REFERENCES
Altschul,
S.F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990).
Basic
local alignment search tool. Journal of Molecular Biology , 215,
403-410. http://dx.doi.org/10.1016/S0022-2836(05)80360-2
Attwood,
T., & Beck, M. (1994).
Prints–a
protein motif fingerprint database. Protein Engineering , 7,
841-848. http://dx.doi.org/10.1093/protein/7.7.841
Bairoch,
A. (1991).
PROSITE:
a dictionary of sites and patterns in proteins. Nucleic Acids
Research , 19. 2241. http://dx.doi.org/10.1093/nar/19.suppl.2241
Birney,
E., Clamp, M., & Durbin, R. (2004).
GeneWise
and genomewise. Genome Research , 14, 988-995.
http://dx.doi.org/10.1101/gr.1865504
Blanco,
E., Parra, G., & Guigó., R. (2007).
Using
geneid to identify genes. Current Protocols in Bioinformatics ,
4.3.1-4.3.28. http://dx.doi.org/10.1002/0471250953.bi0403s18
Boeckmann,
B., Bairoch, A., Apweiler, R., Blatter, M-C., Estreicher, A., Gasteiger,
E., … Schneider, M.
(2003).
The
SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.Nucleic Acids Research , 31, 365-370.
http://dx.doi.org/10.1093/nar/gkg095
Breria,
C. M., Hsieh, C. H., Yen, J. Y., Nair, R., Lin, C. Y., Huang, S. M., …
Schafleitner, R. (2020a).
Population
structure of the world vegetable center mungbean mini core collection
and genome-wide association mapping of loci associated with variation of
seed coat luster. Tropical Plant Biology , 13(1), 1-12.
doi:10.1007/s12042-019-09236-0
Breria,
C. M., Hsieh, C. H., Yen, T. B., Yen, J. Y., Noble, T. J., &
Schafleitner, R. (2020b). A SNP-based genome-wide association study to
mine genetic loci associated to salinity tolerance in mungbean
(Vigna radiata L.). Genes (Basel), 11(7).
doi:10.3390/genes11070759
Bru,
C., Courcelle, E., Carrère, S., Beausse, Y., Dalmar, S.,
&
Kahn, D. (2005)
The
ProDom database of protein domain families: more emphasis on 3D.Nucleic Acids Research , 33, 212-215. doi:10.1093/nar/gki034
Bruce,
J., Walker, T. A., Terrance, S., Margaret, P., Amr, A., Sharadha, S.,
… Ashlee, M. E. (2014).
Pilon:
an integrated tool for comprehensive microbial variant detection and
genome assembly improvement. PLoS One , 9(11), e112963.
https://doi.org/10.1371/journal.pone.0112963
Burge,
C., & Karlin, S. (1997).
Prediction
of complete gene structures in human genomic DNA. Journal of
Molecular Biology , 268, 78-94. https://doi.org/10.1006/jmbi.1997.0951
Joshua, N. B., Andrew, A., Rupali, P. P., Ruolan, Q., Jacob, O. K., &
Jay, S.
(2013).
Chromosome-scale
scaffolding of de novo genome assemblies based on chromatin
interactions. Naturenature Biotechnology , 31(12), 1119-1125.
https://doi.org/10.1038/nbt.2727
Campbell,
M. A., Haas, B. J., Hamilton, J. P., Mount, S. M., & Buell, C. R.
(2006).
Comprehensive
analysis of alternative splicing in rice and comparative analyses withArabidopsis . BMC Genomics , 7, 327.
http://dx.doi.org/10.1186/1471-2164-7-327
Chotechung,
S., Somta, P., Chen, J., Yimram, T., Chen, X., & Srinives, P. (2016).
A
gene encoding a polygalacturonase-inhibiting protein (PGIP) is a
candidate gene for bruchid (Coleoptera: bruchidae) resistance in
mungbean (Vigna radiata ). Theor Appl Genet , 129(9),
1673-1683. doi:10.1007/s00122-016-2731-1
De,
B. T., Cristianini, N., Demuth, J. P.,
&
Hahn, M. W. (2006).
CAFE:
a computational tool for the study of gene family evolution.Bioinformatics , 22, 1269-1271. doi: 10.1093/bioinformatics/btl097
Dimmer,
E. C., Huntley, R. P., Alam-Faruque, Y., Sawford, T., O’Donovan, C.,
Martin, M. J., … Eberhardt, R. (2012).
The
UniProt-GO annotation database in 2011. Nucleic Acids Research ,
40, 565-570. http://dx.doi.org/10.1093/nar/gkr1048
Edgar,
R. C. (2004).
MUSCLE:
multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Research , 32, 1792-1797.
http://dx.doi.org/10.1093/nar/gkh340
Felipe,
A. S., Robert, M. W., Panagiotis, I., Evgenia, V. K., & Evgeny, M. Z.
(2015).
