Impacts of stand density on diversity of understory plant and soil seed banks in a Pinus massoniana plantation.

Stand density is a critical factor impacting the diversity of understory plants. We analyzed the diversity of understory plants and soil seed banks, as well as their relationship by setting up three planting densities in a Pinus massoniana plantation, including low density (1575 trees·hm-2, D1), medium (2474 trees·hm-2, D2), and high (3550 trees·hm-2, D3). It aimed to provide a scientific basis for the implementation of the multi-objective sustainable development of plantations. The results showed that there were 70 species of herbs and shrubs belonging to 42 families and 62 genera. D1 was dominated by heliophiles, whereas both the D2 and D3 were dominated by shade-tolerant species. The Margalef (M), Shannon (H), Simpson (D), Pielou (Jsw), and Altalo (Al) indices of the herbs and shrubs exhibited a downward trend with increasing stand den-sity. In the herb layer, D1 and D3 showed significant difference in H, D, Jsw and Al. There were significant differences of Jsw and Al in the shrub layer among the three stand densities, but no diffe-rence of H and D. H, D, Jsw and Al in the soil seed bank first decreased and then increased with increasing stand density, with species richness and diversity being the highest in D1. The similarity coefficient of Jaccard and Sorensen among different stand densities was low. In the herb layer, M was positively correlated with Jsw. The correlations between stand density and H, D, Jsw and Al were greater in the shrub layer than in the herb layer. There was significant negative correlation between stand density and Jsw both in the shrub and herb layers. The stand density of 1575 trees·hm-2 was comparatively beneficial for the development of understory, plant diversity, and sustainability of P. massoniana plantation.

Mitochondrial analysis of oribatid mites provides insights into their atypical tRNA annotation, genome rearrangement and evolution.

BACKGROUND: The mitochondrial (mt) genomes of Sarcoptiformes mites typically contain 37 genes. Although the loss of genes is rare in Sarcoptiformes mite mitogenomes, two of the six previously reported oribatid mites (Acariforms: Sarcoptiformes) are reported to have lost parts of their tRNA genes. To confirm whether the tRNA genes were indeed lost and whether the loss is universal, we re-annotated the available oribatid mite sequences and sequenced the mitogenome of Oribatula sakamorii. METHODS: The mitogenome of O. sakamorii was sequenced using an Illumina HiSeq sequencer. The mt tRNA gene was annotated using multi-software combined with a manual annotation approach. Phylogenetic analyses were performed using the maximum likelihood and Bayesian inference methods with concatenated nucleotide and amino acid sequences. RESULTS: The mitogenomes of O. sakamorii contained 37 genes, including 22 tRNA genes. We identified all mt tRNA genes that were reported as "lost" in Steganacarus magnus and Paraleius leontonychus and revealed certain atypical tRNA annotation errors in oribatid mite sequences. Oribatid mite mitogenomes are characterized by low rates of genetic rearrangement, with six or seven gene blocks conserved between the mitogenome of all species and that of ancestral arthropods. Considering the relative order of the major genes (protein-coding genes and rRNAs), only one or two genes were rearranged with respect to their positions in the ancestral genome. We explored the phylogenetic relationships among the available oribatid mites, and the results confirmed the systematic position of Hermannia in the Crotonioidea superfamily. This was also supported by the synapomorphic gene-derived boundaries. CONCLUSIONS: The tRNA "lost" phenomenon is not universal in oribatid mites. Rather, highly atypical secondary structure of the inferred mt tRNA genes made them unidentifiable using a single type of tRNA search program. The use of multi-software combined with a manual annotation approach can improve the accuracy of tRNA gene annotation. In addition, we identified the precise systematic position of Hermannia and validated that Astigmata is nested in Oribatida.

Engineering CrtW and CrtZ for improving biosynthesis of astaxanthin in Escherichia coli.

This study engineered ß-carotene ketolase CrtW and ß-carotene hydroxylase CrtZ to improve biosynthesis of astaxanthin in Escherichia coli. Firstly, crtW was randomly mutated to increase CrtW activities on conversion from ß-carotene to astaxanthin. A crtW* mutant with A6T, T105A and L239M mutations has improved 5.35-fold astaxanthin production compared with the wild-type control. Secondly, the expression levels of crtW* and crtZ on chromosomal were balanced by simultaneous modulation RBS regions of their genes using RBS library. The strain RBS54 selected from RBS library, directed the pathway exclusively towards the desired product astaxanthin as predominant carotenoid (99%). Lastly, the number of chromosomal copies of the balanced crtW-crtZ cassette from RBS54 was increased using a Cre-loxP based technique, and a strain with 30 copies of the crtW*-crtZ cassette was selected. This final strain DL-A008 had a 9.8-fold increase of astaxanthin production compared with the wild-type control. Fed-batch fermentation showed that DL-A008 produced astaxanthin as predominant carotenoid (99%) with a specific titer of 0.88 g·L-1 without addition of inducer. In conclusion, through constructing crtW mutation, balancing the expression levels between crtW* and crtZ, and increasing the copy number of the balanced crtW*-crtZ cassette, the activities of ß-carotene ketolase and ß-carotene hydroxylase were improved for conversion of ß-carotene to astaxanthin with higher efficiency. The series of conventional and novel metabolic engineering strategies were designed and applied to construct the astaxanthin hetero-producer strain of E. coli, possibly offering a general approach for the construction of stable hetero-producer strains for other natural products.

