Identification of genes under positive selection reveals evolutionary adaptation of Ulva mutabilis

Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Until now,the Ulva mutabilis genome is the only Ulva genome to have been sequenced.To obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from U.mutabilis,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in U.mutabilis.We detected 63 orthologs in U.mutabilis that were considered to be under positive selection.Functional analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.

Gene duplication and functional divergence of new genes contributed to the polar acclimation of Antarctic green algae

Psychrophilic microalgae successfully survive in the extreme and highly variable polar ecosystems,which represent the energy base of most food webs and play a fundamental role in nutrient cycling.The success of microalgae is rooted in their adaptive evolution.Revealing how they have evolved to thrive in extreme polar environments will help us better understand the origin of life in polar ecosystems.We isolated a psychrophilic unicellular green alga,Microglena sp.YARC,from Antarctic sea ice which has a huge genome.Therefore,we predicted that gene replication may play an important role in its polar adaptive evolution.We found that its protein-coding gene number significantly increased and the duplication time was dated between 37 and 48 million years ago,which is consistent with the formation of the circumpolar Southern Ocean.Most duplicated paralogous genes were enriched in pathways related to photosynthesis,DNA repair,and fatty acid metabolism.Moreover,there were a total of 657 Microglena-specific families,including collagen-like proteins.The divergence in the expression patterns of the duplicated and species-specific genes reflects sub-and neo-functionalization during stress acclimation.Overall,key findings from this study provide new information on how gene duplication and their functional novelty contributed to polar algae adaptation to the highly variable polar environmental conditions.

A type of polarimetric parameter for evaluating the reliability of model-based decomposition result and its application

The reliability of the model-based decomposition result,which is seldom investigated,is a key factor in determining whether decomposition parameters can be effectively applied to polarimetric synthetic aperture radar(PolSAR)applications.In this paper,a type of polarimetric parameter for evaluating the reliability of model-based decomposition result is proposed.It originates from the degree of correlation between the scattering models.The main idea is whether the measured power can be assigned to the corresponding scattering model.The more the measured power that can be allocated to the corresponding scattering model,the more reliable the decomposition result.The C-band Radarsat-2,L-band UAVSAR,X-band TerraSAR-X,and L-band E-SAR PolSAR data are selected for experiments.The results show that the type of polarimetric parameter can effectively represent the reliability of the decomposition result.The reliabilities of surface and double-bounce scattering are high in the ocean and orthogonal buildings,respectively.For oriented buildings,the reliability of the decomposition result is lower owing to the overestimation of volume scattering.For forested areas,reliability is generally higher if volume scattering is not overestimated.Furthermore,the results show that the reliability of soil moisture retrieval is positively correlated with surface scattering reliability.

Heterogeneous Parallel Algorithm Design and Performance Optimization for WENO on the Sunway TaihuLight Supercomputer

A Weighted Essentially Non-Oscillatory scheme(WENO) is a solution to hyperbolic conservation laws,suitable for solving high-density fluid interface instability with strong intermittency. These problems have a large and complex flow structure. To fully utilize the computing power of High Performance Computing(HPC) systems, it is necessary to develop specific methodologies to optimize the performance of applications based on the particular system’s architecture. The Sunway TaihuLight supercomputer is currently ranked as the fastest supercomputer in the world. This article presents a heterogeneous parallel algorithm design and performance optimization of a high-order WENO on Sunway TaihuLight. We analyzed characteristics of kernel functions, and proposed an appropriate heterogeneous parallel model. We also figured out the best division strategy for computing tasks,and implemented the parallel algorithm on Sunway TaihuLight. By using access optimization, data dependency elimination, and vectorization optimization, our parallel algorithm can achieve up to 172× speedup on one single node, and additional 58× speedup on 64 nodes, with nearly linear scalability.

MetaOJ: A Massive Distributed Online Judge System

Online Judge(OJ) systems are a basic and important component of computer education. Here, we present MetaOJ, an OJ system that can be used for holding massive programming tests online. MetaOJ is designed to create a distributed, fault-tolerant, and easy-to-scale OJ system from an existing ordinary OJ system by adding several interfaces into it and creating multiple instances of it. Our case on modifying the TUOJ system shows that the modification adds no more than 3% lines of code and the performance loss on a single OJ instance is no more than 12%. We also introduce mechanisms to integrate the system with cloud infrastructure to automate the deployment process. MetaOJ provides a solution for those OJ systems that are designed for a specific programming contest and are now facing performance bottlenecks.

