Vatanparast, M. et al. First molecular phylogeny of the pantropical genus Dalbergia: implications for infrageneric circumscription and biogeography. S. Afr. J. Bot. 89, 143–149 (2013).
Saha, S. et al. Ethnomedicinal, phytochemical, and pharmacological profile of the genus Dalbergia L. (Fabaceae). Phytopharmacology 4, 291–346 (2013).
Sprent, J. I. Legume Nodulation: A Global Perspective (Wiley, Hoboken, 2009).
Bhagwat, R. M., Dholakia, B. B., Kadoo, N. Y., Balasundaran, M. & Gupta, V. S. Two new potential barcodes to discriminate Dalbergia species. PLoS ONE 10, 1–18 (2015).
EIA. Routes of Extinction: The Corruption and Violence Destroying SIAMESE Rosewood in the Mekong (Environmental Investigation Agency, London, 2014).
EIA. The Hongmu Challenge: A Briefing for the 66th Meeting of the CITES Standing Committee, January 2016 (2016).
Winfield, K., Scott, M. & Graysn, C. Global status of Dalbergia and Pterocarpus rosewood producing species in trade. in Convention on International Trade in Endangered Species 17th Conference of Parties – Johannesburg (2016).
Bentham, G. Synopsis of Dalbergieae, a Tribe of Leguminosae. J. Proc. Linn. Soc. Lond. Bot. 4, 1–128 (1860).
Lavin, M. et al. The dalbergioid legumes (Fabaceae): delimitation of a pantropical monophyletic clade. Am. J. Bot. 88, 503 (2001).
Hartvig, I. et al. Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life-history traits. Ecol. Evol. 8, 530–545 (2018).
Hartvig, I., Czako, M., Kjær, E. D., Nielsen, L. R. & Theilade, I. The use of DNA barcoding in identification and conservation of rosewood (Dalbergia spp.). PLoS ONE 10, e0138231 (2015).
Wattoo, J. I., Saleem, M. Z., Shahzad, M. S., Arif, A. & Hameed, A. DNA barcoding: amplification and sequence analysis of rbcl and matK genome regions in three divergent plant species. Adv. Life Sci. 4, 03–07 (2016).
Phong, D. T., Tang, D. V., Hien, V. T. T., Ton, N. D. & Van, H. N. Nucleotide diversity of a nuclear and four chloroplast DNA regions in rare tropical wood species of dalbergia in Vietnam: a DNA barcode identifying utility. Asian J. Appl. Sci. 02, 116–125 (2014).
Resende, L. C., Ribeiro, R. A. & Lovato, M. B. Diversity and genetic connectivity among populations of a threatened tree (Dalbergia nigra) in a recently fragmented landscape of the Brazilian Atlantic Forest. Genetica 139, 1159–1168 (2011).
Buzatti, R. S. O., Ribeiro, R. A., Filho, J. P. L. & Lovato, M. B. Fine-scale spatial genetic structure of Dalbergia nigra (Fabaceae), a threatened and endemic tree of the Brazilian Atlantic Forest. Genet. Mol. Biol. 35, 838–846 (2012).
Liu, F.-M. et al. De novo transcriptome analysis of Dalbergia odorifera and transferability of SSR markers developed from the transcriptome. Forests 10, 98 (2019).
Xu, D.-P., Xu, S.-S., Zhang, N.-N., Yang, Z.-J. & Hong, Z. Chloroplast genome of Dalbergia cochinchinensis (Fabaceae), a rare and Endangered rosewood species in Southeast Asia. Mitochondrial DNA B 4, 1144–1145 (2019).
Wariss, H. M., Yi, T.-S., Wang, H. & Zhang, R. Characterization of the complete chloroplast genome of Dalbergia odorifera (Leguminosae), a rare and critically endangered legume endemic to China. Conserv. Genet. Resour. https://doi.org/10.1007/s12686-017-0866-2 (2017).
Liu, Y., Huang, P., Li, C.-H., Zang, F.-Q. & Zheng, Y.-Q. Characterization of the complete chloroplast genome of Dalbergia cultrata (Leguminosae). Mitochondrial DNA B 4, 2369–2370 (2019).
Deng, C., Xin, G., Zhang, J. & Zhao, D. Characterization of the complete chloroplast genome of Dalbergia hainanensis (Leguminosae), a vulnerably endangered legume endemic to China. Conserv. Genet. Resour. 1, 105–108 (2018).