De novo sequence of the mitochondrial genome of Tyrophagus putrescentiae (Acari: Sarcoptiformes) including 22 tRNA sequences and the largest non-coding region.

In this study, we de novo sequenced and analyzed the circular mitochondrial genome (mitogenome) of Tyrophagus putrescentiae. It was 14,156 bp long and contained a complete set of 37 genes, contrary to the initial published sequences; it included 22 tRNA sequences and the largest non-coding region. The mtDNA gene order of T. putrescentiae was found to be identical to that of Aleuroglyphus ovatus, Caloglyphus berlesei, and Rhizoglyphus robini (all Acaroidea). Most tRNAs of T. putrescentiae lack at least a D-arm or T-arm. Tyrophagus putrescentiae tRNAs also shared considerable structural and sequence similarity with the tRNAs of other reported Acaroidea species that have the full set of tRNAs. The largest non-coding region was located between trnF and trnS1, and it contained a microsatellite-like (AT)n sequence, short palindromic sequences, and several hairpin loops, as observed in other reported Acaroidea species (excepting Tyrophagus longior).

A histone K-lysine acetyltransferase CqKAT2A-like gene promotes white spot syndrome virus infection by enhancing histone H3 acetylation in red claw crayfish Cherax quadricarinatus.

In contrast to that hypoacetylation of histones is associated with condensed chromatin and gene silencing, the hyperacetylation of histones can promote an "open chromatin" conformation and transcriptional activation, which is recruited by some viruses to enhance the viral genome replication in host cells. However, the function of histone acetylation modification in the infection of white spot syndrome virus (WSSV), one of the most virulent pathogens for crustaceans like shrimp and crayfish at present, is still unknown. Previously, we found that the transcript of a histone K-Lysine acetyltransferase CqKAT2A-like gene was down-regulated in a differentially expressed transcriptome library of the haematopietic tissue (Hpt) cells from red claw crayfish Cherax quadricarinatus upon WSSV infection at 12 hpi. To further reveal its possible role in anti-WSSV response, CqKAT2A-like gene was then identified with an open reading frame (ORF) of 2523 bp encoding 840 amino acids, which contained a conserved PCAF-N domain, acetyltransf1 domain and bromo domain. Gene expression analysis showed that CqKAT2A-like was distributed in all tissues examined with high presence in haemocyte and muscle, and the transcript was significantly down-regulated after WSSV infection in Hpt cells. Furthermore, the level of histone H3 acetylation (H3ac) was strongly reduced by gene silencing of CqKAT2A-like, which was accompanied with the significantly decreased gene expression of WSSV in Hpt cells, suggesting that CqKAT2A-like gene can promote the activity H3ac and the replication of WSSV. When the H3ac was induced by histone deacetyltransferase inhibitor TSA, the transcription of WSSV genes including both IE1 and VP28 genes was significantly increased, indicating that H3ac participated in WSSV infection in Hpt cells. Taken together, these data suggest that CqKAT2A-like gene might promote the replication of WSSV by regulating H3ac, which sheds new light on the pathogenesis of WSSV in crustaceans.

Cellular entry of white spot syndrome virus and antiviral immunity mediated by cellular receptors in crustaceans.

Enveloped virus usually utilizes the receptor-mediated multiple endocytic routes to enter permissive host cells for successful infection. Cellular receptors are cell surface molecules, either by helping viral attachment to cell surface followed by internalization or by triggering antiviral immunity, participate in the viral-host interaction. White spot syndrome virus (WSSV), the most lethally viral pathogen with envelope and double strand DNA genome in crustacean farming, including shrimp and crayfish, has been recently found to recruit various endocytic routes for cellular entry into host cells. Meanwhile, other than the typical pattern recognition receptors for recognition of WSSV, more and more putative cellular receptors have lately been characterized to facilitate or inhibit WSSV entry. In this review, recent findings on the endocytosis-dependent WSSV entry, viral entry mediated by putative cellular receptors, the molecular interplay between WSSV and cellular receptors, and the following anti-WSSV immunity are summarized and discussed, which may provide us a better understanding of the WSSV pathogenesis and further possible antiviral control of white spot disease in crustacean farming.