samples, DNA fragment with a length of 2 kb to cross-species
capture is suitable for enrichment of high variable loci since the
control regions are less than the length of 2 kb. It is possible that a
fragment length of>3 kb could be captured, but it is not recom-
mended to exceed>10 kb, because extremely high-quality and
high-quantity DNA samples are required to shear.
One shortage of the LR-LCH is it cannot be applied to
museum specimens and ancient samples. DNA in these samples
already naturally degraded to small pieces (<500 bp, [27]).
Another shortage is the complicated experiment as compared to
the similar strategy of library preparation for single-molecule DNA
sequencing that allows the user to sequence long library. Karami-
tros and Magiorkinis use long library capture method for two long
loci of interest fromphage lambdaandEscherichia coliand followed
sequencing by using Oxford Nanopore MinION. The efficiency of
their method is very well with 92.5% capture specificity and 99.73%
capture sensitivity [20].
We see capture hybridization becomes a more important
method in many fields, except phylogenetics and ancient DNA
research; the new fields include metagenomics, genetic mapping
of phenotypic traits, and structural variation of some function
region in pathogenic bacteria and human cancer cell lines [2, 4,
20 , 28–31]. LR-LCH as a new kind of capture hybridization may
provide the user obtaining better sequence quality and longer
contigs. We hope this pipeline could help biologist insight of
various scientific problems in these fields.Acknowledgments
We thank Jing Che’s research group for specimen collection and
identification, and especially Hong-man Chen who examined spe-
cies information and its CO1 sequence. We thank Dong Wang,
Chun-Yan Yang, Kong-Wah Sing, and Elizabeth Georgian for
reviewing the manuscript. This work was supported by the Ministry
of Science and Technology of China (MOST no. 2012FY110800
to W.W.) and the National Natural Science Foundation of China
(NSFC no. 31090251 to Y.Z.). Raw data from next-generation
sequencing is available at SRA (http://www.ncbi.nlm.nih.gov/sra)
under accession number SRP090718.References
- Mason VC et al (2011) Efficient cross-species
capture hybridization and next-generation
sequencing of mitochondrial genomes from
noninvasively sampled museum specimens.
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2. Jones MR, Good JM (2016) Targeted capture
in evolutionary and ecological genomics. Mol
Ecol 25:185–202
3. Tsangaras K et al (2014) Hybridization capture
reveals evolution and conservation across the
42 Xing Chen et al.