BUSCO:
assessing genome assembly and annotation completeness with single-copy
orthologs. Bioinformatics , 31(19), 3210-3212. DOI:
10.1007/978-1-4939-9173-0_14
Finn,
R. D., Mistry, J., Schuster-Böckler, B., Griffiths-Jones, S., Hollich,
V., Lassmann, T., … Durbin, R. (2006).
Pfam:
clans, web tools and services. Nucleic Acids Research, 34,
247-251. http://dx.doi.org/10.1093/nar/gkj149
Parra,
G., Bradnam, K., & Korf, I. (2007).
CEGMA:
a pipeline to accurately annotate core genes in eukaryotic genomes.Bioinformatics , 23, 1061-1067.
http://dx.doi.org/10.1093/bioinformatics/btm071
Gough,
J., & Chothia, C. (2002).
SUPERFAMILY:
HMMs representing all proteins of known structure. SCOP sequence
searches, alignments and genome assignments. Nucleic Acids
Research , 30, 268-272. http://dx.doi.org/10.1093/nar/30.1.268
Griffiths-Jones,
S., Moxon, S., Marshall, M., Khanna, A., Eddy, S. R., & Bateman, A.
(2005).
Rfam:
annotating non-coding RNAs in complete genomes. Nucleic Acids
Research , 33, 121-124. http://dx.doi.org/10.1093/nar/gki081
Guindon,
S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel,
O. (2010).
New
algorithms and methods to estimate maximum-likelihood phylogenies:
assessing the performance of PhyML 3.0. Systematic Biology , 59,
307-321. http://dx.doi.org/10.1093/sysbio/syq010
Haas,
B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., Orvis, J.,
… Wortman, J.R. (2008).
Automated
eukaryotic gene structure annotation using EVidenceModeler and the
Program to Assemble Spliced Alignments. Genome Biology , 9, R7.
http://dx.doi.org/10.1186/gb-2008-9-1-r7
Haft,
D. H., Selengut, J. D., & White, O. (2003).
The
TIGRFAMs database of protein families. Nucleic Acids Research ,
31, 371-373. http://dx.doi.org/10.1093/nar/gkg128
Hoede,
C., Arnoux, S., Moisset, M., Chaumier, T., Inizan, O., Jamilloux, V., &
Quesneville, H. (2014).
PASTEC:
an automatic transposable element classification tool. PLoS One ,
9(5), e91929. https://doi.org/10.1371/journal.pone.0091929
Jiao,
K. Y., Li, X., Guo, W. X., Yuan, X. X., Cui, X. Y., & Chen, X. (2016).
Genome
re-sequencing of two accessions and fine mapping the locus of lobed
leaflet margins in mungbean. Molecular Breeding , 36(9). doi:ARTN
128 10.1007/s11032-016-0552-1
Jurka,
J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., &
Walichiewicz, J. (2005).
Repbase
Update, a database of eukaryotic repetitive elements. Cytogenetic
and Genome Research , 110, 462-467. http://dx.doi.org/10.1159/000084979
Kaewwongwal,
A., Chen, J., Somta, P., Kongjaimun, A., Yimram, T., Chen, X., &
Srinives, P. (2017).
Novel
alleles of two tightly linked genes encoding
polygalacturonase-inhibiting proteins (VrPGIP1 and VrPGIP2) associated
with the br locus that confer bruchid (Callosobruchus spp.)
resistance to mungbean (Vigna radiata ) accession V2709.Frontiers
in Plant Science , 8, 1692. doi:10.3389/fpls.2017.01692
Keatinge, J. D. H., Easdown, W. J., Yang, R. Y., Chadha, M. L., &
Shanmugasundaram, S. (2011).
Overcoming
chronic malnutrition in a future warming world: the key importance of
mungbean and vegetable soybean. Euphytica , 180(1), 129-141.
doi:10.1007/s10681-011-0401-6
Keilwagen,
J., Hartung, F., Paulini, M., Twardziok, S. O., & Grau, J. (2018).
Combining
RNA-seq data and homology-based gene prediction for plants, animals and
fungi. BMC Bioinformatics , 19(1), 189.
http://dx.doi.org/10.1186/s12859-018-2203-5
Kanehisa,
M., & Goto, S. (2000).
KEGG:
kyoto encyclopedia of genes and genomes. Nucleic Acids Research ,
28, 27-30. http://dx.doi.org/10.1093/nar/28.1.27
Kang,
Y. J., Kim, S. K., Kim, M. Y., Lestari, P., Kim, K. H., Ha, B. K.,
… Lee, S. H. (2014).
Genome
sequence of mungbean and insights into evolution within Vignaspecies. Nature Communications , 5, 5443.
http://dx.doi.org/10.1038/ncomms6443
Kang.