Song, Y., Zhang, Y., Xu, J., Li, W. & Li, M. F. Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications. Sci. Rep. 9, 1–10 (2019).
Lateef, A., Prabhudas, S. K. & Natarajan, P. RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways. Sci. Rep. 8, 15375 (2018).
Keilwagen, J., Hartung, F., Paulini, M., Twardziok, S. O. & Grau, J. Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC Bioinform. 19, 189 (2018).
Wang, B., Kumar, V., Olson, A. & Ware, D. Reviving the transcriptome studies: an insight into the emergence of single-molecule transcriptome sequencing. Front. Genet. 10, 384 (2019).
Lamble, S. et al. Improved workflows for high throughput library preparation using the transposome-based nextera system. BMC Biotechnol. 13, 104 (2013).
Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).
Buffalo, V. Scythe—a Bayesian adapter trimmer (version 0.994 BETA) [Software] (2011). https://github.com/vsbuffalo/scythe.
Joshi, N. A. & Fass, J. N. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software] (2011). https://github.com/najoshi/sickle.
Carruthers, M. et al. De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics 19, 32 (2018).
Haas, B. J. et al. De novo transcript sequence reconstruction from RNA seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 (2013).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Haas, B. J. TransDecoder (2018). https://github.com/TransDecoder/TransDecoder.
Kriventseva, E. V. et al. OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucl. Acids Res. 47, D807–D811 (2019).
Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35, 543 (2017).
Bertioli, D. J. et al. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat. Genet. 48, 438–446 (2016).
Smith-Unna, R., Boursnell, C., Patro, R., Hibberd, J. M. & Kelly, S. TransRate: reference-free quality assessment of de novo transcriptome assemblies. Genome Res. 26, 1134–1144 (2016).
UniProt: a worldwide hub of protein knowledge. Nucl. Acids Res.47, D506–D515 (2019).
Cheng, C.-Y. et al. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J. 89, 789–804 (2017).
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucl. Acids Res. 47, D427–D432 (2019).
Almagro Armenteros, J. J. et al. SignalP 50 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37, 420–423 (2019).
Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001).
Emms, D. M. & Kelly, S. OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences. BioRxiv https://doi.org/10.1101/466201 (2018).
Guo, L. et al. The opium poppy genome and morphinan production. Science 362, 343–347 (2018).
Nakamura, T., Yamada, K. D., Tomii, K. & Katoh, K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 34, 2490–2492 (2018).
Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucl. Acids Res. 34, W609–W612 (2006).
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. jModelTest 2: more models, new heuristics and high-performance computing. Nat. Methods 9, 772 (2012).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Bouckaert, R. et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15, e1006650 (2019).
Brea, M., Zamuner, A. B., Matheos, S. D., Iglesias, A. & Zucol, A. F. Fossil wood of the Mimosoideae from the early Paleocene of Patagonia, Argentina. Alcheringa An Australas. J. Palaeontol. 32, 427–441 (2008).
Hane, J. K. et al. A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution. Plant Biotechnol. J. 15, 318–330 (2017).
Lavin, M., Herendeen, P. S. & Wojciechowski, M. F. Evolutionary rates analysis of leguminosae implicates a rapid diversification of lineages during the tertiary. Syst. Biol. 54, 575–594 (2005).
Moretzsohn, M. C. et al. A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers. Ann. Bot. 111, 113–126 (2013).
Ye, J. et al. WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. Nucl. Acids Res. 46, W71 (2018).
De Bie, T., Cristianini, N., Demuth, J. P. & Hahn, M. W. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22, 1269–1271 (2006).
Mi, H., Muruganujan, A. & Thomas, P. D. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucl. Acids Res. 41, D377–D386 (2013).
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B (Methodological) 57(1), 289–300 (1995).
Sun, J. et al. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nat. Ecol. Evol. 1, 0121 (2017).
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. ClusterProfiler: an R package for comparing biological themes among gene clusters. Omi. A J. Integr. Biol. 16, 284–287 (2012).
Soltis, D. E., Soltis, P. S., Bennett, M. D. & Leitch, I. J. Evolution of genome size in the angiosperms. Am. J. Bot. 90, 1596–1603 (2003).
