Comparison of Two Reef Sites on the North Coast of Jamaica over a 15-Year Period

This paper compares two reef sites near Discovery Bay, Jamaica, Dairy Bull and Dancing Lady, from 2000 to 2015. At Dairy Bull reef, with low macroalgal cover (8% in 2002 falling to 1% in 2015) and significant number of Diadema antillarum urchins (c. 5 m-2), live coral cover increased from 13% ± 5% in 2006 after the bleaching event in 2005, to 31% ± 7% in 2008, while live Acropora cervicornis increased from 2% ± 2% in 2006 to 28% ± 5% in 2015. Coral cover levels were at least maintained until 2015, owing mostly to a slight increase in A. cervicornis. Dancing Lady reef however was dominated by macroalgae throughout this period (cover of c. 76% ± 7%), with no D. antillarum and showed little decrease in the already low (6% ± 1%) coral cover in 2005. Growth rates for Siderastrea siderea were similar for both sites (7 mm·yr-1), while growth rates of A. cervicornis and A. palmata were 120.0 ± 30 mm·yr-1 and 71.0 ± 29 mm·yr-1 respectively at Dairy Bull in 2015. At Dancing Lady reef, A. cervicornis colonies which were present from 2003 to 2005 had disappeared in 2006, possibly as a result of the mass bleaching event. It appears that A. cervicornis was the most impacted species during the 2005 bleaching event, but was also the species that recovered fastest after its decline at Dairy Bull.

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements （TEs） have no longer been totally considered as ＂junk DNA＂ for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Tech- nologies based on 3C （chromosome conformation capture） have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions （hESC： r= 0.9, P〈 2.2 × 10^16; IMRg0 fibroblasts： r= 0.94, P 〈 2.2 ×10^16） and also have asignificant positive correlation with some remote functional DNA elements like enhancers and promoters （Enhancer： hESC： r= 0.997, P= 2.3× 10^-4; IMR90： r- 0.934, P= 2 × 10^-2; Promoter： hESC： r= 0.995, P= 3.8 × 10^-4; IMR90： r= 0.996, P = 3.2 × 10^-4）. Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes.

Discovery of a high-altitude ecotype and ancient lineage of Arabidopsis thaliana from Tibet

Arabidopsis thaliana（A, thaliana） has long been a model species for dicotyledon study, and was the first flowering plant to get its genome completed sequenced . Although most wild A. thaliana are collected in Europe, several studies have found a rapid A. thaliaria west-east expansion from Central Asia . The Qinghai-Tibet Plateau （QTP） is close to Central Asia and known for its high altitude, unique environments and biodiversity . However, no wild-type A. thaliana had been either discovered or sequenced from QTP. Studies on the A. thaliana populations collected under 2000 m asl have shown that the adaptive variations associated with climate and altitudinal gradients .