Abstract:
:Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole-genome sequences are currently available for three species. In this study, we have generated a chromosome-level genome assembly of the fourth species, the Asian coastal horseshoe crab (Tachypleus gigas; genome size 2.0 Gb). The genome assembly has a scaffold N50 value of 140 Mb with ~97% of the assembly mapped to 14 scaffolds representing 14 chromosomes of T. gigas. In addition, we have generated the complete mitochondrial genome sequence and deep-coverage transcriptome assemblies for four tissues. A total of 26,159 protein-coding genes were predicted in the genome. The T. gigas genome contains five Hox clusters similar to the mangrove horseshoe crab (Carcinoscorpius rotundicauda), suggesting that the common ancestor of horseshoe crabs already possessed five Hox clusters. Phylogenomic and divergence time analysis suggested that the American and Asian horseshoe crab lineages shared a common ancestor around the Silurian period (~436 Ma). Comparison of the T. gigas genome with those of other horseshoe crab species with chromosome-level assemblies provided insights into the chromosomal rearrangement events that occurred during the emergence of these species. The genomic resources of T. gigas will be useful for understanding their genetic diversity and population structure and would help in designing strategies for managing and conserving their stocks across Asia.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Shingate P,Ravi V,Prasad A,Tay BH,Venkatesh Bdoi
10.1111/1755-0998.13233subject
Has Abstractpub_date
2020-11-01 00:00:00pages
1748-1760issue
6eissn
1755-098Xissn
1755-0998journal_volume
20pub_type
杂志文章abstract::The rice leaffolder, Cnaphalocrocis medinalis Guenée (Crambidae, Lepidoptera), is an important agricultural pest that causes serious losses to rice production in rice-growing regions with high humidity and temperature. However, a lack of genomic resources limits in-depth understanding of its biological characteristics...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13274
更新日期:2021-02-01 00:00:00
abstract::Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years; however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy next-generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequence...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12953
更新日期:2019-01-01 00:00:00
abstract::Stegodyphus lineatus spiders live in groups consisting of closely related individuals. There appears to be no discrimination against related individuals as mates but females mate multiply, despite the fact that matings are shown to carry a cost. We have developed eight polymorphic dinucleotide microsatellite markers t...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02296.x
更新日期:2009-01-01 00:00:00
abstract::A novel set of microsatellite markers for mungbean [Vigna radiata (L.) Wilczek] was developed from the public sequence database. Seventy-eight primers were designed and evaluated for polymorphism among 22 cultivated accessions. Eight polymorphic loci detected two to three alleles per locus with an average of 2.25. The...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02655.x
更新日期:2009-05-01 00:00:00
abstract::To enable the accurate sexing of individuals of introduced populations of the small Indian mongoose, Herpestes auropunctatus, we designed a primer set for the amplification of the sex-specific fragments EIF2S3Y and EIF2S3X. Using this primer set, the expected amplification products were obtained for all samples of gen...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02931.x
更新日期:2011-03-01 00:00:00
abstract::The Chilean isopod Excirolana hirsuticauda is a marine benthic brooder with wide distributional range and low potential for long-distance dispersal. Eleven microsatellite markers were developed for E. hirsuticauda using enriched libraries. Characterization of those loci in 35 individuals from Playa Blanca beach showed...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02186.x
更新日期:2008-09-01 00:00:00
abstract::DNA-based identifications have been employed across broad taxonomic ranges and provide an especially useful tool in cases where external identification may be problematic. This study explored the utility of DNA barcoding in resolving skate species found in Atlantic Canadian waters. Most species were clearly resolved, ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03034.x
更新日期:2011-11-01 00:00:00
abstract::QST , a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if QST for a trait is sufficiently larger than the mean FST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12303
更新日期:2015-03-01 00:00:00
abstract::We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cr...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02364.x
更新日期:2009-03-01 00:00:00
abstract::Restriction-site-associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a f...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12206
更新日期:2014-05-01 00:00:00
abstract::Introgression can be an important evolutionary force but it can also lead to species extinction and as such is a crucial issue for species conservation. However, introgression is difficult to detect, morphologically as well as genetically. Hybridization with domestic cats (Felis silvestris catus) is a major concern fo...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12075
更新日期:2013-05-01 00:00:00
abstract::Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was a...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13291
更新日期:2020-11-05 00:00:00
abstract::The longheaded eagle ray, Aetobatus flagellum feeds mainly on bivalves, and there have been some indications that the current reduction in the bivalve population in southern Japan may be due to an increase in the number of longheaded eagle rays. Consequently, the 'predator control programme' for reducing the longheade...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02568.x
