Abstract:
:Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes in various aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community.
journal_name
Nat Communjournal_title
Nature communicationsauthors
Wang K,Wang D,Zheng X,Qin A,Zhou J,Guo B,Chen Y,Wen X,Ye W,Zhou Y,Zhu Ydoi
10.1038/s41467-019-12575-xsubject
Has Abstractpub_date
2019-10-17 00:00:00pages
4714issue
1issn
2041-1723pii
10.1038/s41467-019-12575-xjournal_volume
10pub_type
杂志文章abstract::Selection rules are of vital importance in determining the basic optical properties of atoms, molecules and semiconductors. They provide general insights into the symmetry of the system and the nature of relevant electronic states. A two-dimensional electron gas in a magnetic field is a model system where optical tran...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-16844-y
更新日期:2020-06-10 00:00:00
abstract::Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-16282-w
更新日期:2020-05-15 00:00:00
abstract::Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms14860
更新日期:2017-03-30 00:00:00
abstract::Thousands of tons of isotopic mixtures are processed annually for heavy-water production and tritium decontamination. The existing technologies remain extremely energy intensive and require large capital investments. New approaches are needed to reduce the industry's footprint. Recently, micrometre-size crystals of gr...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms15215
更新日期:2017-05-09 00:00:00
abstract::Graphene has an extremely high in-plane strength yet considerable out-of-plane softness. High crystalline order of graphene assemblies is desired to utilize their in-plane properties, however, challenged by the easy formation of chaotic wrinkles for the intrinsic softness. Here, we find an intercalation modulated plas...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-16494-0
更新日期:2020-05-27 00:00:00
abstract::Classic, model-based theory of land-atmosphere interactions across the Sahel promote positive vegetation-rainfall feedbacks dominated by surface albedo mechanism. However, neither the proposed positive vegetation-rainfall feedback nor its underlying albedo mechanism has been convincingly demonstrated using observation...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-017-02021-1
更新日期:2017-11-30 00:00:00
abstract::In Drosophila, a complex consisting of Calypso and ASX catalyzes H2A deubiquitination and has been reported to act as part of the Polycomb machinery in transcriptional silencing. The mammalian homologs of these proteins (BAP1 and ASXL1/2/3, respectively), are frequently mutated in various cancer types, yet their preci...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-018-08255-x
更新日期:2019-01-21 00:00:00
abstract::Artificially improving traits of cultivated alfalfa (Medicago sativa L.), one of the most important forage crops, is challenging due to the lack of a reference genome and an efficient genome editing protocol, which mainly result from its autotetraploidy and self-incompatibility. Here, we generate an allele-aware chrom...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-16338-x
更新日期:2020-05-19 00:00:00
abstract::Some Bacteroidetes and other human colonic bacteria can degrade arabinoxylans, common polysaccharides found in dietary fiber. Previous work has identified gene clusters (polysaccharide-utilization loci, PULs) for degradation of simple arabinoxylans. However, the degradation of complex arabinoxylans (containing side ch...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-20737-5
更新日期:2021-01-19 00:00:00
abstract::Schwann cells (SCs) generate the myelin wrapping of peripheral nerve axons and are promising candidates for cell therapy. However, to date a renewable source of SCs is lacking. In this study, we show the conversion of skin fibroblasts into induced Schwann cells (iSCs) by driving the expression of two transcription fac...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms14088
更新日期:2017-02-07 00:00:00
abstract::β-Diguetoxin-Dc1a (Dc1a) is a toxin from the desert bush spider Diguetia canities that incapacitates insects at concentrations that are non-toxic to mammals. Dc1a promotes opening of German cockroach voltage-gated sodium (Nav) channels (BgNav1), whereas human Nav channels are insensitive. Here, by transplanting common...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms5350
更新日期:2014-07-11 00:00:00
abstract::The strong metal-support interaction (SMSI) has long been studied in heterogonous catalysis on account of its importance in stabilizing active metals and tuning catalytic performance. As a dynamic process taking place at the metal-support interface, the SMSI is closely related to the metal surface properties which are...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-19484-4
更新日期:2020-11-16 00:00:00
abstract::Zeolite catalysis is determined by a combination of pore architecture and Brønsted acidity. As Brønsted acid sites are formed by the substitution of AlO4 for SiO4 tetrahedra, it is of utmost importance to have information on the number as well as the location and neighbouring sites of framework aluminium. Unfortunatel...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms8589
更新日期:2015-07-02 00:00:00
abstract::The cycling of iron and organic matter (OM) is thought to have been a major biogeochemical cycle in the early ferruginous oceans which contributed to the deposition of banded iron formations (BIF). However, BIF are deficient in OM, which is postulated to be the result of near-complete oxidation of OM during iron reduc...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-019-12975-z
更新日期:2019-11-04 00:00:00
abstract::Quantum Hall edge channels offer an efficient and controllable platform to study quantum transport in one dimension. Such channels are a prospective tool for the efficient transfer of quantum information at the nanoscale, and play a vital role in exposing intriguing physics. Electric current along the edge carries ene...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-019-11888-1
