Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes

Marine Genomics - Tập 45 - Trang 64-71 - 2019
Han Ming Gan1,2,3, Stuart M. Linton2, Christopher M. Austin1,2,3
1Deakin Genomics Centre, Deakin University, Geelong, 3220 Victoria, Australia
2School of Life and Environmental Sciences, Deakin University, Geelong 3220, Victoria, Australia
3School of Science, Monash University Malaysia, Bandar Sunway, 47500, Selangor, Malaysia

Tài liệu tham khảo

Abascal, 2010, TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations, Nucleic Acids Res., 38, W7, 10.1093/nar/gkq291 Aberer, 2014, ExaBayes: massively parallel Bayesian tree inference for the whole-genome era, Mol. Biol. Evol., 31, 2553, 10.1093/molbev/msu236 Adamczewska, 2001, Ecology and behavior of Gecarcoidea natalis, the Christmas Island red crab, during the annual breeding migration, Biol. Bull., 200, 305, 10.2307/1543512 Aird, 2011, Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries, Genome Biol., 12, R18, 10.1186/gb-2011-12-2-r18 Arakawa, 2018, The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae), Mitochondr. DNA Part B, 3, 812, 10.1080/23802359.2018.1495119 Ashton, 2015, MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island, Nat. Biotechnol., 33, 296, 10.1038/nbt.3103 Austin, 2016, The complete mitogenome of the whale shark parasitic copepod Pandarus rhincodonicus Norman, Newbound & Knott (Crustacea; Siphonostomatoida; Pandaridae)–a new gene order for the copepoda, Mitochondr. DNA Part A, 27, 694, 10.3109/19401736.2014.913147 Austin, 2017, De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read, Gigascience, 6, 1, 10.1093/gigascience/gix063 Basso, 2017, The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura, Sci. Rep., 7, 4096, 10.1038/s41598-017-04168-9 Bernt, 2013, MITOS: improved de novo metazoan mitochondrial genome annotation, Mol. Phylogenet. Evol., 69, 313, 10.1016/j.ympev.2012.08.023 Capella-Gutiérrez, 2009, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, 25, 1972, 10.1093/bioinformatics/btp348 Carver, 2011, Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data, Bioinformatics, 28, 464, 10.1093/bioinformatics/btr703 Chandler, 2017, Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis, F1000Research, 6, 10.12688/f1000research.10545.1 Dierckxsens, 2016, NOVOPlasty: de novo assembly of organelle genomes from whole genome data, Nucleic Acids Res., 45, e18 Fisher-Reid, 2011, What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades, BMC Evol. Biol., 11, 300, 10.1186/1471-2148-11-300 Gan, 2012, Genome sequence of Hydrogenophaga sp. strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, J. Bacteriol., 194, 4759, 10.1128/JB.00990-12 Gan, 2014, Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes, BMC Evol. Biol., 14, 19, 10.1186/1471-2148-14-19 Gan, 2016, The complete mitogenome of the hermit crab Clibanarius infraspinatus (Hilgendorf, 1869),(Crustacea; Decapoda; Diogenidae)–a new gene order for the Decapoda, Mitochondr. DNA Part A, 27, 4099, 10.3109/19401736.2014.1003862 Gan, 2017, Nanopore long-read guided complete genome assembly of Hydrogenophaga intermedia, and genomic insights into 4-aminobenzenesulfonate, p-aminobenzoic acid and hydrogen metabolism in the genus Hydrogenophaga, Front. Microbiol., 8, 1880, 10.3389/fmicb.2017.01880 Gan, 2018, Transcriptome-guided identification of carbohydrate active enzymes (CAZy) from the Christmas Island red crab, Gecarcoidea natalis and a vote for the inclusion of transcriptome-derived crustacean CAZys in comparative studies, Mar. Biotechnol., 20, 654, 10.1007/s10126-018-9836-2 Gan, 2018, More evolution underground: accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae), Mol. Phylogenet. Evol., 118, 88, 10.1016/j.ympev.2017.09.022 Gan, 2018, High-quality draft genome sequence of the type strain of Allorhizobium vitis, the primary causal agent of grapevine crown gall, Microbiol. Res. Announc., 7 Gong, 2018, Picky comprehensively detects high-resolution structural variants in nanopore long reads, Nat. Methods, 15, 455, 10.1038/s41592-018-0002-6 Green, 1997, Red crabs in rain forest on Christmas Island, Indian Ocean: activity patterns, density and biomass, J. Trop. Ecol., 13, 17, 10.1017/S0266467400010221 Green, 2008, Recruitment dynamics in a rainforest seedling community: context-independent impact of a keystone consumer, Oecologia, 156, 373, 10.1007/s00442-008-0992-3 Guo, 2015, Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes, BMC Genomics, 16, 727, 10.1186/s12864-015-1929-y Haas, 2013, De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis, Nat. Protoc., 8, 1494, 10.1038/nprot.2013.084 Hahn, 2013, Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach, Nucleic Acids Res., 41, e129, 10.1093/nar/gkt371 Harrisson, 2016, Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species, Heredity, 116, 506, 10.1038/hdy.2016.8 Hartnoll, 1988, 1 Kalyaanamoorthy, 2017, ModelFinder: fast model selection for accurate phylogenetic estimates, Nat. Methods, 14, 587, 10.1038/nmeth.4285 Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010 Krishnan, 2016, Genome-wide profiling of transfer RNAs and their role as novel prognostic markers for breast cancer, Sci. Rep., 6, 32843, 10.1038/srep32843 Lai, 2017, The systematics of land crabs of the genus Gecarcoidea and recognition of a pseudocryptic