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With the development of high-throughput sequencing platforms, such as the GS-FLX (Roche, Branford, CT, USA), microsatellite marker development has recently become fast and efficient [1] [3] and the advance has also allowed the identification of these loci in highly degraded ancient DNA (aDNA), where traditional enrichment procedures have been unsuccessful [2].
Though genetic marker development has facilitated construction of detailed linkage maps in dengue virus vector, Aedes aegypti [9] [12] and the Plasmodium falciparum vector, Anopheles gambiae [13] [16] mosquitoes, genetic studies based on linkage analyses in Cx. pipiens are limited due to the paucity of available marker loci [8], [17].
Despite the economic and ecological importance of the genus Pinus, the progress of entire genome sequencing and associated marker development has been limited [ 6, 7].
In recent years, with the rapid increase of ESTs in public databases and the advent of bioinformatics tools, SSR marker development has become easier and more cost-effective.
The application of transcriptome deep sequencing in metabolic pathway reconstruction and gene marker development has already shown great promise in Camellia sinesis[ 5], Cicer arietinum[ 6], Sphenodon punctatus[ 7], and Anopheles funestus[ 8].
Marker development has improved significantly and has become much less expensive [ 6].
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However, currently no blackberry sequences that might be used for molecular marker development have been deposited in GenBank.
With the introduction of new sequencing technologies, traditional low-throughput methods of marker development have been superseded [ 2].
Previous efforts in oat marker development have always led to large proportions of ambiguous markers and/or low success rates [ 29- 31, 35].
Usefulness of these genomic resources for SNP or microsatellite markers development has largely been proven [19], [20], [21], [22].
Importance of size of the genomic fragments used for construction of genomic library/SSR-marker development has also been shown earlier in groundnut [ 16].
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