A Comparative Analysis on Weibo and Twitter

Weibo is the Twitter counterpart in China that has attracted hundreds of millions of users. We crawled an almost complete Weibo user network that contains 222 million users and 27 billion links in 2013. This paper analyzes the structural properties of this network, and compares it with a Twitter user network. The topological properties we studied include the degree distributions, connected components, distance distributions, reciprocity,clustering coefficient, Page Rank centrality, and degree assortativity. We find that Weibo users have a higher diversity index, higher Gini index, but a lower reciprocity and clustering coefficient for most of the nodes. A surprising observation is that the reciprocity of Weibo is only about a quarter of the reciprocity of the Twitter user network. We also show that Weibo adoption rate correlates with economic development positively, and Weibo network can be used to quantify the connections between provinces and regions in China. In particular, point-wise mutual information is shown to be accurate in quantifying the strength of connections. We developed an interactive analyzing software framework for this study, and released the data and code online.

Cacheap:Portable and Collaborative I/O Optimization for Graph Processing

Increasingly there is a need to process graphs that are larger than the available memory on today's machines.Many systems have been developed with grapli representations that are efficient and compact for out-of-core processing.A necessary task in these systems is memory management.This paper presents a system called Cacheap which automatically and efficiently manages the available memory to maximize the speed of grapli processing,minimize the amount of disk access,and maximize the utilization of memory for graph data.It has a simple interface that can be easily adopted by existing graph engines.The paper describes the new system,uses it in recent graph engines,and demonstrates its integer factor improvements in the speed of large-scale grapli processing.

Adaptive Bird-like Genome Miniaturization During the Evolution of Scallop Swimming Lifestyle

Genome miniaturization drives key evolutionary innovations of adaptive traits in vertebrates,such as the flight evolution of birds.However,whether similar evolutionary processes exist in invertebrates remains poorly understood.Derived from the second-largest animal phylum,scallops are a special group of bivalve molluscs and acquire the evolutionary novelty of the swimming lifestyle,providing excellent models for investigating the coordinated genome and lifestyle evolution.Here,we show for the first time that genome sizes of scallops exhibit a generally negative correlation with locomotion activity.To elucidate the co-evolution of genome size and swimming lifestyle,we focus on the Asian moon scallop(Amusium pleuronectes)that possesses the smallest known scallop genome while being among scallops with the highest swimming activity.Whole-genome sequencing of A.pleuronectes reveals highly conserved chromosomal macrosynteny and microsynteny,suggestive of a highly contracted but not degenerated genome.Genome reduction of A.pleuronectes is facilitated by significant inactivation of transposable elements,leading to reduced gene length,elevated expression of genes involved in energy-producing pathways,and decreased copy numbers and expression levels of biomineralization-related genes.Similar evolutionary changes of relevant pathways are also observed for bird genome reduction with flight evolution.The striking mimicry of genome miniaturization underlying the evolution of bird flight and scallop swimming unveils the potentially common,pivotal role of genome size fluctuation in the evolution of novel lifestyles in the animal kingdom.

Auxo: A Temporal Graph Management System

As real-world graphs are often evolving over time, interest in analyzing the temporal behavior of graphs has grown. Herein, we propose Auxo, a novel temporal graph management system to support temporal graph analysis. It supports both efficient global and local queries with low space overhead. Auxo organizes temporal graph data in spatio-temporal chunks. A chunk spans a particular time interval and covers a set of vertices in a graph.We propose chunk layout and chunk splitting designs to achieve the desired efficiency and the abovementioned goals. First, by carefully choosing the time split policy, Auxo achieves linear complexity in both space usage and query time. Second, graph splitting further improves the worst-case query time, and reduces the performance variance introduced by splitting operations. Third, Auxo optimizes the data layout inside chunks, thereby significantly improving the performance of traverse-based graph queries. Experimental evaluation showed that Auxo achieved 2:9 to 12:1 improvement for global queries, and 1:7 to 2:7 improvement for local queries, as compared with state-of-the-art open-source solutions.