Draft genome of the endangered visayan spotted deer ( <i>Rusa alfredi)</i>, a Philippine endemic species

Javier, Ma. Carmel F.; Noblezada, Albert C.; Sienes, Persie Mark Q.; Guino-o, Robert S.; Palomar-Abesamis, Nadia; Malay, Maria Celia D.; del Castillo, Carmelo S; Ferriols, Victor Marco Emmanuel N.; Javier, Ma. Carmel

doi:10.46471/gigabyte.150

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Draft genome of the endangered visayan spotted deer ( Rusa alfredi), a Philippine endemic species

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Author(s): Ma. Carmel F. Javier ¹ , Albert C. Noblezada ¹ , Persie Mark Q. Sienes ² ^, ^* ^, , Robert S. Guino-o ³ , Nadia Palomar-Abesamis ² , Maria Celia D. Malay ⁴ , Carmelo S. del Castillo ⁵ ^, ⁶ , Victor Marco Emmanuel N. Ferriols ¹ ^, ⁵ ^, ^* ^,

Publication date (Electronic): 24 February 2025

Journal: GigaByte

Publisher: GigaScience Press

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Abstract

The Visayan Spotted Deer (VSD), or Rusa alfredi, is an endangered and endemic species in the Philippines. Despite its status, genomic information on R. alfredi, and the genus Rusa in general, is missing. This study presents the first draft genome assembly of the VSD using the Illumina short-read sequencing technology. The resulting RusAlf_1.1 assembly has a 2.52 Gb total length, with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genome’s completeness, and includes the annotation of 24,531 genes. Our phylogenetic analysis based on single-copy orthologs revealed a close evolutionary relationship between R. alfredi and the genus Cervus. RusAlf_1.1 represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, potentially contributing to more effective conservation and management strategies for this endangered species.

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.

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Author and article information

Contributors

Ma. Carmel F. Javier:

ORCID: https://orcid.org/0009-0006-9546-5055

Role: Formal analysisRole: Data curationRole: InvestigationRole: MethodologyRole: Project administrationRole: VisualizationRole: Writing - original draft

Albert C. Noblezada:

ORCID: https://orcid.org/0009-0008-2955-1486

Role: Data curationRole: Formal analysisRole: SoftwareRole: VisualizationRole: Writing - original draft

Persie Mark Q. Sienes:

ORCID: https://orcid.org/0009-0006-1004-0809

Role: MethodologyRole: Data curationRole: Writing - review editing

Robert S. Guino-o:

ORCID: https://orcid.org/0000-0003-1622-0836

Role: ConceptualizationRole: SupervisionRole: Writing - review editing

Nadia Palomar-Abesamis:

ORCID: https://orcid.org/0000-0001-6881-8421

Role: ConceptualizationRole: SupervisionRole: Writing - review editing

Maria Celia D. Malay:

ORCID: https://orcid.org/0000-0003-0219-4788

Role: ConceptualizationRole: SupervisionRole: Writing - review editing

Carmelo S. del Castillo:

ORCID: https://orcid.org/0000-0001-6786-4004

Role: ConceptualizationRole: SupervisionRole: Writing - review editing

Victor Marco Emmanuel N. Ferriols:

ORCID: https://orcid.org/0000-0002-7427-1298

Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing - review editing

Journal

Journal ID (nlm-ta): GigaByte

Journal ID (iso-abbrev): GigaByte

Journal ID (publisher-id): Gigabyte

Title: GigaByte

Publisher: GigaScience Press (Sha Tin, New Territories, Hong Kong SAR )

ISSN (Electronic): 2709-4715

Publication date (Electronic): 24 February 2025

Publication date Collection: 2025

Volume: 2025

Electronic Location Identifier: gigabyte150

Affiliations

[ ¹ ] Philippine Genome Center Visayas, University of the Philippines Visayas ( https://ror.org/00800dw77) , Miagao Iloilo, Philippines

[ ² ] Biology Department, Silliman University ( https://ror.org/01ry6r150) , Dumaguete, Philippines

[ ³ ] Angelo King Center for Research and Environmental Management, Silliman University ( https://ror.org/01ry6r150) , Dumaguete, Philippines

[ ⁴ ] Marine Science Institute, University of the Philippines Diliman ( https://ror.org/03tbh6y23) , Quezon City, Philippines

[ ⁵ ] Institute of Aquaculture , College of Fisheries and Ocean Sciences, University of the Philippines Visayas ( https://ror.org/00800dw77) , Miagao Iloilo, Philippines

[ ⁶ ] National Institute of Molecular Biology and Biotechnology, University of the Philippines Visayas ( https://ror.org/00800dw77) , Miagao Iloilo, Philippines

Author notes

[ ^* ] Corresponding authors. E-mail: persieqsienes@ 123456su.edu.ph ; vnferriols@ 123456up.edu.ph

Author information

Ma. Carmel F. Javier https://orcid.org/0009-0006-9546-5055

Albert C. Noblezada https://orcid.org/0009-0008-2955-1486

Persie Mark Q. Sienes https://orcid.org/0009-0006-1004-0809

Robert S. Guino-o https://orcid.org/0000-0003-1622-0836

Nadia Palomar-Abesamis https://orcid.org/0000-0001-6881-8421

Maria Celia D. Malay https://orcid.org/0000-0003-0219-4788

Carmelo S. del Castillo https://orcid.org/0000-0001-6786-4004

Victor Marco Emmanuel N. Ferriols https://orcid.org/0000-0002-7427-1298

Article

Publisher-manuscript ID: DRR-202410-02 Publisher ID: 150

DOI: 10.46471/gigabyte.150

PMC ID: 11876970

PubMed ID: 40041424

SO-VID: 8d95f67a-22d4-4dcd-8431-826e2968589d

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 11 October 2024

Date accepted : 18 February 2025

Funding

Funded by: Philippine Genome Center Visayas, University of the Philippines Visayas;

This work was supported by the Philippine Genome Center Visayas, University of the Philippines Visayas.

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Draft genome of the endangered visayan spotted deer ( Rusa alfredi), a Philippine endemic species

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Abstract

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Genome Integrity

Most cited references 69

Trimmomatic: a flexible trimmer for Illumina sequence data

Fast and accurate short read alignment with Burrows–Wheeler transform

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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