Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

Serba, Desalegn D.; Uppalapati, Srinivasa Rao; Krom, Nick; Mukherjee, Shreyartha; Tang, Yuhong; Mysore, Kirankumar S.; Saha, Malay C.

doi:10.1186/s12864-016-3377-8

BMC Genomics

Table 1 Photosynthetic efficiency related gene transcripts differentially upregulated in lowlands as compared to upland switchgrass with more than two-fold change (q-value ≤ 0.01)

From: Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

No	Rice homolog	Protein function description	Average FPKM_ Lowland	Average FPKM_ VS16	Average Fold change
1	Peroxiredoxin	Antioxidant defense system	280	98	2.9
2	Peptidyl-prolyl cis-trans isomerase	Catalysis of the geometric or structural changes within one molecule	540	211	2.6
3	NAD dependent epimerase/dehydratase family protein	Catalytic activity and coenzyme binding	308	121	2.5
4	Glutathione S-transferase	Detoxication and toxification mechanisms	351	122	2.9
5	Ftsh protease	Eliminating abnormal membrane proteins in chloroplast	1005	401	2.5
6	AAA-type atpase family protein	F-type ATPase	308	68	4.8
7	ATP synthase B chain, chloroplast precursor	F-type ATPase	780	314	2.5
8	ATP synthase F1, delta subunit family protein	F-type ATPase	489	168	2.9
9	ATP-dependent Clp protease ATP-binding subunit clpa homolog, chloroplast precursor	F-type ATPase	690	336	2.1
10	Glyceraldehyde-3-phosphate dehydrogenase	Glycolysis	893	356	2.6
11	Cysteine proteinase 1 precursor	Hydrolysis of peptide bonds in a polypeptide chain	409	107	4.2
12	B-box zinc finger family protein	Intracellular protein transport	310	118	2.6
13	Chlorophyll A-B binding protein	LHC-Antana protein	2111	794	5.9
14	Zinc finger A20 and AN1 domain-containing stress-associated protein	Metal ion and DNA binding	347	139	2.5
15	Metallothionein	Metal ion binding	4704	1446	5.2
16	Metallothionein-like protein 3B	Metal ion binding	1471	94	14.3
17	NDH-M H Plastoquinine dehydrogenase	Photosynthetic electron transport	276	92	3.0
18	2Fe-2S iron-sulfur cluster binding domain containing protein	Photosynthetic electron transport	462	136	3.4
19	Calvin cycle protein CP12	Photosynthetic electron transport	1664	402	4.1
20	Carbonic anhydrase, chloroplast precursor	Photosynthetic electron transport	1229	300	4.5
21	Ferredoxin--NADP reductase, chloroplast precursor	Photosynthetic electron transport	523	210	2.6
22	Fructose-1,6-bisphosphatase	Photosynthetic electron transport	282	106	2.7
23	Fructose-bisphospate aldolase isozyme	Photosynthetic electron transport	1724	714	2.6
24	Phosphoglycerate kinase protein	Photosynthetic electron transport	312	106	3.1
25	Phosphoribulokinase/Uridine kinase family protein	Photosynthetic electron transport	285	72	4.2
26	Pyruvate, phosphate dikinase, chloroplast precursor	Photosynthetic electron transport	885	376	2.4
27	Ribulose bisphosphate carboxylase small chain, chloroplast precursor	Photosynthetic electron transport	2367	1113	2.2
28	Ribulose-phosphate 3-epimerase, chloroplast precursor	Photosynthetic electron transport	321	98	3.3
29	Thioredoxin	Photosynthetic electron transport	725	237	3.9
30	Transketolase, chloroplast precursor	Photosynthetic electron transport	399	135	3.2
31	Proton gradient regulation 5 (pgr5)	Photosynthetic electron transport in photosystem I	294	128	2.3
32	Photosystem I reaction center subunit, chloroplast precursor	Photosystem I subunits	892	416	2.2
33	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor	Photosystem II main subunits	624	153	4.1
34	Cytochrome b6f complex subunit	Photosystem II main subunits	284	96	2.9
35	Oxygen evolving enhancer protein 3 domain containing protein	Photosystem II subunits	233	84	3.0
36	Photosystem II reaction center W protein, chloroplast precursor	Photosystem II subunits	555	176	3.6
37	Dehydrin	Plant response and adaptation to abiotic stresses	299	111	2.7
38	Fatty acid desaturase	Plant responses to abiotic stresses	263	102	2.6
39	Enzyme of the cupin superfamily protein	Protect plants from the effects of oxidative stress	447	205	2.2
40	Tetratrico peptide repeat region TPR domain protein	Protein binding	239	77	3.1
41	60S acidic ribosomal protein	Protein synthesis	281	114	2.5
42	Elongation factor	Protein synthesis in the process of cell cycle and elongation	274	82	3.6
43	Hypoxia-responsive family protein	regulation of growth and and developmnt	711	148	4.8
44	Glycine-rich protein A3	RNA-binding	351	158	2.2
45	RNA recognition motif containing protein	RNA-binding domain	905	311	3.0
46	BBTI8 - Bowman-Birk type bran trypsin inhibitor precursor	Serine-type endopeptidase inhibitor activity	316	95	3.6
47	Egg apparatus-1	Small secretory proteins and pollen tube guidance	227	63	4.4
48	Elongation factor thermo unstable (EF-Tu)	Synthesizes new proteins by translation at the ribosome	484	232	2.1
49	Oryzain gamma chain precursor	cysteine-type peptidase activity	546	148	3.6
50	Ubiquitin family protein	Targeted protein degradation	477	200	2.4
51	Ubiquitin-conjugating enzyme	Targets a protein for degradation via the proteasome	386	110	4.0
52	CCT/B-box zinc finger protein	Transcription factor	291	114	2.6
53	Ribosomal protein L35	Translation, ribosomal component	273	116	2.4
54	Aquaporin protein	Transport of water and small solutes	1022	239	4.8
55	Membrane protein	Water and nutrient transport across membranes	799	255	3.1

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ISSN: 1471-2164

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