The identified genes were compared with the database of essential genes (DEG), and 40 genes were found to share high homology with genes identified by DEG (identity ≥ 40%, E-value ≤ 1.0E-30; Table 2). One gene, UTP-glucose-1-phosphate uridylyltransferase (MA-090-485), is involved in the synthesis of the cell wall component 1,3-beta-D-glucan (Table 2). MA-090-485 is highly homologous with the Saccharomyces cerevisiae enzyme (sequence identity = 62.58%, e-value = 0) identified in the DEG search. Similarly, nucleoside diphosphate kinase (MA-120-261), which is involved in the synthesis of CTP and GTP, also shared high homology with one of the essential genes identified by DEG (identity = 66.89%, e-value = 2.0E-68). Besides, in MG, there were 46 genes that did not match with DEG (Additional file 3). Of these, when nitrate was used as nitrogen source, nitrate reductase (MA-291-2) and nitrite reductase (MA-291-3), which together convert nitrate into NH3 for cell growth, were essential under this condition. Another two essential genes, delta 5 desaturase (MA-326-160) and delta 12 desaturase (MA-334-414) are vital for the synthesis of ARA in M. alpina. In addition, most of these essential genes were distributed in the Amino Acid Metabolism category (28.3%). This was understandable since essential gene identified by DEG were in a rich medium in which genes involving amino acid synthesis may not be essential. Table 2 Essential genes identified on different mediums which are high homology with DEG Gene Enzyme Essentiality Subsystem MG YE MA-133-4 Ribose-5-phosphate isomerase E E Carbohydrate metabolism MA-090-485 UTP-glucose-1-phosphate uridylyltransferase E E MA-101-200 Mannose-6-phosphate isomerase E E MA-120-141 Phosphoacetylglucosamine mutase E E MA-184-380 Acetyl-CoA carboxylase E E MA-072-196 Argininosuccinate lyase E NE Amino acid metabolism MA-213-50 Adenylosuccinate synthase E E MA-213-539 Adenylosuccinate lyase E E MA-326-6 Aspartate carbamoyltransferase E E MA-334-434 Phosphoribosylanthranilate isomerase E NE MA-120-148 2-Acetolactate methylmutase E NE MA-090-434 Dihydroxy-acid dehydratase E NE MA-139-331 Homoaconitate hydratase E NE MA-323-77 Saccharopine dehydrogenase E NE MA-326-106 Ornithine carbamoyltransferase E NE MA-101-393 Imidazole-4-carboxamide isomerase E NE MA-184-558 Imidazoleglycerol-phosphate dehydratase E NE MA-090-452 Glutamine amidotransferase:cyclase E NE MA-320-159 3-dehydroquinate synthase E NE MA-139-157 Chorismate synthase E NE MA-073-62 3-deoxy-7-phosphoheptulonate synthase E NE MA-213-547 Tryptophan synthase E NE MA-297-40 Chorismate mutase E NE MA-120-157 Thioredoxin reductase E E MA-173-30 Purine-nucleoside phosphorylase E E Nucleotide metabolism MA-213-65 IMP dehydrogenase E E MA-120-261 Nucleoside diphosphate kinase E E MA-139-347 Guanylate kinase E E MA-120-138 Ribonucleoside-diphosphate reductase E E MA-055-211 Ribonucleoside-diphosphate reductase E E MA-323-58 Ribonucleoside-diphosphate reductase E E MA-334-356 Thymidylate synthase E E MA-153-455 3(2),5-bisphosphate nucleotidase E NE MA-111-23 phosphoadenylyl-sulfate reductase E NE Energy metabolism MA-182-360 6,7-dimethyl-8-ribityllumazine synthase E E Cofactors and vitamins MA-184-368 Riboflavin synthase E E MA-210-311 Aspartate dehydrogenase E E MA-055-340 Fatty-acyl-CoA synthase E E Lipid metabolism MA-162-131 Palmitoyl-protein thioesterase E E MA-334-239 Very-long-chain enoyl-CoA reductase E E E: essential gene; NE: non-essential gene. MG: minimal medium; YE: yeast extract medium.