Severe Bottleneck Research Articles

Blow to the Northeast? Intraspecific differentiation of Populus davidiana suggests a north‐eastward skew of a phylogeographic break in East Asia

AbstractAimThere is increasing interest in the role that biological traits, and historical and biogeographic processes, play in the formation of phylogeographic patterns. An arid belt that once existed in northern China might have affected many plants, but this has yet to be tested in an arid‐tolerant, wind‐dispersed species. Here, we tested how intrinsic and extrinsic factors have affected the phylogeography of Populus davidiana.LocationEast Asia.MethodsGenetic variation was surveyed across 40 populations (555 individuals) covering the Chinese range of P. davidiana, using 16 nuclear microsatellite loci (nSSRs) and four chloroplast fragments (cpDNA). Demographic and migration hypotheses were tested using coalescent‐based approaches, and the present and past potential distributions were predicted using species distribution modelling.ResultsMolecular data divide P. davidiana into two lineages, north‐eastern China (NECR) and central and northern China (CNCR); however, the dividing line is around 118ºE for nSSRs, but 122ºE for cpDNA. The range and habitat of the two lineages barely overlap at present, and their ecological separation may have initiated around the Pliocene‐Quaternary boundary, when major intraspecific cpDNA clades diverged. NECR and CNCR experienced post‐glacial north‐eastward and northward range shifts respectively. Bi‐directional historical gene flow was detected between NECR and CNCR for both bi‐parentally inherited nSSRs and maternally inherited cpDNA. Demographic inferences suggest a severe bottleneck for CNCR and especially NECR, around the latest Pleistocene.Main conclusionsThe phylogeographic break within P. davidiana reflects the impacts of biogeographic history, climate and biological traits. Its plumed, wind‐dispersed seeds might be especially significant because prevailing south‐western spring winds may have moved the NECR‐CNCR boundary further east than similar phylogenetic breaks in other species, and also moved the cpDNA boundary relative to that for nuclear markers. Biological traits, therefore, should also be considered when examining the genetic and ecological differentiation between closely related taxa.

Cultivated Tomato (Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes.

In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest (Solanum pimpinellifolium) and most distantly related (S. neorickii) species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships. A dramatic reduction in genetic diversity was detected in cultivated tomatoes, nonetheless, a few de novo mutations, which still differentiated the cultivated tomatoes from the closest wild relative S. pimpinellifolium, were detected and are potentially utilizable as diagnostic markers. Phylogenetic analyses confirmed that S. pimpinellifolium is the closest ancestor of all cultivated tomatoes. Local accessions all clustered together and were strictly related with other cultivated tomatoes (S. lycopersicum group). Noteworthy, S. lycopersicum var. cerasiforme resulted in a mixture of both cultivated and wild tomato genotypes since one of the two analyzed accessions clustered with cultivated tomato, whereas the other with S. pimpinellifolium. Overall, our results revealed a very reduced cytoplasmic variability in cultivated tomatoes and suggest the occurrence of a cytoplasmic bottleneck during their domestication.

Operationalizing smart specialization in a Portuguese follower region

The inability of the European Union (EU) to grow has raised questions regarding the effectiveness of competitiveness and growth policies. To increase efficacy, the EU has determined that regions must undergo an exercise in smart specialization and devise a strategy for the same. However, particularly in follower regions facing severe locked-in problems and structural bottlenecks, the application of smart specialization may require adjustments and a more dynamic vision, especially with regard to the follower regions. Furthermore, many operational issues arise in the programming and policy-devising stages. This article aims to contribute to this debate by proposing a framework to guide the selection of priorities and by applying the proposed framework to the Portuguese North region.

Genetic Markers of Adaptation of Plasmodium falciparum to Transmission by American Vectors Identified in the Genomes of Parasites from Haiti and South America.

