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Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola

https://doi.org/10.1101/164574
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Definition and Relationships of Lipotyphla
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Venomous mammals
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Human DNA polymorphisms and methods of analysis
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The reduction of genetic diversity in threatened vertebrates and new recommendations regarding IUCN conservation rankings
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Evolution: Natural Selection in the Evolution of Humans and Chimps
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The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data
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Basic Local Alignment Search Tool
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The neutral theory in the genomic era
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Nocturnin, a Deadenylase in Xenopus laevis Retina
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Canidae
inferredcites →https://doi.org/10.1017/s0030605308001324openalex-snapshot
Continued survival of Hispaniolan solenodon Solenodon paradoxus in Haiti
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Mesozoic origin for West Indian insectivores
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The sequence and de novo assembly of the giant panda genome
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Erratum: The sequence and de novo assembly of the giant panda genome
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Inference of human population history from individual whole-genome sequences
inferredcites →https://doi.org/10.1038/nbt.2023openalex-snapshot
How to apply de Bruijn graphs to genome assembly
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The tiger genome and comparative analysis with lion and snow leopard genomes
inferredcites →https://doi.org/10.1038/ng.3280openalex-snapshot
The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.4267openalex-snapshot
Genome-wide profiling of heritable and de novo STR variations
inferredcites →https://doi.org/10.1038/nrg3117openalex-snapshot
Repetitive DNA and next-generation sequencing: computational challenges and solutions
inferredcites →https://doi.org/10.1038/nrg981openalex-snapshot
Sequencing the chimpanzee genome: insights into human evolution and disease
inferredcites →https://doi.org/10.1038/srep31173openalex-snapshot
Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon
inferredcites →https://doi.org/10.1073/pnas.0701705104openalex-snapshot
More genes underwent positive selection in chimpanzee evolution than in human evolution
inferredcites →https://doi.org/10.1089/cmb.1995.2.275openalex-snapshot
Toward Simplifying and Accurately Formulating Fragment Assembly
inferredcites →https://doi.org/10.1093/bib/bbq015openalex-snapshot
A survey of sequence alignment algorithms for next-generation sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/bti1114openalex-snapshot
The fragment assembly string graph
inferredcites →https://doi.org/10.1093/bioinformatics/btm071openalex-snapshot
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btq683openalex-snapshot
Scaffolding pre-assembled contigs using SSPACE
inferredcites →https://doi.org/10.1093/bioinformatics/btr011openalex-snapshot
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/bts280openalex-snapshot
Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btt310openalex-snapshot
Informed and automated k -mer size selection for genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu280openalex-snapshot
Ragout—a reference-assisted assembly tool for bacterial genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/emph/eov005openalex-snapshot
Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?
inferredcites →https://doi.org/10.1093/genetics/158.3.1227openalex-snapshot
Positive and Negative Selection on the Human Genome
inferredcites →https://doi.org/10.1093/hmg/2.8.1123openalex-snapshot
Mutation of human short tandem repeats
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/mst062openalex-snapshot
The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC
inferredcites →https://doi.org/10.1093/mspecies/sev010openalex-snapshot
Solenodon paradoxus(Soricomorpha: Solenodontidae)
inferredcites →https://doi.org/10.1093/nar/25.5.955openalex-snapshot
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
inferredcites →https://doi.org/10.1093/nar/27.2.573openalex-snapshot
Tandem repeats finder: a program to analyze DNA sequences
inferredcites →https://doi.org/10.1093/nar/gkh036openalex-snapshot
The Gene Ontology (GO) database and informatics resource
