SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.

Synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) generates combinatorial genomic diversity through rearrangements at designed recombinase sites. We applied SCRaMbLE to yeast synthetic chromosome arm synIXR (43 recombinase sites) and then used a computational pipeline to infer or unscramble the sequence of recombinations that created the observed genomes. Deep sequencing of 64 synIXR SCRaMbLE strains revealed 156 deletions, 89 inversions, 94 duplications, and 55 additional complex rearrangements; several duplications are consistent with a double rolling circle mechanism. Every SCRaMbLE strain was unique, validating the capability of SCRaMbLE to explore a diverse space of genomes. Rearrangements occurred exclusively at designed loxPsym sites, with no significant evidence for ectopic rearrangements or mutations involving synthetic regions, the 99% nonsynthetic nuclear genome, or the mitochondrial genome. Deletion frequencies identified genes required for viability or fast growth. Replacement of 3' UTR by non-UTR sequence had surprisingly little effect on fitness. SCRaMbLE generates genome diversity in designated regions, reveals fitness constraints, and should scale to simultaneous evolution of multiple synthetic chromosomes.

Complexity Analysis of Carbon Market Using the Modified Multi-Scale Entropy.

Carbon markets provide a market-based way to reduce climate pollution. Subject to general market regulations, the major existing emission trading markets present complex characteristics. This paper analyzes the complexity of carbon market by using the multi-scale entropy. Pilot carbon markets in China are taken as the example. Moving average is adopted to extract the scales due to the short length of the data set. Results show a low-level complexity inferring that China's pilot carbon markets are quite immature in lack of market efficiency. However, the complexity varies in different time scales. China's carbon markets (except for the Chongqing pilot) are more complex in the short period than in the long term. Furthermore, complexity level in most pilot markets increases as the markets developed, showing an improvement in market efficiency. All these results demonstrate that an effective carbon market is required for the full function of emission trading.

Reference-assisted chromosome assembly.

One of the most difficult problems in modern genomics is the assembly of full-length chromosomes using next generation sequencing (NGS) data. To address this problem, we developed "reference-assisted chromosome assembly" (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. Evaluation of results using simulated and real genome assemblies indicates that our approach can substantially improve genomes generated by a wide variety of de novo assemblers if a good reference assembly of a closely related species and outgroup genomes are available. We used RACA to reconstruct 60 Tibetan antelope (Pantholops hodgsonii) chromosome fragments from 1,434 SOAPdenovo sequence scaffolds, of which 16 chromosome fragments were homologous to complete cattle chromosomes. Experimental validation by PCR showed that predictions made by RACA are highly accurate. Our results indicate that RACA will significantly facilitate the study of chromosome evolution and genome rearrangements for the large number of genomes being sequenced by NGS that do not have a genetic or physical map.

Persistence and vertical distribution of neonicotinoids in soils under different citrus orchards chrono sequences from southern China.

Continual input of neonicotinoid insecticides occurs in the citrus orchards from southern China. However, it is still unknown about the variations in the distribution and accumulation of neonicotinoids in soil profiles along a long-term chronosequence of cultivation and the driving factors contributing to these shifts. Here, changes of neonicotinoids in the 0-100 cm soil profiles with distinct orchard cultivation age (1, 10, and 20 years) were investigated, and their related factors were further determined. The results showed that the total levels of five target neonicotinoids (∑5NEOs) in the soil profiles were in the range of 0-25.76 ng/g dw. Imidacloprid was the most dominating neonicotinoid, followed by thiamethoxam. We observed higher neonicotinoid accumulations in the soil profiles from the citrus orchards after 10 and 20 years of cultivation. Neonicotinoids migrated deeper into the soil profiles in orchards with a longer time since cultivation. Imidacloprid, thiamethoxam, and the total amount of neonicotinoid (∑5NEOs) were mainly affected by the cultivation age of citrus orchards (accounting for 58.9% variance; P < 0.001); whereas clothianidin, acetamiprid, and thiacloprid were mainly influenced by soil depths (accounting for 66.9-85.2% variance; P < 0.05). Redundancy analyzes further indicated that the enhanced accumulation of neonicotinoids was mainly correlated with the increase of soil organic carbon (SOC) content and soil porosity, and the reduction of bulk density in the profiles of citrus orchards with increasing cultivation age. This study highlights the finding that we should give more concerns about the contamination and ecological risks of neonicotinoids in the orchards with a long cultivation age.

Draft genome sequence of the Tibetan antelope.

The Tibetan antelope (Pantholops hodgsonii) is endemic to the extremely inhospitable high-altitude environment of the Qinghai-Tibetan Plateau, a region that has a low partial pressure of oxygen and high ultraviolet radiation. Here we generate a draft genome of this artiodactyl and use it to detect the potential genetic bases of highland adaptation. Compared with other plain-dwelling mammals, the genome of the Tibetan antelope shows signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission. Both the highland American pika, and the Tibetan antelope have signals of positive selection for genes involved in DNA repair and the production of ATPase. Genes associated with hypoxia seem to have experienced convergent evolution. Thus, our study suggests that common genetic mechanisms might have been utilized to enable high-altitude adaptation.