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) |