Genome reference sequences and sRNA-Seq datasets are two prerequisites for miRNA annotation, we browsed all public databases including NCBI, Phytozome, etc., and found that there were around 100 plant species meeting with these two prerequisites. They are listed as the following.
Taxon | Organism |
Chlorophytes | Volvox carteri |
Chlorophytes | Chlamydomonas reinhardtii |
Embryophytes; Bryophytes | Physcomitrella patens |
Embryophytes; Tracheophytes; Lycophytes | Selaginella moellendorffii |
Embryophytes; Tracheophytes; Spermatophytes | Picea abies |
Embryophytes; Tracheophytes; Spermatophytes | Ginkgo bioba |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta | Amborella trichopoda |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Magnoliidae | Persea americana |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Actinidiaceae | Actinidia chinensis |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Asteraceae | Carthamus tinctorius |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Asteraceae | Lactuca sativa |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Arabidopsis halleri |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Arabidopsis lyrata |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Arabidopsis thaliana |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Brassica juncea |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Brassica napus |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Brassica nigra |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Brassica oleracea |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Brassica rapa |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Capsella rubella |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Brassicaceae | Eutrema salsugineum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Caricaceae | Carica papaya |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Caryophyllaceae | Silene latifolia |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Convolvulaceae | Ipomoea batatas |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Cucurbitaceae | Citrullus lanatus |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Cucurbitaceae | Cucumis melo |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Cucurbitaceae | Cucumis sativus |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Cucurbitaceae | Cucurbita maxima |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Cucurbitaceae | Cucurbita moschata |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Cucurbitaceae | Lagenaria siceraria |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Euphorbiaceae | Hevea brasiliensis |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Euphorbiaceae | Jatropha curcas |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Euphorbiaceae | Manihot esculenta |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Euphorbiaceae | Ricinus communis |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Fabaceae | Cicer arietinum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Fabaceae | Glycine max |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Fabaceae | Lotus japonicus |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Fabaceae | Medicago truncatula |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Fabaceae | Phaseolus vulgaris |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Fabaceae | Pisum sativum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Fagaceae | Quercus robur |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Fagaceae | Vigna unguiculata |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Lythraceae | Punica granatum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Malvaceae | Gossypium arboreum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Malvaceae | Gossypium barbadense |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Malvaceae | Gossypium hirsutum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Malvaceae | Hibiscus syriacus |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Nelumbonaceae | Nelumbo nucifera |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Oleaceae | Fraxinus excelsior |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Oleaceae | Olea europaea |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Phrymaceae | Erythranthe guttata |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Rosaceae | Fragaria vesca |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Rosaceae | Fragaria ananassa |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Rosaceae | Prunus persica |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Rutaceae | Citrus clementina |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Rutaceae | Citrus maxima |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Rutaceae | Citrus sinensis |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Salicaceae | Populus euphratica |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Salicaceae | Populus trichocarpa |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Capsicum annuum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Nicotiana benthamiana |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Nicotiana tabacum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Solanum habrochaites |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Solanum lycopersicum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Solanum melongena |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Solanum pennellii |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Solanum pimpinellifolium |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Solanaceae | Solanum tuberosum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Eudicotyledons; Vitaceae | Vitis vinifera |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Araceae | Spirodela polyrhiza |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Arecaceae | Phoenix dactylifera |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Asparagaceae | Asparagus officinalis |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Musaceae | Musa acuminata |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Orchidaceae | Phalaenopsis aphrodite |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Brachypodium distachyon |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Oryza glaberrima |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Oryza nivara |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Oryza rufipogon |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Oryza sativa |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Panicum hallii |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Panicum virgatum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Saccharum hybrid cultivar |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Setaria italica |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Sorghum bicolor |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Triticum aestivum |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Poaceae | Zea mays |
Embryophytes; Tracheophytes; Spermatophytes; Magnoliophyta; Liliopsida; Zosteraceae | Zostera marina |
At the beginning of June 2018, we started to download reference sequences, sRNA-Seq datasets, PARE-Seq datasets, and other related information. The whole process lasted around 4 or 5 months. Meanwhile, with our pipelines, Zheng Kuang and Zhonglong Guo started to process these data. During this period, we really appreciate members in Dr. Yang and Dr. Li lab who get involved in the project. Many thanks to their diligent effort.