Andrews S.2010.FastQC:A quality control tool for high throughput sequence data.In:Babraham Bioinformatics,Babraham Institute.Cambridge,United Kingdom. Bolger A M,Lohse M,Usadel B.2014.Trimmomatic:A flexible trimmer for Illumina sequence data.Bioinformatics,30:2114-2120. Burgin C,He K.2018.Family Soricidae (Shrews).Barcelona:Lynx Edicions,332-551. Bushnell B.2014.BBMap:A fast,accurate,splice-aware aligner.In:Lawrence Berkeley National Lab.(LBNL),Berkeley,CA (United States). Camacho C,Coulouris G,Avagyan V,Ma N,Papadopoulos J,Bealer K,Madden T L.2009.BLAST+:Architecture and applications.BMC Bioinformatics,10:421-421. Dress A W M,Flamm C,Fritzsch G,Grünewald S,Kruspe M,Prohaska S J,Stadler P F.2008.Noisy:Identification of problematic columns in multiple sequence alignments.Algorithms for Molecular Biology,3:7. Emms D M,Kelly S.2015.OrthoFinder:solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.Genome Biology,16:157. Fan H,Xiao Y,Yang Y,Xia W,Mason A S,Xia Z,Qiao F,Zhao S,Tang H.2013.RNA-Seq analysis of Cocos nucifera:transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.PLoS ONE,8:e59997. Grabherr M G,Haas B J,Yassour M,Levin J Z,Thompson D A,Amit I,Adiconis X,Fan L,Raychowdhury R,Zeng Q,Chen Z,Mauceli E,Hacohen N,Gnirke A,Rhind N,di Palma F,Birren B W,Nusbaum C,Lindblad-Toh K,Friedman N,Regev A.2011.Full-length transcriptome assembly from RNA-Seq data without a reference genome.Nature Biotechnology,29:644-652. Haas B J,Papanicolaou A,Yassour M,Grabherr M,Blood P D,Bowden J,Couger M B,Eccles D,Li B,Lieber M,MacManes M D,Ott M,Orvis J,Pochet N,Strozzi F,Weeks N,Westerman R,William T,Dewey C N,Henschel R,LeDuc R D,Friedman N,Regev A.2013.De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.Nature Protocols,8:1494-1512. Hutterer R.1985.Anatomical adaptations of shrews.Mammal Review,15:43-55. Jain A,Tuteja G.2019.TissueEnrich:Tissue-specific gene enrichment analysis.Bioinformatics,35:1966-1967. Joshi S,Singh A R,Durden D L.2014.MDM2 regulates hypoxic hypoxia-inducible factor 1α stability in an E3 ligase,proteasome,and PTEN-phosphatidylinositol 3-kinase-AKT-dependent manner.The Journal of Biological Chemistry,289:22785-22797. Katoh K,Misawa K,Kuma K,Miyata T.2002.MAFFT:A novel method for rapid multiple sequence alignment based on fast Fourier transform.Nucleic Acids Research,30:3059-3066. Langmead B,Salzberg S L.2012.Fast gapped-read alignment with Bowtie2.Nature Methods,9:357-359. Li B,Dewey C N.2011.RSEM:Accurate transcript quantification from RNA-Seq data with or without a reference genome.BMC Bioinformatics,12:323-323. Li W,Godzik A.2006.Cd-hit:a fast program for clustering and comparing large sets of protein or nucleotide sequences.Bioinformatics,22:1658-1659. Liang H,He S,Yang J,Jia X,Wang P,Chen X,Zhang Z,Zou X,McNutt M A,Shen W H,Yin Y.2014.PTENα,a PTEN isoform translated through alternative initiation,regulates mitochondrial function and energy metabolism.Cell Metabolism,19:836-848. Moreno-Santillan D D,Machain-Williams C,Hernandez-Montes G,Ortega J.2019.De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats.Scientific Reports,9. Nishimura O,Hara Y,Kuraku S.2017.gVolante for standardizing completeness assessment of genome and transcriptome assemblies.Bioinformatics,33:3635-3637. Nowak R M.1999.Walker's Mammals of the World.Baltimore:Johns Hopkins University Press Prakash A,Jeffryes M,Bateman A,Finn R.2017.The HMMER web server for protein sequence similarity search.Current Protocols in Bioinformatics,60:3.15.11-13.15.23. Robinson M D,McCarthy D J,Smyth G K.2010.edgeR:A Bioconductor package for differential expression analysis of digital gene expression data.Bioinformatics,26:139-140. Semenza G L.2012.Hypoxia-inducible factors in physiology and medicine.Cell,148:399-408. Simão F A,Waterhouse R M,Ioannidis P,Kriventseva E V,Zdobnov E M.2015.BUSCO:Assessing genome assembly and annotation completeness with single-copy orthologs.Bioinformatics,31:3210-3212. Smith-Unna R,Boursnell C,Patro R,Hibberd J M,Kelly S.2016.TransRate:Reference-free quality assessment of de novo transcriptome assemblies.Genome Research,26:1134-1144. Smith A T,Xie Y.2008.A Guide to the Mammals of China.Princeton:Princeton University Press Stamatakis A.2014.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies.Bioinformatics,30:1312-1313. Takagi H,King G L,Ferrara N,Aiello L P.1996.Hypoxia regulates vascular endothelial growth factor receptor KDR/Flk gene expression through adenosine A2 receptors in retinal capillary endothelial cells.Investigative Ophthalmology Visual Science,37:1311-1321. Warnes G R,Bolker B,Bonebakker L,Gentleman R,Huber W,Liaw A,Lumley T,Maechler M,Magnusson A,Moeller S.2009.gplots:Various R programming tools for plotting data.R Package Version,2:1. Ye J,Fang L,Zheng H,Zhang Y,Chen J,Zhang Z,Wang J,Li S,Li R,Bolund L.2006.WEGO:a web tool for plotting GO annotations.Nucleic Acids Research,34:W293-W297. Zhao Q Y,Wang Y,Kong Y M,Luo D,Li X,Hao P.2011.Optimizing de novo transcriptome assembly from short-read RNA-Seq data:a comparative study.BMC Bioinformatics,12:S2-S2. 刘少英,吴毅.2019.中国兽类图鉴.福州市:海峡书局. |