更新日期:2009-05-01 00:00:00
abstract::We developed a total of 50 microsatellite markers for the three fungal pathogens causing the most important leaf spot diseases of banana: 32 loci for Mycosphaerella fijiensis are presented, and nine loci each for Mycosphaerella musicola and Mycosphaerella eumusae. All these loci were polymorphic within each species on...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02180.x
更新日期:2008-09-01 00:00:00
abstract::With the advent of next generation sequencing technologies, transcriptome level sequence collections are arising as prominent resources for the discovery of gene-based molecular markers. In a previous study more than 15,000 simple sequence repeats (SSRs) in expressed sequence tag (EST) sequences resulting from 454 pyr...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03102.x
更新日期:2012-05-01 00:00:00
abstract::Understanding how landscape features affect gene flow has implications for numerous fields including molecular and evolutionary ecology. Despite this, modelling landscape resistance surfaces has remained a significant challenge. The R package resistancega was developed to provide a framework for optimizing landscape r...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13217
更新日期:2020-11-01 00:00:00
abstract::Biodiversity analyses based on next-generation sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of suc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12472
更新日期:2016-03-01 00:00:00
abstract::We report the characterization of eight microsatellite markers in the big-headed ant Pheidole megacephala, a pest ant registered in the list of '100 of the world's worst invasive alien species'. An enrichment protocol was used to isolate microsatellite loci, and polymorphism was explored with 36 individuals collected ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02116.x
更新日期:2008-07-01 00:00:00
abstract::We describe primers and polymerase chain reaction conditions to amplify 22 microsatellite loci from the Barrow's goldeneye (Bucephala islandica). The primers were tested on 27 individuals from a population breeding in British Columbia, Canada. The developed primer pairs yielded an average of 6.11 alleles per locus (ra...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02225.x
更新日期:2009-05-01 00:00:00
abstract::Thirty-four novel microsatellite markers developed for wood cricket (Nemobius sylvestris) were tested and optimized. Twenty-five microsatellite loci were polymorphic, exhibiting between two and nine alleles. Observed heterozygosities ranged from 0.038 to 0.925. The microsatellites were also tested in a species belongi...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02269.x
更新日期:2008-11-01 00:00:00
abstract::Understanding the genetics of biological diversification across micro- and macro-evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant f...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12945
更新日期:2019-01-01 00:00:00
abstract::The emergence of third-generation sequencing (3GS; long-reads) is bringing closer the goal of chromosome-size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of nonmodel organisms. However, long-read technologies result in higher sequenc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13176
更新日期:2020-09-01 00:00:00
abstract::The brushtail possum is a major agricultural and ecological pest in New Zealand. A novel noninvasive DNA sampling tool for detecting its presence (WaxTags, or WT) was tested. DNA was recovered from saliva left on WT, and two lengths (407 bp and 648 bp) of the cytochrome c oxidase I (COI) barcoding region were amplifie...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02498.x
更新日期:2009-03-01 00:00:00
abstract::Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morpholo...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12401
更新日期:2015-11-01 00:00:00
abstract::The plant family Labiatae (Lamiaceae) is known for its fine medicinal and aromatic herbs like lavender, mint, oregano, sage and thyme and is a rich source of essential oils for the food, pharmaceutical and cosmetic industry. Besides its great economic importance, the Labiatae family contributes significantly to the en...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03129.x
更新日期:2012-07-01 00:00:00
abstract::Genomic data sets are increasingly central to ecological and evolutionary biology, but far fewer resources are available for invertebrates. Powerful new computational tools and the rapidly decreasing cost of Illumina sequencing are beginning to change this, enabling rapid genome assembly and reference marker extractio...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13146
更新日期:2020-05-01 00:00:00
abstract::We describe 10 microsatellite loci for Panulirus argus (Caribbean spiny lobster). The number of alleles at each locus ranged from four to 39 (mean = 21.8) in 89 juvenile specimens collected at two different times at a recruitment site in south Florida. Levels of expected and observed heterozygosities ranged from 0.48 ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.02032.x
更新日期:2008-05-01 00:00:00
abstract::Recent advances in high-throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27 556 single ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12476
更新日期:2016-05-01 00:00:00
abstract::Bactrocera cucurbitae (Coquillett) is an important insect pest of melon fruit causing extensive losses of production in Asia and Pacific areas. Twelve polymorphic microsatellite loci were isolated from an enriched DNA library of this species and their amplification characteristics are described. Genetic parameters wer...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02678.x
更新日期:2009-09-01 00:00:00
abstract::High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12077
更新日期:2013-05-01 00:00:00