake Sunmcuo, fit several of the key characteristics of the sympatric speciation model. We used combined mitochondrial control region sequences and the cytochrome b gene (1894 bp) to address the phylogenetics and population genetics of 232 specimens of G. e. eckloni and G. e. scoliostomus, as well as all of its closely related sister species. We found that: (i) a total of four old lineages were uncovered in the widespread G. e. eckloni, of which only one was shown to be shared with all G. e. scoliostomus individuals and (ii) the new subspecies (G. e. scoliostomus) evolved in Lake Sunmcuo from the ancestral G. e. eckloni population within approximately 0.057 Ma. These two taxa of the species complex are morphologically distinct, and reproductive isolation is further suggested. Ecological disruptive selection based on morphological traits (e.g. mouth cleft characters) and food utilization may be a mechanism of incipient speciation of two sympatric populations within Lake Sunmcuo. This study provides the first genetic evidence for sympatric speciation in the schizothoracine fish.

Assessment effects of cage culture on nitrogen and phosphorus dynamics in relation to fallowing in a shallow lake in China

Nitrogen and phosphorus dynamics in relation to fallowing in a fish cage farm was investigated in a shallow lake in China. Four sampling sites were set: beneath the cages, at the cage sides, and 50 and 100 m east of the cage farm. Total nitrogen (TN) and total phosphorus (TP) in lake water and sediment were analyzed during a 2-year rearing cycle. The cage culture had a fish yield of 16.3-39.2 tonnes in the study period. Based on the mass balance equation, 1533-3084 kg TN and 339-697 kg TP were contributed to the lake environment. Nitrogen and phosphorous concentrations showed greater increase in the first culture period than in the second rearing cycle. No obvious changes were found at the sampling sites 50 and 100 m east of the cages during the study periods. Main impacts were found close to the cages (beneath the cages and at the cage side); the sampling points at the cage side showed relatively high TN and TP sedimentation. After 3 months of fallowing, water TN and TP decreased significantly but the sediment TN and TP contents remained high. Therefore, recovery seems to happen during fallowing but attention should be paid to whether the culture continues to operate in the future.

Pseudobagrus fui Miao, a valid bagrid species from the Yangtze River drainage, South China (Teleostei: Bagridae)

Pseudobagrus fui Miao is a valid bagrid species that can be separated from all its congeners in having 27-33 anal-fin rays. Among the species of Pseudobagrus, it forms part of a group of approximately 20 species putatively characterized by having a smooth anterior margin of the pectoral-fin spine and short maxillary barbels not extending to the base of the pectoral-fin spine. Pseudobagrus fui, together with P. nitidus and P. vachelli, can be differentiated from all other fork-tailed species of this group by having no fewer than 20 branched anal-fin rays, the posterior end of the anal-fin base posterior to the vertical through the posterior end of the adipose-fin base, and anal-fin base longer than the adipose-fin base. It further differs from P. nitidus in having a gas bladder without beaded lateral and posterior margins, and from P. vachelli in having short maxillary barbels not extending to the base of the pectoral-fin spine. Pseudobagrus fui is currently known from the main stream of the upper Yangtze River and its tributaries, the Min River, Jialing River, Tuo River, Wu River and Chishui River in Sichuan Province, Guizhou Province, and the Chongqing City. The identity and nomenclature of Pseudobagrus nitidus is also discussed.

Food Consumption by In Situ Pen-Cultured Planktivorous Fishes and Effects on an Algal Bloom in Lake Taihu, China

Silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) were used as a new pen-cultureed biomanipulation technique to control algal blooms in Meiliang Bay of Lake Taihu. In order to evaluate the capacity of these two fishes to decrease algal blooms, diel feeding samplings were carried out in May (without algal blooms) and September (with algal blooms) in 2005. Based on estimated food consumption by the Elliott-Persson model, silver carp increased daily food consumption from 2.07 g dry weight per 100 g wet body weight in May before the outbreak of algal blooms to 4.98 g dry weight per 100 g wet body weight in September during algal blooms outbreak. However, no obvious variation of food consumption was observed in bighead carp during the study period. This species 1.88 and 1.54 g dry weight of plankton per 100 g wet body weight in May and September, respectively. Silver carp had a higher feeding capacity for plankton than bighead carp. Biotic factors (i.e., fish size and conspecific competition with natural species in the lake) may affect the feeding behaviors of both carps as well as seasonal variation of plankton communities in the pen.

Peridiniopsis niei sp nov (Dinophyceae), a new species of freshwater red tide dinoflagellates from China

A new freshwater phototrophic species of the dinoflagellate genus Peridiniopsis, P. niei sp. nov., is described based on morphology. The new species appeared during spring with densities up to 1.48 x 10(7) cells L-1 in some tributaries and gullies of Three Gorge Reservoir and Lake Donghu, China, forming red tides. Peridiniopsis niei is a cyst-producing freshwater dinoflagellate that belongs to the group Penardii. The plate tabulation is po+x+4 '+0a+6 ''+5c+5s+5 '''+2 '''' and the plate pattern is symmetric. The cells of P. niei are pentagonal in ventral view, the epitheca is larger than the hypotheca, making up about 2/3 the length of the cell. Plate 3 ' is hexangular. The closest species to P. niei is P. penardii (Lemmermann) Bourrelly, but cells of the former are pentagonal, very compressed dorsoventrally, and the hypotheca is truncated with one transparent, robust spine on each antapical plate.

Study on freshwater genus Peridinium (Dinophyta) from China

Peridinium is an important genus of freshwater armoured dinoflagellates with two more intercalary plates (sensu Bourrelly). A few species of Peridinium were known from China heretofore. The plate pattern is one of the important criteria for the taxonomy of Peridinium, and it was difficult to visualize their plate patterns under normal light microscope. For editing of Flora Algarum Sinicarum Aquae Dulcis, 11 species of Peridinium collected from various freshwater habitats of China are described. Among them, 6 species are first reported from China. They are P. gatunense Nygaard, P. gutwinskii Woloszynska, P. lomnickii Woloszynska, P. palatinum Lauterborn, P. striolatum Playfair, and P. zonatum Playfair. Epifluorescence microscopy and scanning electron microscopy, and also light microscopy were employed for their structure and patterns of thecal plates.