AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.

Inland lakes are major surface water resource in arid regions of Central Asia. The area changes in these lakes have been proved to be the results of regional climate changes and recent human activities. This study aimed at investigating the area variations of the nine major lakes in Central Asia over the last 30 years. Firstly, multi-temporal Landsat imagery in 1975, 1990, 1999, and 2007 were used to delineate lake extents automatically based on Normalized Difference Water Index (NDWI) threshold segmentation, then lake area variations were detailed in three decades and the mechanism of these changes was analyzed with meteorological data and hydrological data. The results indicated that the total surface areas of these nine lakes had decreased from 91,402.06 km(2) to 46,049.23 km(2) during 1975-2007, accounting for 49.62% of their original area of 1975. Tail-end lakes in flat areas had shrunk dramatically as they were induced by both climate changes and human impacts, while alpine lakes remained relatively stable due to the small precipitation variations. With different water usage of river outlets, the variations of open lakes were more flexible than those of other two types. According to comprehensive analyses, different types of inland lakes presented different trends of area changes under the background of global warming effects in Central Asia, which showed that the increased human activities had broken the balance of water cycles in this region.

Verticillium wilt (VW), caused by the soil‐borne fungus Verticillium dahliae Kleb., is one of the most destructive diseases in Upland cotton (Gossypium hirsutum L.) production in the U.S. and worldwide. Development of VW‐resistant cultivars remains the only economic option for controlling the disease. The objective of this review was to summarize the progress in screening methods, resistance sources, and genetics, quantitative trait locus (QTL) mapping, marker‐assisted selection (MAS) and breeding for VW resistance in cotton. Even though Gossypium barbadense L. carries high levels of resistance, its resistance has not been transferred into commercial Upland cultivars. Many Acala cotton cultivars developed in New Mexico and California between the 1940s and the 1990s, and some commercial transgenic cultivars are tolerant or moderately resistant to VW. However, due to difficulties in achieving consistent and uniform inoculation and infection with V. dahliae, both qualitative and quantitative inheritance of VW resistance have been reported in numerous studies for resistant G. barbadense and Upland genotypes. Several QTL analyses have shown the existence of VW resistance QTLs on almost all the tetraploid cotton chromosomes; however, QTLs have most frequently been detected on c5, c7, c8, c11, c16, c17, c19, c21, c23, c24, and c26. This has led to MAS for progeny with favorable QTL alleles for VW resistance in several experiments. Phenotypic selection for VW resistance has been inefficient, while the effectiveness and efficiency of MAS remain to be validated. There is an urgent need for the development of better plant inoculation and screening methods, and for more molecular mapping studies to discern the genetic basis of VW resistance in cotton.

Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (L-D 1 ), which is responsible for the major leaf shapes in cotton. The L-D 1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the L-D 1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virusinduced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype. cotton | leaf shape | okra | gene cloning

Two alkane hydroxylase-rubredoxin fusion gene homologs (alkW1 and alkW2) were cloned from a Dietzia strain, designated DQ12-45-1b, which can grow on crude oil and n-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1-and AlkG2-type Rds. Expression of the alkW1 gene in DQ12-45-1b was induced when cells were grown on C 8 to C 32 n-alkanes as sole carbon sources, but expression of the alkW2 gene was not detected. Functional heterologous expression in an alkB deletion mutant of Pseudomonas fluorescens KOB2⌬1 suggested the alkW1 could restore the growth of KOB2⌬1 on C 14 and C 16 n-alkanes and induce faster growth on C 18 to C 32 n-alkanes than alkW1⌬Rd, the Rd domain deletion mutant gene of alkW1, which also caused faster growth than KOB2⌬1 itself. In addition, the artificial fusion of AlkB from the Gram-negative P. fluorescens CHA0 and the Rds from both Gram-negative P. fluorescens CHA0 and Gram-positive Dietzia sp. DQ12-45-1b significantly increased the degradation of C 32 alkane compared to that seen with AlkB itself. In conclusion, the alkW1 gene cloned from Dietzia species encoded an alkane hydroxylase which increased growth on and degradation of n-alkanes up to C 32 in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain n-alkanes (such as C 32 ) in the Gram-negative bacterium.Alkane hydroxylation is the key step in alkane degradation in microorganisms, and alkane hydroxylases play an important role in the microbial degradation of alkanes (34). There are three classes of alkane hydroxylases in microorganisms, depending on the chain length of the alkane substrate. The soluble nonheme di-iron monooxygenases (sMMO) and membrane-bound particulate copper-containing enzymes (pMMO) are the main enzymes that catalyze the oxygenation of alkanes C 1 to C 5 in length (21). The integral-membrane alkane monooxygenase (AlkB)-related alkane hydroxylases (37) and cytochrome P450 enzymes (35) found in fungi and bacteria can oxidize long-chain alkanes with up to 16 carbon atoms. Among the members of the third class of enzymes, which can catalyze the oxidation of alkanes longer than C 18 , only one C 15 to C 36 alkane monooxygenase (LadA) found in Geobacillus thermodenitrificans NG80-2, which is distinct from other known AlkBtype alkane hydroxylases, has been cloned and the activities of purified LadA on alkanes with different chain lengths have been previously identified (8). In the AlkB system, three individual...