HTS High-throughput sequencing
K2P Kimura 2-parameter
kb Kilobase
LR-LCH Long-range library capture hybridization
LR-PCR Long-range polymerase chain reaction
mtDNA Mitochondrial DNA
Mitogenome Mitochondrial genome
ND1 NADH dehydrogenase subunit 1
ND2 NADH dehydrogenase subunit 2
ND3 NADH dehydrogenase subunit 3
ND4 NADH dehydrogenase subunit 4
ND5 NADH dehydrogenase subunit 5
ND6 NADH dehydrogenase subunit 6
PGM Ion Torrent Personal Genome Machine
1 Introduction
Capture hybridization coupled with high-throughput sequencing
(HTS) has become one of the most popular approaches to address
some scientific problems not only for fundamental evolution but
also for ecology and human disease in recent years [1–5]. Except
restriction-site-associated DNA sequencing (RAD-seq, [5–7]) and
whole-transcriptome shotgun sequencing (RNA-seq, [8]), capture
hybridization coupled with HTS is a powerful approach that
enables user cost- and time-effective for enriching and sequencing
a massive amount of target loci (10s–1000s) distributed separately
in a whole simultaneously [1, 5, 9]. According to target loci of
interest, there exist versatile approaches, including exon capture,
ultraconservative elements, hyRAD, and homemade probe capture
for any specific gene [1, 6, 10–12]. As compared to RAD-seq and
RNA-seq, the combined approaches have some merits: (1) it gen-
erated high-quality data, such as longer assembled contigs, lower
variance in target coverage, and more accurate SNP calling [5, 12,
13 ]; (2) it allows user to align DNA/RNA sequence from widely
taxonomic samples and infer complex and higher-level phylogenies
[5, 14]. However, the combined method is not perfect. One short-
age of the method is limitation of probe ability for cross-species
capture, especially in divergent gene [10, 15].
Two decades ago, Jacobsen used capture hybridization method
to enrich a single locusluxgene in microorganism genome from
soil samples (Pseudomonas fluorescens,[16]). The number of locus
for the capture hybridization greatly increased a decade ago because
it incorporated HTS [17]. To date, the combined method has
simplified and consists of four general steps: (1) prepare probe;30 Xing Chen et al.