Y., J., & Ha, J. (2020) Mungbean genome and synteny with other genomes.
In: Nair R, Schafleitner R, Lee SH, editors. The mungbean genome.
Compendium of plant genomes . Berlin: Springer; 2020.125-127.
https://doi.org/10.1007/978-3-030-20008-4
Keilwagen,
J., Wenk, M., Erickson, J. L., Schattat, M. H., Jan, G., & Frank, H.
(2016).
Using
intron position conservation for homology-based gene prediction.Nucleic Acids Research , 44, e89.
http://dx.doi.org/10.1093/nar/gkw092
Kent,
W. J.
(2002).
BLAT–the
BLAST-like alignment tool. Genome Research , 12(4), 656-664.
http://dx.doi.org/10.1101/gr.229202
Kim,
D., Langmead, B., & Salzberg, S. L. (2015).
HISAT:
a fast spliced aligner with low memory requirements. Nature
Methods , 12, 357-360. http://dx.doi.org/10.1038/nmeth.3317
Koonin,
E. V., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Krylov, D. M.,
Makarova, K. S., … Natale, D. A. (2004).
A
comprehensive evolutionary classification of proteins encoded in
complete eukaryotic genomes. Genome Biology , 5, R7.
https://doi.org/10.1186/gb-2004-5-2-r7
Koren,
S., Walenz, B. P., Berlin, K., Miller, J. R., & Phillippy, A. M.
(2017).
Canu:
scalable and accurate long-read assembly via adaptive k-mer weighting
and repeat separation. Genome Research , 27(5), 722-736.
http://dx.doi.org/10.1101/gr.215087.116
Korf,
I. (2004).
Gene
finding in novel genomes. BMC Bioinformatics , 5, 59. DOI:
10.1186/1471-2105-5-59
Lees,
J., Yeats, C., Perkins, J., Sillitoe, I., Rentzsch, R., Dessailly, B.
H., & Orengo, C. (2012).
Gene3D:
a domain-based resource for comparative genomics, functional annotation
and protein network analysis. Nucleic Acids Research , 40,
465-471. http://dx.doi.org/10.1093/nar/gkr1181
Letunic,
I., Copley, R. R., Schmidt, S., Ciccarelli, F. D., Doerks, T., Schultz,
J., … Bork, P. (2004).
SMART
4.0: towards genomic data integration. Nucleic Acids Research ,
32, 142-144. http://dx.doi.org/10.1093/nar/gkh088
Li, H. (2013).
Aligning
sequence reads, clone sequences and assembly contigs with bwa-mem. arXiv
e-prints.
Li,
H., & Richard, D. (2009).
Fast
and accurate short read alignment with Burrows–Wheeler transform.Bioinformatics , 25(14), 1754-1760.
http://dx.doi.org/10.1093/bioinformatics/btp324
Li, L., Stoeckert, C. J., & Roos, D. S. (2003).
OrthoMCL:
identification of ortholog groups for eukaryotic genomes. Genome
Research , 13, 2178-2189. http://dx.doi.org/10.1101/gr.1224503
Lima,
T., Auchincloss, A. H., Coudert, E., Keller, G., Michoud, K., Rivoire,
C., … Baratin, D. (2009)
HAMAP:
a database of completely sequenced microbial proteome sets and manually
curated microbial protein families in UniProtKB/Swiss-Prot.Nucleic Acids Research , 37, 471-478.
http://dx.doi.org/10.1093/nar/gkn661
Lowe,
T. M.,
&
Eddy, S. R. (1997).
tRNAscan-SE:
a program for improved detection of transfer RNA genes in genomic
sequence. Nucleic Acids Research , 25, 0955-0964.
http://dx.doi.org/10.1093/nar/25.5.955
Majoros,
W. H., Pertea, M., & Salzberg, S. L. (2004).
TigrScan
and GlimmerHMM: two open source ab initio eukaryotic gene-finders.Bioinformatics , 20, 2878-2879. doi: 10.1093/bioinformatics/bth315
Marchler-Bauer,
A., Lu, S., Anderson, J. B., Chitsaz, F., Derbyshire, M. K.,
DeWeese-Scott, C., … Gonzales, N. R. (2011).
CDD:
a Conserved Domain Database for the functional annotation of proteins.Nucleic Acids Research , 39,
225-229.
http://dx.doi.org/10.1093/nar/gkq1189
Nair,
R.,
&
Schreinemachers, P. (2020). Global status and economic importance of
mungbean.
In:
Nair R, Schafleitner R, Lee SH, editors. The mungbean genome.
Compendium of plant genomes . Berlin: Springer; 2020.1-6.
https://doi.org/10.1007/978-3-030-20008-4
Pertea,
M., Pertea, G. M., Antonescu, Corina, M., Chang, T.-C., Mendell, J. T.,
& Salzberg, S. L.
(2015).
