@article{fdi:010058172,
  title = {{D}eep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton},
  author = {{L}acape, {J}. {M}. and {C}laverie, {M}. and {V}idal, {R}. {O}. and {C}arazzolle, {M}. {F}. and {P}ereira, {G}. {A}. {G}. and {R}uiz, {M}. and {P}re, {M}. and {L}lewellyn, {D}. and {A}l-{G}hazi, {Y}. and {J}acobs, {J}. and {D}ereeper, {A}lexis and {H}uguet, {S}. and {G}iband, {M}. and {L}anaud, {C}.},
  editor = {},
  language = {{ENG}},
  abstract = {{C}otton ({G}ossypium) fiber is the most prevalent natural product used in the textile industry. {T}he two major cultivated species, {G}. hirsutum ({G}h) and {G}. barbadense ({G}b), are allotetraploids with contrasting fiber quality properties. {T}o better understand the molecular basis for their fiber differences, {EST} pyrosequencing was used to document the fiber transcriptomes at two key development stages, 10 days post anthesis (dpa), representing the peak of fiber elongation, and 22 dpa, representing the transition to secondary cell wall synthesis. {T}he 617,000 high quality reads (89% of the total 692,000 reads) from 4 libraries were assembled into 46,072 unigenes, comprising 38,297 contigs and 7,775 singletons. {F}unctional annotation of the unigenes together with comparative digital gene expression ({DGE}) revealed a diverse set of functions and processes that were partly linked to specific fiber stages. {G}lobally, 2,770 contigs (7%) showed differential expression (>2-fold) between 10 and 22 dpa (irrespective of genotype), with 70% more highly expressed at 10 dpa, while 2,248 (6%) were differentially expressed between the genotypes (irrespective of stage). {T}he most significant genes with differential {DGE} at 10 dpa included expansins and lipid transfer proteins (higher in {G}b), while at 22 dpa tubulins, cellulose, and sucrose synthases showed higher expression in {G}b. {DGE} was compared with expression data of 10 dpa-old fibers from {A}ffymetrix microarrays. {A}mong 543 contigs showing differential expression on both platforms, 74% were consistent in being either over-expressed in {G}h (242 genes) or in {G}b (161 genes). {F}urthermore, the unigene set served to identify 339 new {SSR}s and close to 21,000 inter-genotypic {SNP}s. {S}ubsets of 88 {SSR}s and 48 {SNP}s were validated through mapping and added 65 new loci to a {RIL} genetic map. {T}he new set of fiber {EST}s and the gene-based markers complement existing available resources useful in basic and applied research for crop improvement in cotton.},
  keywords = {},
  booktitle = {},
  journal = {{P}los {O}ne},
  volume = {7},
  numero = {11},
  pages = {e48855},
  ISSN = {1932-6203},
  year = {2012},
  DOI = {10.1371/journal.pone.0048855},
  URL = {https://www.documentation.ird.fr/hor/fdi:010058172},
}