@article{fdi:010048265,
  title = {{M}occa{DB} - an integrative database for functional, comparative and diversity studies in the {R}ubiaceae family},
  author = {{P}lechakova, {O}. and {T}ranchant {D}ubreuil, {C}hristine and {B}enedet, {F}. and {C}ouderc, {M}. and {T}inaut, {A}. and {V}iader, {V}. and {D}e {B}lock, {P}. and {H}amon, {P}erla and {C}ampa, {C}laudine and {K}ochko, {A}lexandre de and {H}amon, {S}erge and {P}oncet, {V}al{\'e}rie},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {I}n the past few years, functional genomics information has been rapidly accumulating on {R}ubiaceae species and especially on those belonging to the {C}offea genus (coffee trees). {A}n increasing number of expressed sequence tag ({EST}) data and {EST}- or genomic-derived microsatellite markers have been generated, together with {C}onserved {O}rtholog {S}et ({COS}) markers. {T}his considerably facilitates comparative genomics or map-based genetic studies through the common use of orthologous loci across different species. {S}imilar genomic information is available for e. g. tomato or potato, members of the {S}olanaceae family. {S}ince both {R}ubiaceae and {S}olanaceae belong to the {E}uasterids {I} (lamiids) integration of information on genetic markers would be possible and lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality, and maturation, or adaptation. {O}ur goal was to develop a comprehensive web data source for integrated information on validated orthologous markers in {R}ubiaceae. {D}escription: {M}occa{DB} is an online {M}y{SQL}-{PHP} driven relational database that houses annotated and/or mapped microsatellite markers in {R}ubiaceae. {I}n its current release, the database stores 638 markers that have been defined on 259 {EST}s and 379 genomic sequences. {M}arker information was retrieved from 11 published works, and completed with original data on 132 microsatellite markers validated in our laboratory. {DNA} sequences were derived from three {C}offea species/hybrids. {M}icrosatellite markers were checked for similarity, in vitro tested for cross-amplification and diversity/polymorphism status in up to 38 {R}ubiaceae species belonging to the {C}inchonoideae and {R}ubioideae subfamilies. {F}unctional annotation was provided and some markers associated with described metabolic pathways were also integrated. {U}sers can search the database for marker, sequence, map or diversity information through multi-option query forms. {T}he retrieved data can be browsed and downloaded, along with protocols used, using a standard web browser. {M}occa{DB} also integrates bioinformatics tools ({CM}ap viewer and local {BLAST}) and hyperlinks to related external data sources ({NCBI} {G}en{B}ank and {P}ub{M}ed, {SOL} {G}enomic {N}etwork database). {C}onclusion: {W}e believe that {M}occa{DB} will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of {R}ubiaceae and {S}olanaceae species, in particular.},
  keywords = {},
  booktitle = {},
  journal = {{B}mc {P}lant {B}iology},
  volume = {9},
  numero = {},
  pages = {123},
  ISSN = {1471-2229},
  year = {2009},
  DOI = {10.1186/1471-2229-9-123},
  URL = {https://www.documentation.ird.fr/hor/fdi:010048265},
}