Small RNA regulation of ovule development in the cotton plant, G. hirsutum L.
BACKGROUND
The involvement of small RNAs in cotton fiber development is under explored. The objective of this work was to directly clone, annotate, and analyze small RNAs of developing ovules to reveal the candidate small interfering RNA/microRNAs involved in cotton ovule and fiber development.


RESULTS
We cloned small RNA sequences from 0-10 days post anthesis (DPA) developing cotton ovules. A total of 6691 individual colonies were sequenced from 11 ovule small RNA libraries that yielded 2482 candidate small RNAs with a total of 583 unique sequence signatures. The majority (362, 62.1%) of these 583 sequences were 24 nt long with an additional 145 sequences (24.9%) in the 21 nt to 23 nt size range. Among all small RNA sequence signatures only three mirBase-confirmed plant microRNAs (miR172, miR390 and ath-miR853-like) were identified and only two miRNA-containing clones were recovered beyond 4 DPA. Further, among all of the small RNA sequences obtained from the small RNA pools in developing ovules, only 15 groups of sequences were observed in more than one DPA period. Of these, only five were present in more than two DPA periods. Two of these were miR-172 and miR-390 and a third was identified as 5.8S rRNA sequence. Thus, the vast majority of sequence signatures were expressed in only one DPA period and this included nearly all of the 24 nt sequences. Finally, we observed a distinct DPA-specific expression pattern among our clones based upon sequence abundance. Sequences occurring only once were far more likely to be seen in the 0 to 2 DPA periods while those occurring five or more times were the majority in later periods.


CONCLUSIONS
This initial survey of small RNA sequences present in developing ovules in cotton indicates that fiber development is under complex small RNA regulation. Taken together, the results of this initial small RNA screen of developing cotton ovules is most consistent with a model, proposed by Baulcombe, that there are networks of small RNAs that are induced in a cascade fashion by the action of miRNAs and that the nature of these cascades can change from tissue to tissue and developmental stage to developmental stage.
Abdurakhmonov
Ibrokhim Y
IY
Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan. ibrokhim_a@yahoo.com
Devor
Eric J
EJ
Buriev
Zabardast T
ZT
Huang
Lingyan
L
Makamov
Abdusalom
A
Shermatov
Shukhrat E
SE
Bozorov
Tohir
T
Kushanov
Fakhriddin N
FN
Mavlonov
Gafurjon T
GT
Abdukarimov
Abdusattor
A
D003001:Cloning, Molecular; D030561:Databases, Nucleic Acid; D035264:Flowers / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development; D035683:MicroRNAs / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D017423:Sequence Analysis, RNA
D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering
Curr Biol. 2006 May 9;16(9):939-44
16682356
J Genet Genomics. 2007 Apr;34(4):347-54
17498633
PLoS Genet. 2008 Apr 25;4(4):e1000056
18437202
Int J Plant Genomics. 2008;2008:742304
18288253
Planta. 2008 Jan;227(2):319-29
17849148
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W701-4
15980567
Eur J Neurosci. 2006 Dec;24(11):2978-86
17156359
Plant Cell. 2007 May;19(5):1507-21
17526749
Cell. 2006 Nov 3;127(3):565-77
17081978
Lipids. 2005 Aug;40(8):773-85
16296396
Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12191-6
16873546
Genes Dev. 2006 Dec 15;20(24):3407-25
17182867
Plant Physiol. 1995 Jun;108(2):669-76
7610164
Funct Integr Genomics. 2008 May;8(2):165-74
18043952
BMC Plant Biol. 2007 May 16;7:22
17506877
Plant Physiol. 2007 Dec;145(4):1303-10
18056866
Int J Dev Biol. 2005;49(5-6):773-80
16096981
Hum Mol Genet. 2004 Aug 1;13(15):1535-49
15175272
Am J Bot. 1999 Jun;86(6):776-9
10371719
Gene. 2007 Jun 15;395(1-2):49-61
17408884
Mol Genet Genomics. 2008 Jan;279(1):75-85
17943315
J Exp Bot. 2007;58(3):473-81
17122407
Trends Genet. 2008 Mar;24(3):133-41
18262675
Biochim Biophys Acta. 1998 Jul 9;1398(3):342-6
9655931
Plant Physiol. 1995 Dec;109(4):1285-1293
12228669
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18054-9
17110445
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11
14681370
Plant Physiol. 2003 Oct;133(2):580-8
12972649
Cell. 1993 Dec 3;75(5):843-54
8252621
Plant Physiol. 2001 Dec;127(4):1361-6
11743074
Cell Res. 2005 Jun;15(6):465-73
15987605
Cell. 1993 Dec 3;75(5):855-62
8252622
Plant Cell. 2001 Jan;13(1):47-60
11158528
Curr Opin Plant Biol. 2007 Oct;10(5):503-11
17709279
Plant Physiol. 2003 Jun;132(2):709-17
12805599
Plant Physiol. 2001 Jul;126(3):981-92
11457949
Front Biosci. 2007 May 01;12:3975-82
17485351
Plant Cell Physiol. 1999 Feb;40(2):155-63
10202811
Biochim Biophys Acta. 2004 Sep 17;1679(3):214-21
15358513
Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12637-42
8901635
Plant Physiol. 2004 Dec;136(4):4104-13
15557097
Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4559-64
18339806
Science. 2006 Sep 15;313(5793):1596-604
16973872
J Cell Physiol. 2007 Feb;210(2):279-89
17096367
Gene. 2007 Aug 1;397(1-2):26-37
17574351
Plant J. 2006 Sep;47(5):761-75
16889650
Plant Physiol. 1996 Dec;112(4):1491-1497
12226460
RNA. 2003 Mar;9(3):277-9
12592000
New Phytol. 2007;175(3):462-471
17635221
Cold Spring Harb Symp Quant Biol. 2006;71:13-20
17381275
Cell. 2004 Jan 23;116(2):281-97
14744438
Plant Cell. 2007 Nov;19(11):3692-704
17993622
Ann Bot. 2007 Dec;100(7):1391-401
17905721