Genome survey of sago palm (Metroxylon sagu Rottboll)

Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing

“…Genome size is one of the important attributes of the genome of an organism, and before commencing genome sequencing, accurate estimations of nuclear genome sizes are prerequisites [ 28 , 29 , 30 ]. There are several methods to predict the genome size, such as feulgen spectrophotometry, pulsed-field gel electrophoresis (PFGE), and flow cytometry [ 19 ]. Though flow cytometry has become a well-recognized technique for predicting genome size before plant genome sequencing due to its low material requirements, short analysis time, and high accuracy, there is still some technical error that will hinder exact quantification [ 21 , 31 ].…”

“…Though flow cytometry has become a well-recognized technique for predicting genome size before plant genome sequencing due to its low material requirements, short analysis time, and high accuracy, there is still some technical error that will hinder exact quantification [ 21 , 31 ]. With the rapid development of NGS technology, k-mer analysis, which is based on whole-genome sequencing reads, has become an effective and economical method to obtain genome sizes of non-model or emerging species [ 32 ], which has been proven successful for many plant species, such as Metroxylon sagu Rottboll [ 19 ], Rhododendron micranthum [ 14 ], Pistacia vera [ 15 ], and Akebia trifoliata [ 33 ]. Therefore, using both methods to measure genome size can improve the reliability of the results.…”

“…GC content exceeding the normal range (>65% or <25%) will result in reduced coverage in sequencing regions, which can seriously affect genome assembly [ 35 ]. In this study, the GC content of I. chinensis was medium, which fell within the general range of 30 to 47% for most plants [ 19 , 36 ], and would not influence the quality of the genome sequence during the sequencing process [ 18 , 27 ].…”

“…Exploring the genes related to the effective components and excellent agronomic characters of plants, and analyzing the metabolic pathways and regulatory mechanisms from the genome-wide level, can lay the foundation for the improvement of medicinal plant varieties and the protection of genetic resources [ 14 , 17 ]. Owing to recent advances in DNA sequencing techniques, draft genomes have been assembled for many plant species as resources for genomic and genetic research efforts [ 18 , 19 , 20 ]. However, the genomes of some plant species, particularly tree species and medicinal plants, are highly heterozygous, and have a complex genetic background [ 12 , 21 , 22 ].…”

Transcriptome dataset of sago palm in peat soil

“…Numerous studies were performed to address the non-trunking sago palm problem such as soil physicochemical properties [2] , soil microbiome [4] and molecular studies [5] , [6] , [7] . The general outcome of the studies revealed that the mineral deficiency causes the non-trunking in sago palm, but how this deficiency affects sago development remains unanswered.…”