Table 2. List of the RNA seq analyses performed in Allium species.

Species	Platform	Tissue	Purpose/observation	Reference
Allium sativum	Illumina HiSeq 2000	Dormant and sprouting bud	Discovery of genes in sulfur assimilation	Sun et al. (2012)
Allium sativum	Illumina HiSeq 2500	Whole plant of 10 and 45 days old	Developed SSR marker in garlic and studied their transferability to other Allium species	Liu et al. (2015)
Allium sativum	MiSeq v3 platform	Leaves, basal plate, roots inflorescence, flowers, cloves	Organ specific transcriptome for identification key gene and mechanism of organ development	Kamenetsky et al. (2015)
Allium sativum	Roche 454-FLX	Leaves, pseudostems, and roots	SNPs and indels discovery	Havey & Ahn (2016)
Allium sativum	Illumina HiSeq 2000	Flower buds of male sterile and fertile lines	Energy deficiency of tapetum cells might be reason of male sterility in garlic	Shemesh-Mayer et al. (2015)
Allium sativum	Illumina HiSeq™ 2000	Shoot apex	Genes differentially expressed in shoot apex were identified	Sun et al. (2013)
Allium cepa	Illumina HiSeq 2500	Leaf	Discovery of NAC transcription factor in onion	Zheng et al. (2016)
Allium cepa	Illumina HiSeq 2000	Outer, intermediate and inner scale	Programmed cell death in onion skin formation	Galsurker et al. (2017)
Allium cepa	Illumina HiSeq 2000	Bulb	ISGAP was used for higher accuracy of transcript annotation	Kim et al. (2015)
Allium cepa	Roche 454 FLX platform	Bulbs, tissue from leaves, unopened umbels, bulbs, and roots	SNP development based on saturated map	Duangjit et al. (2013)
Allium cepa	Illumina HiSeq 2000	Leaf	Differentially expressed genes were identified at freezing temperature and development of SSR and SNPs markers	Han et al. (2016)
Allium cepa	HisSeq™ 2500	Bulb	Dissected sucrose metabolism during bulb formation	Zhang et al. (2016)
Allium cepa	Illumina HiSeq™ 2000	Anthers at the tetrad stage	Identification of differentially expressed gene in anthers of sterile and maintainer line	Yuan et al. (2018)
Allium cepa	Illumina HiSeq 2000	Bulb	The AcPMS 1 involved in DNA mismatch Repair, is the best candidate for fertility restoration	Kim et al. (2015)
Allium cepa	454™ GS-FLX	Leaves and shoot	Developed toolkit for bulk PCR marker designing from transcriptome data	Baldwin et al. (2012b)
Allium cepa	Illumina HiSeq 2000	Scales	Studied differential response of outer and inner scales to the heat treatment	Galsurker et al. (2018)
Allium cepa	Illumina HiSeq 4000	Bulb	Variation in bulb colour	Zhang et al. (2018)
Allium cepa and interspecific hybrids	Illumina HiSeq2000	Leaves	Develoment of SNP markers from interspecific hybrids for introgression breeding	Scholten et al. (2016)
Allium cepa	PacBio_RSII platform, P4-C2 chemistry	Flowers, leaves, bulbs and roots	Long read sequencing was used to construct a draft reference transcripts	Sohn et al. (2016)
Allium porrum	Illumina HiSeq 2500	Leaves	Identification of CONSTANS-like genes which play role in flowering	Liu et al. (2018)
Allium porrum	Illumina MiSeq	Leaves and cloves	Elucidation of organosulfur metabolic pathway	Mehra et al. (2019)
Allium fistulosum	Illumina HiSeq 2500	Bulb	Study of saponin biosynthetic pathway and their possible role in fusarium resistance	Abdelrahman et al. (2017)
Allium fistulosum	Illumina HiSeq 2000	Leaves, false stem, basal plate and root	Gene for sulfur and selenium metabolism were identified, SSR marker were developed	Sun et al. (2016)
Allium fistulosum	GS-FLX and HiSeq 2000	2-week-old seedlings, leaf, roots, basal meristem, immature flower bract, mature bract, opened flowers, immature fruits and sliced pseudostem	EST markers were developed for mapping and these marker will enable comparison with bulb onion	Tsukazaki et al. (2015)
Allium fistulosum	Illumina HiSeq 2000	Leaves	Identified four genes for wax content and developed 1,558 SSR markers	Liu et al. (2014)
Allium fistulosum	Illumina HiSeq 2000	Inflorescences	Differential gene expression in CMS and maintainer line	Liu et al. (2016)
A. fistulosum, shallots and 8 monosomic addition lines	HiSeq 2500	Bulbs	Found hot spot for flavonoid synthesis on chromosome 5A	Abdelrahman et al. (2019)
Allium tuberosum Rottler ex Spr	Illumina HiSeq 2000	Leaves, shoots and roots	Performed gene annotation and SSR identification in Chinese chive	Zhou et al. (2015)
A. sativum, A. porrum, A. tuberosum, A. Fistulosum, A. ascalonicum, A. cepa, A. cepa var. agrogarum, A. chinense, A. macrostemon	Illumina HiSeq 2500	Leaf	PCD might involve in development of fistular leaves	Zhu et al. (2017)
A. ursinum, A. cepa, A. angulosum, A. cernuum, A. ericetorum, A. fistulosum, A. nutans, A. sativum, A. scorodoprasum, A. senescens and A. vineale	Illumina HiSeq 2000	Leaves and roots	Reported that the unusual telomeric sequence present in Allium species, demonstrated the synthesis of telomere by telomerase	Fajkus et al. (2016)
A. nutans, A. cepa, A. ursinum, A. angulosum, A. ericetorum, A. fistulosum, Tulbaghia violacea, Scilla peruviana, and Cestrum elegans	Illumina NextSeq500	Leave sand root	Studied telomeres in order Asparagales	Fajkus et al. (2019)