species, G. humei, from the eastern Indian Ocean (Crustacea: Decapoda: Gecarcinidae), Invertebr. Syst., 31, 406, 10.1071/IS16052 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Lee, 2016, The complete mitogenome of the New Zealand freshwater crayfish Paranephrops planifrons White 1842 (Crustacea: Decapoda: Parastacidae), Mitochondr. DNA Part A, 27, 3333, 10.3109/19401736.2015.1018209 Li, 2018, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, 1, 7 Li, 2015, MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics, 31, 1674, 10.1093/bioinformatics/btv033 Li, 2015, Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences, Sci. Rep., 5, 8527, 10.1038/srep08527 Linton, 2007, A review of feeding and nutrition of herbivorous land crabs: adaptations to low quality plant diets, J. Comp. Physiol. B., 177, 269, 10.1007/s00360-006-0138-z Linton, 2015, A glycosyl hydrolase family 16 gene is responsible for the endogenous production of beta-1,3-glucanases within decapod crustaceans, Gene, 569, 203, 10.1016/j.gene.2015.05.056 Loman, 2015, A complete bacterial genome assembled de novo using only nanopore sequencing data, Nat. Methods, 12, 733, 10.1038/nmeth.3444 Lopes-Lima, 2018, Expansion and systematics redefinition of the most threatened freshwater mussel family, the Margaritiferidae, Mol. Phylogenet. Evol., 127, 98, 10.1016/j.ympev.2018.04.041 Miller, 2004, Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed, Gene, 331, 65, 10.1016/j.gene.2004.01.022 Miller, 2005, Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae), Mar. Biotechnol., 7, 339, 10.1007/s10126-004-4077-8 Musacchia, 2017, De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus, PLoS One, 12, 10.1371/journal.pone.0184090 Nguyen, 2014, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol., 32, 268, 10.1093/molbev/msu300 O'Dowd, 1989, Red crabs in rain forest, Christmas Island: removal and relocation of leaf-fall, J. Trop. Ecol., 5, 337, 10.1017/S0266467400003746 Pan, 2014, DNA polymerase preference determines PCR priming efficiency, BMC Biotechnol., 14, 10, 10.1186/1472-6750-14-10 Payne, 2018, Whale watching with BulkVis: a graphical viewer for Oxford Nanopore bulk fast5 files, bioRxiv, 312256 Pennisi, 2014 Quail, 2008, A large genome center's improvements to the Illumina sequencing system, Nat. Methods, 5, 1005, 10.1038/nmeth.1270 Rang, 2018, From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy, Genome Biol., 19, 90, 10.1186/s13059-018-1462-9 Ranjard, 2018, Complete mitochondrial genome of the green-lipped mussel, Perna canaliculus (Mollusca: Mytiloidea), from long nanopore sequencing reads, Mitochondr. DNA Part B, 3, 175, 10.1080/23802359.2018.1437810 Schalamun, 2018, Harnessing the Min ION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora, Mol. Ecol. Resour., 19, 77, 10.1111/1755-0998.12938 Sherman, 2003, Effects of land crabs on leaf litter distributions and accumulatons in a mainland tropical rain forest1, Biotropica, 35, 365, 10.1111/j.1744-7429.2003.tb00590.x Sokolov, 2000, An improved method for DNA isolation from mucopolysaccharide-rich molluscan tissues, J. Molluscan Stud., 66, 573, 10.1093/mollus/66.4.573 Song, 2016, Capturing the phylogeny of Holometabola with mitochondrial genome data and Bayesian site-heterogeneous mixture models, Genome Biol. Evol., 8, 1411, 10.1093/gbe/evw086 Stöver, 2010, TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses, BMC Bioinforma., 11, 7, 10.1186/1471-2105-11-7 Sullivan, 2011, Easyfig: a genome comparison visualizer, Bioinformatics, 27, 1009, 10.1093/bioinformatics/btr039 Tan, 2015, MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes, Mol. Phylogenet. Evol., 85, 180, 10.1016/j.ympev.2015.02.009 Tan, 2017, Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda), PeerJ, 5, 10.7717/peerj.2982 Tan, 2018, ORDER within the chaos: insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements, Mol. Phylogenet. Evol., 127, 320, 10.1016/j.ympev.2018.05.015 Tan, 2018, Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly, GigaScience, 7, gix137, 10.1093/gigascience/gix137 Tan, 2018, More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda: Glypheidea: Glypheidae), Invertebr. Syst., 32, 448, 10.1071/IS17050 Thorvaldsdóttir, 2013, Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration, Brief. Bioinform., 14, 178, 10.1093/bib/bbs017 Tsang, 2014, Evolutionary history of true crabs (Crustacea: Decapoda: Brachyura) and the origin of freshwater crabs, Mol. Biol. Evol., 31, 1173, 10.1093/molbev/msu068 Velozo Timbó, 2017, Mitogenome sequence accuracy using different elucidation methods, PLoS One, 12, 10.1371/journal.pone.0179971 Wang, 2017, Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles, Sci. Rep., 7, 1814, 10.1038/s41598-017-01835-9 Weeks, 2014, A single panmictic population of endemic red crabs, Gecarcoidea natalis, on Christmas Island with high levels of genetic diversity, Conserv. Genet., 15, 909 Wick, 2015, Bandage: interactive visualization of de novo genome assemblies, Bioinformatics, 31, 3350, 10.1093/bioinformatics/btv383 Wick, 2017, Unicycler: resolving bacterial genome assemblies from short and long sequencing reads, PLoS Comput. Biol., 13, 10.1371/journal.pcbi.1005595 Xia, 2018, DAMBE7: new and improved tools for data analysis in molecular biology and evolution, Mol. Biol. Evol., 35, 1550, 10.1093/molbev/msy073