不同郁闭度控制下马尾松（Pinus massoniana）人工林土壤动物群落特征

采用郁闭度控制方法,形成马尾松人工林郁闭度梯度(0.5,0.6,0.7,0.8,0.9)试验样地,研究不同郁闭度下土壤动物群落特征。运用手捡法、Tullgren法和Baermann法进行土壤动物群落调查。结果显示,1)共捕获土壤动物8 860只,隶属于4门11纲25目111科,其中大型土壤动物589只,以蜚蠊、疣和康叭为优势类群;中小型土壤动物8271只,以等节和丽甲螨为优势类群。2)大型土壤动物以杂食性为主,杂食性在0.9郁闭度显著增加,捕食性显著减少;中小型土壤动物以菌食和腐食性为主,腐食性土壤动物随郁闭度增大逐渐增加,菌食性逐渐减少。中小型捕食性土壤动物在郁闭度0.5—0.7显著增加,0.7—0.9无显著变化。3)大型土壤动物仅5—10 cm土层类群数在0.9郁闭度显著增加;中小型土壤动物总个体数及枯落物层个体数、5—10 cm土层类群数显著增加(0.5—0.7)后减少(0.7—0.9);中小型土壤动物总类群数在郁闭度0.5—0.6显著增加,枯落层类群数在郁闭度0.5—0.8显著增加,0.8—0.9显著减少。4)大型、中小型土壤动物多样性在土层中差异显著。中小型土壤动物Simpson优势度指数随郁闭度增大而减小,Shannon-Wiener多样性指数、Pielou均匀性指数则显著增大,Margalef丰富度指数先显著增高(0.5—0.6)后趋于平稳(0.6—0.9);大型土壤动物Jaccard相似性指数低于中小型。5)CCA分析表明,不同类群土壤动物对环境因子响应不同,郁闭度、含水量、有机质及全P对土壤动物类群影响显著。研究表明,0.7郁闭度马尾松人工林下土壤动物优势度、丰富度适中,林下植被恢复情况较好,该郁闭度可能更有利于土壤动物多样性和群落稳定性。     

The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold

Background

An ornamental plant often seen in gardens and farmhouses, Musa basjoo Siebold can also be used as Chinese herbal medicine. Its pseudostem and leaves are diuretic; its root can be decocted together with ginger and licorice to cure gonorrhea and diabetes; the decoct soup of its pseudostem can help relieve heat, and the decoct soup of its dried flower can treat cerebral hemorrhage. There have not been many chloroplast genome studies on M. basjoo Siebold.

Methods and results

We characterized its complete chloroplast genome using Novaseq 6000 sequencing. This paper shows that the length of the chloroplast genome M. basjoo Siebold is 172,322 bp, with 36.45% GC content. M. basjoo Siebold includes a large single-copy region of 90,160 bp, a small single-copy region of 11,668 bp, and a pair of inverted repeats of 35,247 bp. Comparing the genomic structure and sequence data of closely related species, we have revealed the conserved gene order of the IR and LSC/SSC regions, which has provided a very inspiring discovery for future phylogenetic research.

Conclusions

Overall, this study has constructed an evolutionary tree of the genus Musa species with the complete chloroplast genome sequence for the first time. As can be seen, there is no obvious multi-branching in the genus, and M. basjoo Siebold and Musa itinerans are the closest relatives.

     

SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing

Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.