Documentation

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.