The malaria parasite, Plasmodium falciparum, was introduced into Hispaniola and other regions of the Americas through the slave trade spanning the 16th through the 19th centuries. During this period, more than 12 million Africans were brought across the Atlantic to the Caribbean and other regions of the Americas. Since malaria is holoendemic in West Africa, a substantial percentage of these individuals carried the parasite. St. Domingue on Hispaniola, now modern-day Haiti, was a major port of disembarkation, and malaria is still actively transmitted there. We undertook a detailed study of the phylogenetics of the Haitian parasites and those from Colombia and Peru utilizing whole-genome sequencing. Principal-component and phylogenetic analyses, based upon single nucleotide polymorphisms (SNPs) in protein coding regions, indicate that, despite the potential for millions of introductions from Africa, the Haitian parasites share an ancestral relationship within a well-supported monophyletic clade with parasites from South America, while belonging to a distinct lineage. This result, in stark contrast to the historical record of parasite introductions, is best explained by a severe population bottleneck experienced by the parasites introduced into the Americas. Here, evidence is presented for targeted selection of rare African alleles in genes which are expressed in the mosquito stages of the parasite's life cycle. These genetic markers support the hypothesis that the severe population bottleneck was caused by the required adaptation of the parasite to transmission by new definitive hosts among the Anopheles (Nyssorhynchus) spp. found in the Caribbean and South America.IMPORTANCE Historical data suggest that millions of P. falciparum parasite lineages were introduced into the Americas during the trans-Atlantic slave trade, which would suggest a paraphyletic origin of the extant isolates in the Western Hemisphere. Our analyses of whole-genome variants show that the American parasites belong to a well-supported monophyletic clade. We hypothesize that the required adaptation to American vectors created a severe bottleneck, reducing the effective introduction to a few lineages. In support of this hypothesis, we discovered genes expressed in the mosquito stages of the life cycle that have alleles with multiple, high-frequency or fixed, nonsynonymous mutations in the American populations which are rarely found in African isolates. These alleles appear to be in gene products critical for transmission through the anopheline vector. Thus, these results may inform efforts to develop novel transmission-blocking vaccines by identifying parasite proteins functionally interacting with the vector that are important for successful transmission. Further, to the best of our knowledge, these are the first whole-genome data available from Haitian P. falciparum isolates. Defining the genome of these parasites provides genetic markers useful for mapping parasite populations and monitoring parasite movements/introductions.

Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step.

The ongoing COVID-19 pandemic has created an unprecedented need for rapid diagnostic testing. The World Health Organization (WHO) recommends a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription–quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. The goal of this study was to determine whether SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether. The direct RT-qPCR approach correctly identified 92% of a reference set of blinded NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Importantly, the direct method had sufficient sensitivity to reliably detect those patients with viral loads that correlate with the presence of infectious virus. Thus, this strategy has the potential to ease supply choke points to substantially expand COVID-19 testing and screening capacity and should be applicable throughout the world.

HyCloud: Tweaking Hybrid Cloud Storage Services for Cost-Efficient Filesystem Hosting

Today’s cloud storage infrastructures typically provide two distinct types of services for hosting files: object storage like Amazon S3 and filesystem storage like Amazon EFS. In practice, a cloud storage user often desires the advantages of both—efficient filesystem operations with a low unit storage price. An intuitive approach to achieving this goal is to combine the two types of services, e.g., by hosting large files in S3 and small files together with directory structures in EFS. Unfortunately, our benchmark experiments indicate that the clients’ download performance for large files becomes a severe system bottleneck. In this article, we attempt to address the bottleneck with little overhead by carefully tweaking the usages of S3 and EFS. Guided by two key observations, we design and implement an open-source system called HyCloud. It automatically invokes the data APIs of S3 and EFS on behalf of users, and intelligently schedules the data transfer among S3, EFS and the clients in a distributed manner. Real-world evaluations demonstrate that the unit storage price of HyCloud is close to that of S3, and the filesystem operations are executed as quickly as in EFS in most times (sometimes even more quickly than in EFS).

Ape Origins of Human Malaria.

African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottlenecks followed by rapid population expansion. A putative new Plasmodium species widespread in chimpanzees, gorillas, and bonobos places the origin of Plasmodium malariae in Africa. Here, we review what is known about the origins and evolutionary history of all human-infective Plasmodium species, the time and circumstances of their emergence, and the diversity, host specificity, and zoonotic potential of their ape counterparts.

Infection with multiple HIV-1 founder variants is associated with lower viral replicative capacity, faster CD4+ T cell decline and increased immune activation during acute infection.

