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      The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance

      research-article
      1 , 2 , 3 , 4 , 5 , 3 , 2 , 6 , 7 , 7 , 7 , 1 , 8 , 1 , 1 , 1 , 4 , 9 , 9 , 9 , 2 , 2 , 5 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 7 , 3 , 3 , 3 , 3 , 8 , 7 , 10 , 10 , , 2 , 7 , 8 ,
      BMC Biology
      BioMed Central
      Trachypithecus leucocephalus, Genome assembly, Limestone karsts, Alkali tolerance, Mineral ion binding

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          Abstract

          Background

          Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche.

          Results

          In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies.

          Conclusions

          These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.

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          Most cited references66

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              HISAT: a fast spliced aligner with low memory requirements.

              HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT's hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ∼64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.
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                Author and article information

                Contributors
                cmhuang@ioz.ac.cn
                huyanling@gxmu.edu.cn
                Journal
                BMC Biol
                BMC Biol
                BMC Biology
                BioMed Central (London )
                1741-7007
                8 April 2021
                8 April 2021
                2021
                : 19
                : 67
                Affiliations
                [1 ]Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi 530003 China
                [2 ]GRID grid.256607.0, ISNI 0000 0004 1798 2653, Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, , Guangxi Medical University, ; Nanning, Guangxi 530021 China
                [3 ]GRID grid.459340.f, Annoroad Gene Technology, ; Beijing, 100176 China
                [4 ]Guangxi Chongzuo white headed langur national nature reserve, Chongzuo, Guangxi 532200 China
                [5 ]GRID grid.256607.0, ISNI 0000 0004 1798 2653, School of Information and Management, , Guangxi Medical University, ; Nanning, Guangxi 530021 China
                [6 ]GRID grid.412594.f, Guangxi Reproductive Medical Research Center, , First Affiliated Hospital of Guangxi Medical University, ; Nanning, Guangxi 530021 China
                [7 ]GRID grid.256607.0, ISNI 0000 0004 1798 2653, Life Sciences Institute, , Guangxi Medical University, ; Nanning, Guangxi 530021 China
                [8 ]GRID grid.256607.0, ISNI 0000 0004 1798 2653, Center for Genomic and Personalized Medicine, , Guangxi Medical University, ; Nanning, Guangxi 530021 China
                [9 ]Nanning Animal Zoo, Nanning, Guangxi 530021 China
                [10 ]GRID grid.253663.7, ISNI 0000 0004 0368 505X, College of Life Sciences, Capital Normal University, ; Beijing, 100048 China
                Article
                998
                10.1186/s12915-021-00998-2
                8034193
                33832502
                038d51d2-754b-417d-9abf-0a6f36f3c6ae
                © The Author(s) 2021

                Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 26 November 2020
                : 5 March 2021
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: No. 81472414
                Funded by: Guangxi Forestry Department Foundation
                Award ID: No. 2017001 and No. 2016007
                Funded by: Guangxi Medical University Training Program for Distinguished Young Scholars
                Funded by: by the National Natural Science Foundation of China
                Award ID: No.31672285
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2021

                Life sciences
                trachypithecus leucocephalus,genome assembly,limestone karsts,alkali tolerance,mineral ion binding

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