inferredcites →https://doi.org/10.1093/nar/gkh121openalex-snapshot
The Pfam protein families database
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkj118openalex-snapshot
TreeFam: a curated database of phylogenetic trees of animal gene families
inferredcites →https://doi.org/10.1093/nar/gkl200openalex-snapshot
AUGUSTUS: ab initio prediction of alternative transcripts
inferredcites →https://doi.org/10.1093/nar/gkl315openalex-snapshot
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
inferredcites →https://doi.org/10.1093/nar/gkm1005openalex-snapshot
TreeFam: 2008 Update
inferredcites →https://doi.org/10.1093/nar/gkr367openalex-snapshot
HMMER web server: interactive sequence similarity searching
inferredcites →https://doi.org/10.1093/nar/gku1063openalex-snapshot
Rfam 12.0: updates to the RNA families database
inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
inferredcites →https://doi.org/10.1093/nar/gkw1138openalex-snapshot
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements
inferredcites →https://doi.org/10.1093/sysbio/syv025openalex-snapshot
The Fossil Calibration Database—A New Resource for Divergence Dating
inferredcites →https://doi.org/10.1098/rstb.2009.0219openalex-snapshot
Genome-wide scans for footprints of natural selection
inferredcites →https://doi.org/10.1101/024679openalex-snapshot
Cookiecutter: a tool for kmer-based read filtering and extraction
inferredcites →https://doi.org/10.1101/gr.123356.111openalex-snapshot
Cactus: Algorithms for genome multiple sequence alignment
inferredcites →https://doi.org/10.1111/ddi.12420openalex-snapshot
Independent evolutionary histories in allopatric populations of a threatened Caribbean land mammal
inferredcites →https://doi.org/10.1126/science.aae0344openalex-snapshot
Long-read sequence assembly of the gorilla genome
inferredcites →https://doi.org/10.1146/annurev-animal-090414-014900openalex-snapshot
The Genome 10K Project: A Way Forward
inferredcites →https://doi.org/10.1186/1471-2105-6-31openalex-snapshot
Automated generation of heuristics for biological sequence comparison
inferredcites →https://doi.org/10.1186/1471-2164-10-51openalex-snapshot
Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22
inferredcites →https://doi.org/10.1186/1471-2164-15-599openalex-snapshot
Uncovering adaptive evolution in the human lineage
inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1186/2047-217x-2-10openalex-snapshot
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
inferredcites →https://doi.org/10.1186/gb-2013-14-5-r47openalex-snapshot
REAPR: a universal tool for genome assembly evaluation
inferredcites →https://doi.org/10.1186/s13059-015-0837-4openalex-snapshot
Genomic legacy of the African cheetah, Acinonyx jubatus
inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot
Repbase Update, a database of repetitive elements in eukaryotic genomes
inferredcites →https://doi.org/10.1201/9781420039481.ch16openalex-snapshot
Systematics and Biogeography of the West Indian Genus Solenodon
inferredcites →https://doi.org/10.1371/journal.pone.0130821openalex-snapshot
QuorUM: An Error Corrector for Illumina Reads
inferredcites →https://doi.org/10.1671/0272-4634(2005)025[0936:anbsmc]2.0.co;2openalex-snapshot
A new basal skunk Martinogale (Carnivora, Mephitinae) from Late Miocene Dove Spring Formation, California, and origin of New World mephitines
inferredcites →https://doi.org/10.2475/ajs.s4-24.139.55openalex-snapshot
Notes on the habits and external characters of the Solenodon of San Domingo (Solenodon paradoxus)
inferredcites →https://doi.org/10.26879/424openalex-snapshot
Constraints on the timescale of animal evolutionary history
inferredcites →https://doi.org/10.2992/0097-4463-77.3.321openalex-snapshot
On the Cranial Osteology of the Hispaniolan Solenodon, Solenodon paradoxus Brandt, 1833 (Mammalia, Lipotyphla, Solenodontidae)
inferredcites →https://doi.org/10.3109/24701394.2016.1167891openalex-snapshot
Mitogenomic sequences support a north–south subspecies subdivision within Solenodon paradoxus
inferredcites →https://doi.org/10.5281/zenodo.594183openalex-snapshot
GOATOOLS: Tools for Gene Ontology
inferredcites →https://doi.org/10.5860/choice.191025openalex-snapshot
Mammalogy: adaptation, diversity, ecology
inferredcites →https://doi.org/10.5860/choice.35-5657openalex-snapshot
Classification of mammals: above the species level
inferredcites →https://doi.org/10.5860/choice.44-3275openalex-snapshot
Conservation and the genetics of populations
inferredcites →https://doi.org/10.5962/bhl.title.110496openalex-snapshot
The systematics, biology, and conservation of Solenodon

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inferred← citeshttps://doi.org/10.1073/pnas.1906117116openalex-snapshot
Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals
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