HIV-1 transmission is associated with a severe bottleneck in which a limited number of variants from a pool of genetically diverse quasispecies establishes infection. The IAVI protocol C cohort of discordant couples, female sex workers, other heterosexuals and men who have sex with men (MSM) present varying risks of HIV infection, diverse HIV-1 subtypes and represent a unique opportunity to characterize transmitted/founder viruses (TF) where disease outcome is known. To identify the TF, the HIV-1 repertoire of 38 MSM participants' samples was sequenced close to transmission (median 21 days post infection, IQR 18-41) and assessment of multivariant infection done. Patient derived gag genes were cloned into an NL4.3 provirus to generate chimeric viruses which were characterized for replicative capacity (RC). Finally, an evaluation of how the TF virus predicted disease progression and modified the immune response at both acute and chronic HIV-1 infection was done. There was higher prevalence of multivariant infection compared with previously described heterosexual cohorts. A link was identified between multivariant infection and replicative capacity conferred by gag, whereby TF gag tended to be of lower replicative capacity in multivariant infection (p = 0.02) suggesting an overall lowering of fitness requirements during infection with multiple variants. Notwithstanding, multivariant infection was associated with rapid CD4+ T cell decline and perturbances in the CD4+ T cell and B cell compartments compared to single variant infection, which were reversible upon control of viremia. Strategies aimed at identifying and mitigating multivariant infection could contribute toward improving HIV-1 prognosis and this may involve strategies that tighten the stringency of the transmission bottleneck such as treatment of STI. Furthermore, the sequences and chimeric viruses help with TF based experimental vaccine immunogen design and can be used in functional assays to probe effective immune responses against TF.

Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi (Notiomystis cincta).

To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.

Genetic analysis reveals long-standing population differentiation and high diversity in the rust pathogen Melampsora lini.

A priority for research on infectious disease is to understand how epidemiological and evolutionary processes interact to influence pathogen population dynamics and disease outcomes. However, little is understood about how population adaptation changes across time, how sexual vs. asexual reproduction contribute to the spread of pathogens in wild populations and how diversity measured with neutral and selectively important markers correlates across years. Here, we report results from a long-term study of epidemiological and genetic dynamics within several natural populations of the Linum marginale-Melampsora lini plant-pathogen interaction. Using pathogen isolates collected from three populations of wild flax (L. marginale) spanning 16 annual epidemics, we probe links between pathogen population dynamics, phenotypic variation for infectivity and genomic polymorphism. Pathogen genotyping was performed using 1567 genome-wide SNP loci and sequence data from two infectivity loci (AvrP123, AvrP4). Pathogen isolates were phenotyped for infectivity using a differential set. Patterns of epidemic development were assessed by conducting surveys of infection prevalence in one population (Kiandra) annually. Bayesian clustering analyses revealed host population and ecotype as key predictors of pathogen genetic structure. Despite strong fluctuations in pathogen population size and severe annual bottlenecks, analysis of molecular variance revealed that pathogen population differentiation was relatively stable over time. Annually, varying levels of clonal spread (0–44.8%) contributed to epidemics. However, within populations, temporal genetic composition was dynamic with rapid turnover of pathogen genotypes, despite the dominance of only four infectivity phenotypes across the entire study period. Furthermore, in the presence of strong fluctuations in population size and migration, spatial selection may maintain pathogen populations that, despite being phenotypically stable, are genetically highly dynamic.

Scalable Manufacturing of MXene Films: Moving toward Industrialization

Industry-scale manufacturing techniques hold the key to the ultimate commercialization of MXene products. In Matter, Taylor, Gogotsi, and colleagues demonstrate a drop-casting method to prepare scalable and micro-patternable MXene films on hydrophobic substrates, highlighting the excellent potential for the commercial application in electromagnetic interference shielding.

Evolution of PAPR Reduction Techniques: A Wavelet Based OFDM Approach

Orthogonal frequency division multiplexing (OFDM) is considered among the most suitable multiplexing technique for realizing high speed wireless communication in the present era. Substantially immune to frequency selective fading, high spectral efficiency and superior data rate made OFDM a preferred and popular modulation technique in 3rd generation and 4th generation mobile communication systems. The high value of peak to average power ratio (PAPR) and inter carrier interference (ICI) are the most severe bottleneck for OFDM applications to deliver high performance in communication system. The present work portraits most of conventional and current PAPR reduction techniques through comparative study assisted by simulative analysis which foretells future research potential in wavelet based OFDM to generate more efficient system. PAPR optimization is achieved through hybridization of wavelet with clipping and companding techniques. Different modulation techniques have been analyzed (through Matlab simulation) over proposed hybrid model to observe the PAPR reduction in OFDM system.

Paying attention to speech: The role of working memory capacity and professional experience.

Managing attention in multispeaker environments is a challenging feat that is critical for human performance. However, why some people are better than others in allocating attention appropriately remains highly unknown. Here, we investigated the contribution of two factors-working memory capacity (WMC) and professional experience-to performance on two different types of attention task: selective attention to one speaker and distributed attention among multiple concurrent speakers. We compared performance across three groups: individuals with low (n = 20) and high (n = 25) WMC, and aircraft pilots (n = 24), whose profession poses extremely high demands for both selective and distributed attention to speech. Results suggests that selective attention is highly effective, with good performance maintained under increasingly adverse conditions, whereas performance decreases substantially with the requirement to distribute attention among a larger number of speakers. Importantly, both types of attention benefit from higher WMC, suggesting reliance on some common capacity-limited resources. However, only selective attention was further improved in the pilots, pointing to its flexible and trainable nature, whereas distributed attention seems to suffer from more fixed and severe processing bottlenecks.

