Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species.

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Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei

Poaceae represent the most important group of crops susceptible to abiotic stress. This large family of monocotyledonous plants, commonly known as grasses, counts several important cultivated species, namely wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays) and barley (Hordeum vulgare). These crops, notably, show different behaviors under abiotic stress conditions: wheat and rice are considered sensitive, showing serious yield reduction upon water scarcity and soil salinity, while barley presents a natural drought and salt tolerance. During the green revolution (1940-1960), cereal breeding was very successful in developing high-yield crops varieties; however, these cultivars were maximized for highest yield under optimal conditions, and did not present suitable traits for tolerance under unfavorable conditions. The improvement of crop abiotic stress tolerance requires a deep knowledge of the phenomena underlying tolerance, to devise novel approaches and decipher the key components of agricultural production systems. Approaches to improve food production combining both enhanced water use efficiency (WUE) and acceptable yields are critical to create a sustainable agriculture in the future. This paper analyzes the latest results on abiotic stress tolerance in Poaceae. In particular, the focus will be directed towards various aspects of water deprivation and salinity response efficiency in Poaceae. Aspects related to cell wall metabolism will be covered, given the importance of the plant cell wall in sensing environmental constraints and in mediating a response; the role of silicon (Si), an important element for monocots’ normal growth and development, will also be discussed, since it activates a broad-spectrum response to different exogenous stresses. Perspectives valorizing studies on landraces conclude the survey, as they help identify key traits for breeding purposes.

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Poaceae vs. Abiotic Stress: Focus on Drought and Salt Stress, Recent Insights and Perspectives.

Genome-wide dissection of co-selected UV-B responsive pathways in the UV-B adaptation of qingke

The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called “Qingke” in Chinese and “Ne” in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.

https://www.pnas.org/content/pnas/112/4/1095.full.pdf

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

The blunt snout bream Megalobrama amblycephala is the economically most important cyprinid fish species As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption As a first towards optimizing this aquatic livestock, we present a 1116-Gb draft genome of M amblycephala, with 77954 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 the improvement of M amblycephala livestock, the draft genome sequence offers new insights into the development of intermuscular bone and herbivorous adaptation

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The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet.

Background Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources leads to fewer study progresses in these fields, due to its huge genome of ∼50 GB making it extremely difficult to be assembled. Results We reported the sequenced transcriptome of more than 20 tissues from adult CGS using Illumina Hiseq 2000 technology, and a total of 93 366 no-redundancy transcripts with a mean length of 1326 bp were obtained. We developed for the first time an efficient pipeline to construct a high-quality reference gene set of CGS and obtained 26 135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6% of vertebrate universal single-copy orthologs, and this coding gene set had a higher proportion of completeness CDS with comparable quality of the protein sets of Tibetan frog. Conclusions These highest quality data will provide a valuable reference gene set to the subsequent research of CGS. In addition, our strategy of de novo transcriptome assembly and protein identification is applicable to similar studies.

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Jiang Li

Papers

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet.

A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus.