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2023
Basaldúa, S., Rodriguez-Pilco, M., Gutiérrez-Guerrero, Y., Ortega, J. and Baeza, J.A., 2023. The mitochondrial genome of the endemic and endangered trumpet-nosed bat Musonycteris harrisoni (Chiroptera: Phyllostomidae). Journal of Natural History, 57:1206-1219. https://doi.org/10.1080/00222933.2022.2150581
Baeza, J.A., Rajapakse, D., Pearson, L. and Kreiser, B.R., 2023. Low coverage sequencing provides insights into the key features of the nuclear and mitochondrial genomes of the Alligator Snapping Turtle Macrochelys temminckii. Gene 12;873:147478. https://doi.org/10.1016/j.gene.2023.147478
Baeza, J.A., Macdonald-Shedd, A., Latorre-Cárdenas, M.C., Griffin, E. and Gutiérrez-Rodríguez, C., 2023. The first genomic resource for the ‘near threatened’ Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae. Journal of Natural History, 57(5-8):408-425.
https://doi.org/10.1080/00222933.2023.2186809
Baeza, J.A., R. Barata, D. Rajapakse, J. Penaloza, P. Harrison, and A. Haberski. 2023. Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals. Genes 14(3): 657.
https://doi.org/10.3390/genes14030657
Vargas-Trejo, K.J., Ortega, J., Gutiérrez-Guerrero, Y.T., Gutiérrez, E.G. and Baeza, J.A., 2023. The mitochondrial genomes of big-eared bats, Macrotus waterhousii and Macrotus californicus (Chiroptera: Phyllostomidae: Macrotinae). Gene 863: 147295. https://doi.org/10.1016/j.gene.2023.147295
Manuela Moreno-Carmona, Paula Montaña-Lozano, Carlos F. Prada-Quiroga, and J. Antonio Baeza. 2023. Comparative analysis of mitochondrial genomes reveals family-specific architectures and molecular features in scorpions (Arthropoda: Arachnida: Scorpiones). Gene 859: 147189. https://doi.org/10.1016/j.gene.2023.147189
Colín, Angélica, Carolina Galván-Tirado, Laura Carreón-Palau, Heather D. Bracken-Grissom, and J. Antonio Baeza. 2023. Mitochondrial genomes of the land hermit crab Coenobita clypeatus (Anomura: Paguroidea) and the mole crab Emerita talpoida (Anomura: Hippoidea) with insights into phylogenetic relationships in the Anomura (Crustacea: Decapoda)." Gene 849: 146896. https://doi.org/10.1016/j.gene.2022.146896
2022
Baeza, J. A. 2022. Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera trigis altaica. PeerJ 10:e14428 DOI 10.7717/peerj.14428. https://peerj.com/articles/14428/
Molina-Quirós, José Luis, Sebastián Hernández-Muñoz, and J. Antonio Baeza. 2022. The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes. Gene 845: 146847. https://doi.org/10.1016/j.gene.2022.146847
Ennis, C.C., Ortega, J. and Baeza, J.A., 2022. First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii). PeerJ, 10, p.e13440. https://peerj.com/articles/13440/
Baeza, J.A., M. L. Neo, and D. Huang. 2022. Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea. Genes 13, no. 5: 903. https://doi.org/10.3390/genes13050903
Baeza, J.A., and F. Garcia-De Leon. 2022. Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis. BMC Genomics 23, 320 (2022). https://doi.org/10.1186/s12864-022-08482-z.
Baeza, J.A. 2022. An introduction to the Special Section on Crustacean Mitochondrial Genomics: Improving the assembly, annotation, and characterization of mitochondrial genomes using user-friendly and open-access bioinformatics tools, with decapod crustaceans as an example. Journal of Crustacean Biology 42(1), ruac004, https://doi.org/10.1093/jcbiol/ruac012.
Baeza, J.A., Baker, A.M., and Liu, H. 2022. Genome survey sequencing of the long-legged spiny lobster Panulirus longipes (A. Milne-Edwards, 1868) (Decapoda: Achelata: Palinuridae): improved mitochondrial genome annotation, nuclear repetitive elements classification, and SSR marker discovery. Journal of Crustacean Biology 42(1), ruac006, https://doi.org/10.1093/jcbiol/ruac006.
Cronin, T.J., Conrad, I., Kerkhove, T.R.H., Hellemans, B., De Troch, M., Volckaert, F.A.M., and Baeza, J.A. 2022. Characterization of the complete mitochondrial genome of the Atlantic seabob shrimp Xiphopenaeus kroyeri Heller, 1862 (Decapoda: Dendrobranchiata: Penaeidae), with insights into the phylogeny of Penaeidae. Journal of Crustacean Biology 42(1), ruac004, https://doi.org/10.1093/jcbiol/ruac004.
Cronin, T.J., Jones, S.J.M., and Baeza, J.A., 2022. The complete mitochondrial genome of the spot prawn, Pandalus platyceros Brandt in von Middendorf, 1851 (Decapoda: Caridea: Pandalidae), assembled from linked-reads sequencing. Journal of Crustacean Biology 42(1), ruac007, https://doi.org/10.1093/jcbiol/ruac003.
Collins, S.B., Bracken-Grissom, H.D., and Baeza, J.A. 2022. The complete mitochondrial genome of the pink shrimp Farfantepenaeus duorarum (Burkenroad, 1939) (Decapoda: Dendrobranchiata: Penaeidae). Journal of Crustacean Biology 42(1), ruac007, https://doi.org/10.1093/jcbiol/ruac007.
O’Brien, C., Bracken-Grissom, H.D., and Baeza, J.A. 2022. The complete mitochondrial genome of the Atlantic ghost crab Ocypode quadrata (Fabricius, 1787) (Brachyura: Ocypodidae: Ocypodinae). Journal of Crustacean Biology 42(1), ruac005, https://doi.org/10.1093/jcbiol/ruac005.
Rodriguez-Pilco, M.A., Leśny, P., Podsiadłowski, L., Schubart, C., and Baeza, J.A., 2022. Characterization of The Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae). Genes 13(2), 299; https://doi.org/10.3390/genes13020299.
López-Cuamatzi, I.L., Ortega, J. and Baeza, J.A., 2022. The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico. Molecular Biology Reports, pp.1-9. https://doi.org/10.1007/s11033-021-06940-7
Baeza, J.A., Rodríguez, M.E. and Ortega, J., 2022. A genomic portrait of Sturnira parvidens: mitochondrial chromosome, repetitive elements, and microsatellite discovery. Journal of Mammalogy. https://doi.org/10.1093/jmammal/gyab117
Ma, X., Agudelo, P., Richards, V.P., Baeza, J.A. 2022. Genome survey sequencing of the phyto-parasitic nematode Hoplolaimus galeatus. PeerJ 10:e12749. http://doi.org/10.7717/peerj.12749
2021
Hwang, Hee-seung, Jongwoo, J. and Baeza, J.A., 2021. The mitochondrial genome of Faughnia haani (Stomatopoda): novel organization of the control region and phylogenetic position of the superfamily Parasquilloidea. BMC Genomics, 22:726. https://doi.org/10.1186/s12864-021-08034-x
Vivas-Toro, I., Ortega, J. and Baeza, J.A., 2021. The complete mitochondrial genome of the Honduran white bat Ectophylla alba (Allen 1982) (Chiroptera: Phyllostomidae). Gene, p.145868. https://doi.org/10.1016/j.gene.2021.145868
Ennis, C. C., N. N. Haeffner, C. D. Keyser, S. T. Leonard, A. C. Macdonald-Shedd, A. M. Savoie, T. J. Cronin, W. P. Veldsman, P. Barden, S. T. C. Chak, and J. A. Baeza. 2021. Comparative mitochondrial genomics of sponge-dwelling snapping shrimps in the genus Synalpheus: Exploring differences between eusocial and non-eusocial species and insights into phylogenetic relationships in caridean shrimps. Gene 786: 145624, https://doi.org/10.1016/j.gene.2021.145624
Chak, S.T., Baeza, J.A. and Barden, P., 2021. Eusociality shapes convergent patterns of molecular evolution across mitochondrial genomes of snapping shrimps. Molecular Biology and Evolution. msaa297, https://doi.org/10.1093/molbev/msaa297
Conrad, I., Craft, A., Thurman, C.L. and Baeza, J.A., 2021. The complete mitochondrial genome of the red-jointed brackish-water fiddler crab Minuca minax (LeConte 1855)(Brachyura: Ocypodidae): New family gene order, and purifying selection and phylogenetic informativeness of protein coding genes. Genomics. https://doi.org/10.1016/j.ygeno.2020.09.050
Baeza, J.A., 2021. A first genomic portrait of the Florida stone crab Menippe mercenaria: Genome size, mitochondrial chromosome, and repetitive elements. Marine Genomics, p.100821. https://doi.org/10.1016/j.margen.2020.100821
2020
Baeza, J.A. 2020. Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus. BMC Genomics 21, 882. https://doi.org/10.1186/s12864-020-07292-5
Veldsman, W. P., Wang, Y., Niu, J., Baeza, J. A., & Chu, K. H. (2020). Characterization of the complete mitochondrial genome of a coconut crab, Birgus latro (Linnaeus, 1767)(Decapoda: Anomura: Coenobitidae), from Okinawa, Japan. Journal of Crustacean Biology. https://doi.org/10.1093/jcbiol/ruaa032
Ma, X., Agudelo, P., Richards, V.P. & Baeza, J.A. The complete mitochondrial genome of the Columbia lance nematode, Hoplolaimus columbus, a major agricultural pathogen in North America. Parasites Vectors 13, 321 (2020). https://doi.org/10.1186/s13071-020-04187-y
2019
Chak, S.T.C., Barden, P. & Baeza, J.A. The complete mitochondrial genome of the eusocial sponge-dwelling snapping shrimp Synalpheus microneptunus. Sci Rep 10, 7744 (2020). https://doi.org/10.1038/s41598-020-64269-w
Baeza, J. A., F.A. Sepulveda, M. T. Gonzalez. 2019. The complete mitochondrial genome and description of a new cryptic species of Benedenia Diesing, 1858 (Monogenea: Capsalidae), a major pathogen infecting the yellowtail kingfish Seriola lalandi Valenciennes in the South-East Pacific. Parasites and Vectors 12, 490. doi:10.1186/s13071-019-3711-5
2018
Baeza, J. A. 2018. The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus: purifying selection and phylogenomic informativeness of protein coding genes. Scientific Reports. 8, 17690 (2018). https://doi.org/10.1038/s41598-018-36132-6
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