Genomic Analysis of the Only Blind Cichlid Reveals Extensive Inactivation in Eye and Pigment Formation Genes.

Trait loss represents an intriguing evolutionary problem, particularly when it occurs across independent lineages. Fishes in light-poor environments often evolve “troglomorphic” traits, including reduction or loss of both pigment and eyes. Here, we investigate the genomic basis of trait loss in a blind and depigmented African cichlid, Lamprologus lethops, and explore evolutionary forces (selection and drift) that may have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower Congo River. Available evidence suggests that it inhabits deep, low-light habitats. Using genome sequencing, we show that genes related to eye formation and pigmentation, as well as other traits associated with troglomorphism, accumulated inactivating mutations rapidly after speciation. A number of the genes affected in L. lethops are also implicated in troglomorphic phenotypes in Mexican cavefish (Astyanax mexicanus) and other species. Analysis of heterozygosity patterns across the genome indicates that L. lethops underwent a significant population bottleneck roughly 1 Ma, after which effective population sizes remained low. Branch-length tests on a subset of genes with inactivating mutations show little evidence of directional selection; however, low overall heterozygosity may reduce statistical power to detect such signals. Overall, genome-wide patterns suggest that accelerated genetic drift from a severe bottleneck, perhaps aided by directional selection for the loss of physiologically expensive traits, caused inactivating mutations to fix rapidly in this species.

Population connectivity and genetic structure of Asian green mussel, Perna viridis along Indian waters assessed using mitochondrial markers.

Perna viridis (Linnaeus, 1758), the Asian green mussel, belonging to the family Mytilidae is widely distributed along the Indian coast. The species is majorly found in southeastern countries and is considered an ideal candidate for aquaculture due to its high nutritional value and growth rate. Obtaining their genetic information is essential for their sustainable capture-based production. In the present study, genetic variation, population structure, and demographic processes of the populations across the distribution of this species were assessed using the mitochondrial DNA ATPase6 and cytb gene. In total, we selected 170 samples from five localities across the Indian subcontinent including Andaman Sea. Sequence analysis of partial cytb (885bp) and ATPase6 (714bp) genes revealed 45 and 58 haplotypes, respectively. The significant coefficient of genetic differentiation (FST: 0.255 for cytb and 0.252 for ATPase6) and analyses of molecular variance indicated three varieties of stocks, namely Arabian Sea, Bay of Bengal, and Andaman Sea. All the populations showed low nucleotide diversity, suggesting severe historical bottleneck events and high haplotype diversity, indicating population expansion. The genetic variation and demographic process reported in this study will form the baseline information for framing policies, which can be adopted while planning stock specific ranching and relaying programmes in the Indian subcontinent with view to enhance and manage the fishery.

Urban Food Markets and the Lockdown in India

On March 24, 2020, the Government of India announced a 21-day national lockdown that has since been extended to May 3, 2020. The lockdown has left urban food markets in disarray with severe supply bottlenecks and restrictions on doing business. At a time when food prices in India were declining consistently, supply disruptions consequent to the lockdown have reversed the trend. Based on an analysis of publicly available data on wholesale and retail prices for 22 commodities from 114 Centres, we find that prices have increased since the lockdown and show no signs of reverting to the pre-lockdown levels as of April 21, 2020. Average price increases are to the tune of over 6% for several pulses, over 3.5% for most edible oils, 15% for potato 28% for tomato in the 28 days post-lockdown compared to prices during the month preceding the lockdown. We also find that smaller cities have seen a much higher increase in prices with at least a few cities seeing a rise in retail food prices by as much as 20%. A survey of 50 food retailers in 14 cities reveal serious operational challenges associated with sourcing supplies, transportation and police harassment. At the same time, several innovative arrangements have evolved as well. The paper reviews these briefly and outlines some policy concerns.