Hiremath, S. C. & Nagasampige, M. H. Genome size variation and evolution in some species of Dalbergia Linn.f. (Fabaceae). Caryologia 57, 367–372 (2004).
Lawrence, G. H. M. Taxonomy of Vascular Plants (IBH Publishing Co., Oxford, 1973).
Lombello, R. A. & Forni-Martins, E. R. Chromosome studies and evolution in Sapindaceae. Caryologia 51, 89–93 (1998).
Sheremet’ev, S. N. & Gamalei, Y. V. Towards angiosperms genome evolution in time. arXiv (2013).
Carlquist, S. Anatomy of vine and liana stems: a review and synthesis. In The Biology of Vines (eds Putz, F. E. & Mooney, H. A.) 53–72 (University of Cambridge Press, Cambridge, 1991).
Li, Q. et al. The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes. Holzforschung 71, 939–949 (2017).
Lavin, M. et al. Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes. Philos. Trans. R. Soc. B Biol. Sci. 359, 1509–1522 (2004).
Kučerová, J. Miocénna flóra z lokalít Kalonda a Mučín. Acta Geol. Slovaca 1, 65–70 (2009).
Gao, S.-X. & Zhou, Z.-K. The megafossil legumes from China. In Advances in Legume Systematics (eds Herendeen, P. S. & Dilcher, D. L.) (The Royal Botanic Gardens, Kew, 1992).
de Saporta, G. Dalbergia phleboptera Saporta. Muséum national d’Histoire naturelle (2015). https://science.mnhn.fr/institution/mnhn/collection/f/item/14084.?lang=en_US.
De Bruyn, M. et al. Borneo and Indochina are major evolutionary hotspots for southeast Asian biodiversity. Syst. Biol. 63, 879–901 (2014).
Koenen, E. J. M. et al. The origin and early evolution of the legumes are a complex paleopolyploid phylogenomic tangle closely associated with the cretaceous-paleogene (K-Pg) boundary. biorxiv https://doi.org/10.1101/577957 (2019).
Lespinet, O., Wolf, Y. I., Koonin, E. V. & Aravind, L. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12, 1048–1059 (2002).
Ming, Y. et al. Molecular footprints of inshore aquatic adaptation in Indo-Pacific humpback dolphin (Sousa chinensis). Genomics https://doi.org/10.1016/j.ygeno.2018.07.015 (2018).
Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1545 (1999).
Luengo, T. M., Mayer, M. P. & Rüdiger, S. G. The Hsp70–Hsp90 chaperone cascade in protein folding. Trends Cell Biol. 29(2), 164–177. https://doi.org/10.1016/j.tcb.2018.10.004 (2019).
Jacob, P., Hirt, H. & Bendahmane, A. The heat-shock protein/chaperone network and multiple stress resistance. Plant Biotechnol. J. 15, 405–414 (2017).
Yamada, K. et al. Cytosolic HSP90 regulates the heat shock response that is responsible for heat acclimation in Arabidopsis thaliana. J. Biol. Chem. 282, 37794–37804 (2007).
Clément, M. et al. The cytosolic/nuclear HSC70 and HSP90 molecular chaperones are important for stomatal closure and modulate abscisic acid-dependent physiological responses in arabidopsis. Plant Physiol. 156, 1481–1492 (2011).
Hou, Q. & Bartels, D. Comparative study of the aldehyde dehydrogenase (ALDH) gene superfamily in the glycophyte Arabidopsis thaliana and Eutrema halophytes. Ann. Bot. 115, 465–479 (2015).
Missihoun, T. D. & Kotchoni, S. O. Aldehyde dehydrogenases and the hypothesis of a glycolaldehyde shunt pathway of photorespiration. Plant Signal. Behav. 13, e1449544 (2018).
Estioko, L. P. et al. Differences in responses to flooding by germinating seeds of two contrasting rice cultivars and two species of economically important grass weeds. AoB Plants 6, plu064 (2014).
Brocker, C. et al. Aldehyde dehydrogenase (ALDH) superfamily in plants: Gene nomenclature and comparative genomics. Planta 237, 189–210 (2013).
Sharma, B., Joshi, D., Yadav, P. K., Gupta, A. K. & Bhatt, T. K. Role of ubiquitin-mediated degradation system in plant biology. Front. Plant Sci. 7, 806 (2016).
