######################## Species Abbreviations ######################## Abal -- Abies alba Aeya -- Acer yangbiense Atch -- Actinidia chinensis Aqag -- Aquilaria agallocha Bena -- Betula nana Bepe -- Betula pendula Capa -- Carica papaya Cact -- Carya cathayensis Cail -- Carya illinoinensis Camo -- Castanea mollissima Cika -- Cinnamomum kanehirae Cimi -- Cinnamomum micranthum Coav -- Corylus avellana Elgu -- Elaeis guineensis Euca -- Eucalyptus camaldulensis Eugr -- Eucalyptus grandis Fasy -- Fagus sylvatica Frex -- Fraxinus excelsior Gibi -- Ginkgo biloba Gnmo -- Gnetum montanum Haim -- Handroanthus impetiginosus Hebr -- Hevea brasiliensis Jacu -- Jatropha curcas Jual -- Juglans alianthifolia Juct -- Juglans cathayensis Juci -- Juglans cinerea Juia -- Juglans cinerea x ailantifolia Jucr -- Juglans cinerea x regia Juhi -- Juglans hindsii Juit -- Juglans intermedia Jumj -- Juglans major Jumn -- Juglans mandshurica Jumi -- Juglans microcarpa Juni -- Juglans nigra Jure -- Juglans regia Jusi -- Juglans sigillata Kaob -- Kandelia obovata Lich -- Liriodendron chinense Main -- Macadamia integrifolia Mado -- Malus x domestica Maes -- Manihot esculenta Mono -- Morus notabilis Oleu -- Olea europaea Phda -- Phoenix dactylifera Paab -- Picea abies Pagl -- Picea glauca Pila -- Pinus lambertiana Pita -- Pinus taeda Podl -- Populus deltoides Poep -- Populus euphratica Popr -- Populus pruinosa Pota -- Populus tremula Potl -- Populus tremula x Populus tremuloides Pote -- Populus tremuloides Potr -- Populus trichocarpa Prpe -- Prunus persica Psme -- Pseudotsuga menziesii Ptst -- Pterocarya stenoptera Pugr -- Punica granatum Qulo -- Quercus lobata Quro -- Quercus robur Sese -- Sequoia sempervirens Segi -- Sequoiadendron giganteum Sygl -- Symphonia globulifera Vefo -- Vernicia fordii Vivi -- Vitis vinifera Xaso -- Xanthoceras sorbifolium ######################## FTP Genome Directory Structure ######################## Below is an example of file structure and naming conventions using the ficticious organism Example species (species code Exsp) genome version 1.0. Most files listed are optional and dependent on what files have been made available when the genome was released. Exsp │ └── v1.0    ├──README.txt (optional) - Contains information about the genome project including publication/attribution. If genome was size selected and/or includes masked and unmasked scaffolds it will be noted here.    ├──alignments (optional)    │    ├── Exsp.1_0.gmap.gff    │    ├── Exsp.1_0.tsa.fa - transcript fasta used for gmap run    │    └── README.txt - summary of gmap results from gFACS    ├──annotation    │    ├── Exsp.1_0.cds.fa.gz    │    ├── Exsp.1_0.gff.gz    │    ├── Exsp.1_0.pep.fa.gz   │    ├── Exsp.1_0.repeats.fa.gz (optional) │    ├── Exsp.1_0.repeats.gff.gz (optional)    │    ├── Exsp.1_0.entap_annotations.tsv    │    ├── Exsp.1_0.entap_statistics.txt    │    └── README.txt - rnaQUAST and BUSCO results    ├── genome    │    ├── Exsp.1_0.fa.gz    │    └── README.txt - QUAST and BUSCO results    ├── index    │    ├── gene_index    │    |    └── Exsp.1_0.gene_blast    │    ├── genome_index    │    |    ├── Exsp.1_0.bwa    │    |    ├── Exsp.1_0.genome_blast    │    |    ├── Exsp.1_0.gmap    │    |    ├── Exsp.1_0.hisat2    │    |    └── Exsp.1_0.hisat2_annotation    │    └── protein_index    │       ├── Exsp.1_0.protein_blast    │       └── Exsp.1_0.protein_diamond    ├── plastid (optional)    │ ├── mitochondrial    │ │ ├── Exsp.1_0.mito.gff.gz    │ │ ├── Exsp.1_0.mito.fa.gz    │ │ └── README.txt    │ └── chloroplast    │ ├── Exsp.1_0.chloro.gff.gz    │ ├── Exsp.1_0.chloro.fa.gz    │ └── README.txt    └── supplemental (optional)    ├── Exsp.1_0.annotations.tsv.gz (If original project provides annotation files they will be located in the supplemental directory. In-house annotations are located in the annotation directory.)    ├── Exsp.1_0.snps.vcf.gz    └── Exsp.1_0.polymorphisms.vcf.gz