更新日期:2019-09-02 00:00:00
abstract::China has enacted a series of policies since 2015 to substitute electricity for in-home combustion for rural residential heating. The Electric Heating Policy (EHP) has contributed to significant improvements in air quality, benefiting hundreds of millions of people. This shift, however, has resulted in a sharp increas...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-19854-y
更新日期:2020-11-27 00:00:00
abstract::In LaAlO(3)/SrTiO(3) heterointerfaces, charge carriers migrate from the LaAlO(3) to the interface in an electronic reconstruction. Magnetism has been observed in LaAlO(3)/SrTiO(3), but its relationship to the interface conductivity is unknown. Here we show that reconstruction is necessary, but not sufficient, for the ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms1931
更新日期:2012-06-26 00:00:00
abstract::Noble metal nanoparticles stabilized by organic ligands are important for applications in assembly, site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, molecular recognition and molecular electronics, and catalysis. Here we report crystal structures and theoretical analysis of three Ag...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms3422
更新日期:2013-01-01 00:00:00
abstract::Polarization-driven resistive switching in ferroelectric tunnel junctions (FTJs)--structures composed of two electrodes separated by an ultrathin ferroelectric barrier--offers new physics and materials functionalities, as well as exciting opportunities for the next generation of non-volatile memories and logic devices...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms6518
更新日期:2014-11-24 00:00:00
abstract::Among calcareous nannofossils, important primary producers in Jurassic and Cretaceous oceans, nannoconids were carbonate rock-forming organisms. During the late Barremian and early Aptian (~126 to 122 million years ago), nannoconids went through a crisis culminating during the Oceanic Anoxic Event 1a. Here we present ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms2698
更新日期:2013-01-01 00:00:00
abstract::Hearing relies on mechanical stimulation of stereocilia bundles on the sensory cells of the inner ear. When sound hits the ear, each stereocilium pivots about a neck-like taper near their base. More than three decades of research have established that sideways deflection of stereocilia is essential for converting mech...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms2100
更新日期:2012-01-01 00:00:00
abstract::The interaction of lipids and proteins plays an important role in plasma membrane bioactivity, and much can be learned from their diffusion characteristics. Here we present the combination of super-resolution STED microscopy with scanning fluorescence correlation spectroscopy (scanning STED-FCS, sSTED-FCS) to characte...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms6412
更新日期:2014-11-20 00:00:00
abstract::Ultrafast materials science promises optical control of physical properties of solids. Continuous-wave circularly polarized laser driving was predicted to induce a light-matter coupled state with an energy gap and a quantum Hall effect, coined Floquet topological insulator. Whereas the envisioned Floquet topological i...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms8047
更新日期:2015-05-11 00:00:00
abstract::Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor β-retinoi...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-017-00981-y
更新日期:2017-10-11 00:00:00
abstract::An essential issue in the development of materials presenting an accurately functionalized surface is to achieve control of layer structuring. Whereas the very popular method based on the spontaneous adsorption of alkanethiols on metal faces stability problems, the reductive electrografting of aryldiazonium salts yiel...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms2121
更新日期:2012-01-01 00:00:00
abstract::It is commonly assumed that neural systems efficiently process natural sensory input. However, the mechanisms by which such efficient processing is achieved, and the consequences for perception and behaviour remain poorly understood. Here we show that small conductance calcium-activated potassium (SK) channels enable ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms11353
更新日期:2016-04-18 00:00:00
abstract::The high photon flux and femtosecond pulse duration of hard X-ray free-electron lasers have spurred a large variety of novel and fascinating experiments in physical, chemical and biological sciences. Many of these experiments depend fundamentally on a clean, well-defined wavefront. Here we explore the wavefront proper...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms1950
更新日期:2012-07-10 00:00:00
abstract::The shift from maternal to embryonic control is a critical developmental milestone in preimplantation development. Widespread transcriptomic and epigenetic remodeling facilitate this transition from terminally differentiated gametes to totipotent blastomeres, but the identity of transcription factors (TF) and genomic ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-18508-3
更新日期:2020-09-17 00:00:00
abstract::The immunogenic heat shock proteins (HSPs) gp96, hsp70 and calreticulin (CRT) bind to CD91 on antigen-presenting cells (APCs) for cross-presentation of the HSP-chaperoned peptides. This event leads to priming of T-cell responses. Here we show that CD91 serves as a signalling receptor for these HSPs, allowing for the m...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms1524
更新日期:2011-11-01 00:00:00
abstract::A challenge for neuroscience is to understand the conscious and unconscious processes underlying construction of willed actions. We investigated the neural substrate of human motor awareness during awake brain surgery. In a first experiment, awake patients performed a voluntary hand motor task and verbally monitored t...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-14517-4
更新日期:2020-02-04 00:00:00