Patterns of genotype variation and demographic history in Lindera glauca (Lauraceae), an apomict‐containing dioecious forest tree

AbstractAimThe historical circumstances promoting the transition from sexual to apomictic reproduction in dioecious plant species remain poorly understood. Here, we investigated the divergence and demographic history of Lindera glauca, a dioecious tree generally considered to be obligate sexual in China while comprising only females (apomicts) in Japan.LocationEast Asia (China and Japan).TaxonLindera glauca (Lauraceae)MethodsSamples from 42 populations were genotyped using chloroplast DNA and nuclear microsatellite (nSSR) loci to assess genetic diversity and structure. The nSSR genotypes were also used to detect the mode of reproduction in Chinese and Japanese populations, respectively. Approximate Bayesian Computation on nSSRs and palaeoclimatic niche models provided further insights into the evolutionary and population demographic history.ResultsChinese L. glauca was found to harbour both sexual and asexual genotypes. Chinese and Japanese L. glauca underwent likely severe bottlenecks during a mid‐Pleistocene glacial period, possibly marking the split time of the island lineage from its mainland ancestor. In contrast to Chinese L. glauca, the Japanese lineage experienced a massive range contraction during the Last Glacial Maximum and postglacial expansions.Main ConclusionsWhile reproductive assurance plays an important role in the selection of apomixis in Chinese L. glauca, the lack of male plants in Japan likely reflects population demographic history driven by (Late) Quaternary climate change. Hence, the present study demonstrates a possible link between palaeoclimate change and the transition to exclusively apomictic reproduction in a dioecious tree.

Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high-coverage reference genome for the Siberian roe deer (C. pygargus). We find progressive reductions in effective population size (Ne ), despite very large census sizes in modern C. capreolus populations and show that low Ne has impacted the C. capreolus genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among C. capreolus populations, including a historically documented founder population that has been through a severe bottleneck. During each phylogenetic transition there is evidence for selection (from dN/dS and nucleotide diversity tests), including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even-toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.

Put an elephant into a fridge

In today's data centers, memory-based key-value systems, such as Memcached and Redis, play an indispensable role in providing high-speed data services. The rapidly growing capacity and quickly falling price of DRAM memory in the past years have enabled us to create a large memory-based key-value store, which is able to serve hundreds of Gigabytes to even Terabytes of key-value data all in memory. Unfortunately, CPU cache in modern processors has not seen a similar growth in capacity, still remaining at the level of a few dozens of Megabytes. Such an extremely low cache-to-memory ratio (less than 0.1%) poses a significant new challenge---the limited CPU cache is becoming a severe performance bottleneck that hinders us from fully exploiting the great potential of high-speed memory-based key-value stores. To address this critical challenge, we propose a highly cache-efficient scheme, called Cavast , to optimize the cache utilization of large-capacity in-memory key-value stores. Our goal is to maximize cache efficiency and system performance without any hardware changes. We first present two light-weight, software-only mechanisms to enable user to indirectly control the cache content at application level. Then we propose a set of optimization policies to address several critical design issues that impair cache's efficacy in the current key-value store systems. By carefully reorganizing the data layout in memory, redesigning the hash indexing structure, and offloading garbage collection, we can effectively improve the utilization of the limited cache space. We have developed a module in Linux as a kernel-level support, and implemented two prototypes based on Memcached and Redis with the proposed Cavast scheme. Our experimental studies show promising results. On a 6-core Intel Xeon processor with only 15-MB cache, we can raise the cache hit ratio up to 82.7% with a very small cache-to-memory ratio (0.023%), and significantly increase the key-value system throughput by a factor of up to 4.2.

Layerwise Sparse Coding for Pruned Deep Neural Networks with Extreme Compression Ratio

Deep neural network compression is important and increasingly developed especially in resource-constrained environments, such as autonomous drones and wearable devices. Basically, we can easily and largely reduce the number of weights of a trained deep model by adopting a widely used model compression technique, e.g., pruning. In this way, two kinds of data are usually preserved for this compressed model, i.e., non-zero weights and meta-data, where meta-data is employed to help encode and decode these non-zero weights. Although we can obtain an ideally small number of non-zero weights through pruning, existing sparse matrix coding methods still need a much larger amount of meta-data (may several times larger than non-zero weights), which will be a severe bottleneck of the deploying of very deep models. To tackle this issue, we propose a layerwise sparse coding (LSC) method to maximize the compression ratio by extremely reducing the amount of meta-data. We first divide a sparse matrix into multiple small blocks and remove zero blocks, and then propose a novel signed relative index (SRI) algorithm to encode the remaining non-zero blocks (with much less meta-data). In addition, the proposed LSC performs parallel matrix multiplication without full decoding, while traditional methods cannot. Through extensive experiments, we demonstrate that LSC achieves substantial gains in pruned DNN compression (e.g., 51.03x compression ratio on ADMM-Lenet) and inference computation (i.e., time reduction and extremely less memory bandwidth), over state-of-the-art baselines.