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      Mikania micrantha genome provides insights into the molecular mechanism of rapid growth

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          Abstract

          Mikania micrantha is one of the top 100 worst invasive species that can cause serious damage to natural ecosystems and substantial economic losses. Here, we present its 1.79 Gb chromosome-scale reference genome. Half of the genome is composed of long terminal repeat retrotransposons, 80% of which have been derived from a significant expansion in the past one million years. We identify a whole genome duplication event and recent segmental duplications, which may be responsible for its rapid environmental adaptation. Additionally, we show that M. micrantha achieves higher photosynthetic capacity by CO 2 absorption at night to supplement the carbon fixation during the day, as well as enhanced stem photosynthesis efficiency. Furthermore, the metabolites of M. micrantha can increase the availability of nitrogen by enriching the microbes that participate in nitrogen cycling pathways. These findings collectively provide insights into the rapid growth and invasive adaptation.

          Abstract

          Mikania micrantha is an extremely fast-growing invasive plant species that can cause serious damage to natural ecosystems. Here, the authors assemble its chromosome-scale reference genome and explore possible mechanisms that contribute to its rapid growth.

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          KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

          We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5’ to 3’ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.
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            Synteny and collinearity in plant genomes.

            Correlated gene arrangements among taxa provide a valuable framework for inference of shared ancestry of genes and for the utilization of findings from model organisms to study less-well-understood systems. In angiosperms, comparisons of gene arrangements are complicated by recurring polyploidy and extensive genome rearrangement. New genome sequences and improved analytical approaches are clarifying angiosperm evolution and revealing patterns of differential gene loss after genome duplication and differential gene retention associated with evolution of some morphological complexity. Because of variability in DNA substitution rates among taxa and genes, deviation from collinearity might be a more reliable phylogenetic character.
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              LTR_retriever: a highly accurate and sensitive program for identification of long terminal-repeat retrotransposons

              Long terminal repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. The identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the well-conserved structure, multiple programs were developed for the de novo identification of LTR-RTs; however, these programs are associated with low specificity and high false discovery rates. Here, we report LTR_retriever, a multithreading-empowered Perl program that identifies LTR-RTs and generates high-quality LTR libraries from genomic sequences. LTR_retriever demonstrated significant improvements by achieving high levels of sensitivity (91%), specificity (97%), accuracy (96%), and precision (90%) in rice (Oryza sativa). LTR_retriever is also compatible with long sequencing reads. With 40k self-corrected PacBio reads equivalent to 4.5× genome coverage in Arabidopsis (Arabidopsis thaliana), the constructed LTR library showed excellent sensitivity and specificity. In addition to canonical LTR-RTs with 5'-TG…CA-3' termini, LTR_retriever also identifies noncanonical LTR-RTs (non-TGCA), which have been largely ignored in genome-wide studies. We identified seven types of noncanonical LTRs from 42 out of 50 plant genomes. The majority of noncanonical LTRs are Copia elements, with which the LTR is four times shorter than that of other Copia elements, which may be a result of their target specificity. Strikingly, non-TGCA Copia elements are often located in genic regions and preferentially insert nearby or within genes, indicating their impact on the evolution of genes and their potential as mutagenesis tools.
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                Author and article information

                Contributors
                pengchl@scib.ac.cn
                qianwanqiang@caas.cn
                fanwei@caas.cn
                wanfanghao@caas.cn
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                17 January 2020
                17 January 2020
                2020
                : 11
                : 340
                Affiliations
                [1 ]ISNI 0000 0001 0526 1937, GRID grid.410727.7, Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, , Chinese Academy of Agricultural Sciences, ; Shenzhen, 518120 China
                [2 ]ISNI 0000 0000 9546 5767, GRID grid.20561.30, Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture; College of Natural Resources and Environment, , South China Agricultural University, ; Guangzhou, 510642 China
                [3 ]ISNI 0000 0004 0368 7397, GRID grid.263785.d, Institute of Ecological Science, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development; Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring; School of Life Science, , South China Normal University, ; Guangzhou, 510631 China
                [4 ]ISNI 0000 0000 9546 5767, GRID grid.20561.30, Key Laboratory of Protein Function and Regulation in Agricultural Organisms of Guangdong province, College of Life Science, , South China Agricultural University, ; Guangzhou, 510642 China
                [5 ]ISNI 0000 0001 0526 1937, GRID grid.410727.7, The Institute of Plant Protection, , Chinese Academy of Agricultural Sciences, ; Beijing, 100193 China
                [6 ]Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, 518004 China
                Author information
                http://orcid.org/0000-0002-7840-9450
                http://orcid.org/0000-0002-8754-4195
                http://orcid.org/0000-0002-7023-262X
                http://orcid.org/0000-0001-6385-8862
                http://orcid.org/0000-0001-6149-4989
                http://orcid.org/0000-0001-5036-8733
                Article
                13926
                10.1038/s41467-019-13926-4
                6969026
                31953413
                4ae59c73-db71-4687-a1bd-37fc90315a26
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 29 May 2019
                : 6 December 2019
                Funding
                Funded by: The Science and Technology Planning Project of Guangdong Province, China (2019B030301007)
                Funded by: research program of Urban Management Bureau of Shenzhen Municipality (No. 201914)
                Funded by: National key research and development program of China 2017YFC1200105
                Funded by: National key research and development program of China 2016YFC1200600
                Funded by: Shenzhen science and technology program (JCYJ20170303154245825) Associated fund of Dapeng District (PT20170310 and PT20170309) Agricultural Science and Technology Innovation Program & The Elite Young Scientists Program of CAAS, Fundamental Research Funds for Central Non-profit Scientific Institution (No.Y2017JC01) The Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission (CAAS-XTCX2016) Fund of Key Laboratory of Shenzhen (ZDSYS20141118170111640)
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                dna sequencing,comparative genomics,genome evolution,plant ecology,plant physiology
                Uncategorized
                dna sequencing, comparative genomics, genome evolution, plant ecology, plant physiology

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