StringTie
enables improved reconstruction of a transcriptome from RNA-seq reads.Naturenature Biotechnology , 33, 290-295.
http://dx.doi.org/10.1038/nbt.3122
Prestridge,
D. S. (1991).
Signal
scan: a computer program that scans DNA sequences for eukaryotic
transcriptional elements. Computer Applications in the Bioences
Cabios , 7(2), 203. http://dx.doi.org/10.1093/bioinformatics/7.2.203
Price,
A. L., Jones, N. C., & Pevzner, P. A. (2005).
De
novo identification of repeat families in large genomes.Bioinformatics , 21, 351-358.
http://dx.doi.org/10.1093/bioinformatics/bti1018
Rao,
S., Huntley, M., Durand, N., Stamenova, E., Bochkov, I., Robinson, J., .
. . Aiden, E. (2014).
A
3D map of the human genome at kilobase resolution reveals principles of
chromatin looping. Cell , 159(7), 1665-1680.
http://dx.doi.org/10.1016/j.cell.2014.11.021
Schabauer, H., Valle, M., Pacher, C., Stockinger, H., Stamatakis, A.,
Robinson-Rechavi, M., … Salamin, N. (2012). SlimCodeML: an optimized
version of CodeML for the Branch-Site Model. Paper presented at
the 2012 IEEE 26th International Parallel and Distributed Processing
Symposium Workshops & PhD Forum , 706-714
Servant,
N., Varoquaux, N., Lajoie, B. R., Viara, E., Chen, C. J., Vert, J. P.,
… Barillot, E. (2015).
HiC-Pro:
an optimized and flexible pipeline for Hi-C data processing.Genome Biology , 16, 259.
http://dx.doi.org/10.1186/s13059-015-0831-x
She,
R., Chu, J. S., Wang, K., Pei, J., & Chen, N. (2009).
GenBlastA:
enabling BLAST to identify homologous gene sequences. Genome
Research , 19(1), 143-149.
http://genome.cshlp.org/cgi/doi/10.1101/gr.082081.108
Stanke, M., & Waack, S. (2003).
Gene
prediction with a hidden Markov model and a new intron submodel.Bioinformatics , 19, 215-225.
https://doi.org/10.1093/bioinformatics/btg1080
Tang, S., Lomsadze, A., & Borodovsky, M. (2015).
Identification
of protein coding regions in RNA transcripts. Nucleic Acids
Research , 43(12), e78. https://doi.org/10.1093/nar/gkv227
Tarailo-Graovac, M.,
&
Chen, N. (2009).
Using
RepeatMasker to identify repetitive elements in genomic sequences.Current Protocols in Bioinformatics , 25(1), 4.10.11-14.10.14.
https://doi.org/10.1002/0471250953.bi0410s25
Thomas, P. D., Kejariwal, A., Campbell, M. J., Mi, H., Diemer, K., Guo,
N., … Doremieux, O. (2003).
PANTHER:
a browsable database of gene products organized by biological function,
using curated protein family and subfamily classification. Nucleic
Acids Research , 31(7), 2024-2024. https://doi.org/10.1093/nar/gkg115
Vaser, R., Sovic, I., Nagarajan, N., & Sikic, M. (2017).
Fast
and accurate de novo genome assembly from long uncorrected reads.Genome Research , 27(5), 737-746. doi:10.1101/gr.214270.116
Wu, C. H., Nikolskaya, A., Huang, H. Z., Yeh, L. S. L., Natale, D. A.,
Vinayaka, C. R., … Barker, W. C. (2004).
PIRSF:
family classification system at the Protein Information Resource.Nucleic Acids Research , 32, D112-D114. DOI:10.1093/nar/gkh097
Xu, Z., & Wang, H. (2007).
LTR_FINDER:
an efficient tool for the prediction of full-length LTR
retrotransposons. Nucleic Acids Research , 35, W265-W268.
https://doi.org/10.1093/nar/gkm286
Yang, Z. H. (1997).
PAML:
a program package for phylogenetic analysis by maximum likelihood.Computer Applications in the Biosciences , 13(5), 555-556.
https://doi.org/10.1093/bioinformatics/13.5.555
Yundaeng, C., Somta, P., Chen, J., Yuan, X., Chankaew, S., Srinives, P.,
& Chen, X. (2020).
Candidate
gene mapping reveals VrMLO12 (MLO Clade II) is associated
with powdery mildew resistance in mungbean (Vigna radiata[L.] Wilczek). Plant Science , 298, 110594.
doi:10.1016/j.plantsci.2020.110594
Zdobnov, E. M., & Apweiler, R. (2001).
InterProScan
- an integration platform for the signature-recognition methods in
InterPro. Bioinformatics , 17(9), 847-848. doi:
10.1093/bioinformatics/17.9.847
Table 1. Assembly and annotation statistics of Sulv 1 genome