Walters, K. J., Goh, A. M., Wang, Q., Wagner, G. & Howley, P. M. Ubiquitin family proteins and their relationship to the proteasome: a structural perspective. Biochimica et Biophysica Acta Mol. Cell Res. 1695, 73–87 (2004).
Liu, Z.-B. et al. A novel membrane-bound E3 ubiquitin ligase enhances the thermal resistance in plants. Plant Biotechnol. J. 12, 93–104 (2014).
Macho, A. P. & Zipfel, C. Plant PRRs and the activation of innate immune signaling. Mol. Cell 54, 263–272 (2014).
Martin, G. B., Bogdanove, A. J. & Sessa, G. Understanding the functions of plant disease resistance proteins. Annu. Rev. Plant Biol. 54, 23–61 (2003).
Cohn, J., Sessa, G. & Martin, G. B. Innate immunity in plants. Curr. Opin. Immunol. 13, 55–62 (2001).
Lehmann, P. Structure and evolution of plant disease resistance genes. J. Appl. Genet. 43, 403–414 (2002).
Jeffares, D. C., Tomiczek, B., Sojo, V. & dos Reis, M. A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. in Parasite Genomics Protocols: Second Edition 65–90 (Springer Fachmedien, 2014). https://doi.org/10.1007/978-1-4939-1438-8_4.
Andersen, E. J., Ali, S., Byamukama, E., Yen, Y. & Nepal, M. P. Disease resistance mechanisms in plants. Genes 9(7), 339 (2018).
IUCN. The IUCN Red List of Threatened Species. Veresion 2019–2 (2019). https://www.iucnredlist.org.
Federhen, S. The NCBI taxonomy database. Nucl. Acids Res. 40(D1), D136–D143 (2012).
Brandies, P., Peel, E., Hogg, C. J. & Belov, K. The value of reference genomes in the conservation of threatened species. Genes 10, 846 (2019).
Supple, M. A. & Shapiro, B. Conservation of biodiversity in the genomics era. Genome Biol. 19(1), 1–12 (2018).
Fuentes-Pardo, A. P. & Ruzzante, D. E. Whole-genome sequencing approaches for conservation biology: advantages, limitations and practical recommendations. Mol. Ecol. 26, 5369–5406 (2017).
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).
Bragg, J. G., Potter, S., Bi, K. & Moritz, C. Exon capture phylogenomics: efficacy across scales of divergence. Mol. Ecol. Resour. 16, 1059–1068 (2016).
İpek, A., İpek, M., Ercişli, S. & Tangu, N. A. Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive. Funct. Integr. Genomics 17, 493–501 (2017).
Vatanparast, M., Powell, A., Doyle, J. J. & Egan, A. N. Targeting legume loci: a comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. Appl. Plant Sci. 6, e1036 (2018).
Ouborg, N. J. Integrating population genetics and conservation biology in the era of genomics. Biol. Lett. 6, 3–6 (2010).
CITES. Consideration of Proposals for Amendment of Appendices I and II. Convention on International Trade in Endangered Species of Wild Fauna and Flora. (Convention on International Trade in Endangered Species of Wild Fauna and Flora, 2017).
Asian Regional Workshop (Conservation & Sustainable Management of Trees Viet Nam). Dalbergia cochinchinensis. The IUCN Red List of Threatened Species. e.T32625A9719096 (1998). https://doi.org/10.2305/IUCN.UK.1998.RLTS.T32625A9719096.en.
Bernal, R., Gradstein, S. & Celis, M. Catálogo de plantas y líquenes de Colombia (Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, 2015).
World Conservation Monitoring Centre. Dalbergia melanoxylon. The IUCN Red List of Threatened Species 1998. e.T32504A9710439 (1998). https://doi.org/10.2305/IUCN.UK.1998.RLTS.T32504A9710439.en.
ILDIS. International Legume Database and Information Service V10.39 (2011).
Nghia, N. H. Dalbergia oliveri. The IUCN Red List of Threatened Species 1998. e.T32306A9693932 (1998). https://doi.org/10.2305/IUCN.UK.1998.RLTS.T32306A9693932.en.
Orwa, C., Mutua, A., Kindt, R., Jamnadass, R. & Anthony, S. Agroforestree Database: A Tree Reference and Selection Guide Version 4.0. (2009). https://www.worldagroforestry.org/sites/treedbs/treedatabases.asp.
Source: Ecology - nature.com
